Contacts of the helix formed by residues 74 - 101 (chain B) in PDB entry 4KJQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR 4.5 0.9 + - - +
73B ASP* 1.3 84.0 + - - +
75B TYR* 1.3 53.4 + - - +
76B PRO* 3.2 20.6 - - - +
77B LEU* 2.9 37.5 + - + +
78B LEU* 2.7 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASP 3.2 9.3 + - - +
74B ASN* 1.3 69.9 - - - +
76B PRO* 1.4 72.1 - - + +
78B LEU* 3.3 18.2 - - + +
79B LEU* 2.9 71.7 + - + +
307B PHE* 4.1 13.5 - + - -
308B VAL* 4.1 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASN* 3.2 12.8 - - - +
75B TYR* 1.4 99.0 - - + +
77B LEU* 1.3 57.0 + - - +
79B LEU* 4.1 12.1 - - + +
80B THR* 2.9 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 3.9 28.9 - - + +
73B ASP* 5.2 2.2 - - - +
74B ASN* 2.9 40.1 + - + +
76B PRO* 1.3 75.2 - - - +
78B LEU* 1.3 61.2 + - - +
80B THR* 3.1 11.5 + - + -
81B VAL* 3.1 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 3.6 39.7 - - + +
71B THR* 3.2 31.4 - - - +
72B ALA* 5.1 4.9 - - - -
74B ASN 2.7 14.4 + - - +
75B TYR* 3.3 36.3 - - + +
77B LEU* 1.3 70.0 - - - +
79B LEU* 1.3 71.5 + - + +
80B THR 3.1 1.3 - - - -
81B VAL* 4.4 1.8 - - - -
82B ALA* 3.2 21.0 + - + +
307B PHE* 3.4 42.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 2.9 68.6 + - + +
76B PRO* 4.1 10.1 - - + +
78B LEU* 1.3 83.0 - - + +
80B THR* 1.3 60.8 + - - +
82B ALA* 3.8 3.1 - - - +
83B PHE* 3.3 13.5 + - - +
304B LEU* 3.2 32.6 - - + +
307B PHE* 4.0 5.2 - - + -
308B VAL* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PRO 2.9 17.9 + - - -
77B LEU* 3.1 15.6 + - + +
78B LEU 3.1 0.6 - - - -
79B LEU* 1.3 75.7 - - - +
81B VAL* 1.3 58.1 + - + +
82B ALA 3.1 1.6 - - - -
83B PHE* 2.9 9.8 + - + +
84B LEU* 2.7 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 4.0 23.6 - - + +
68B LEU* 3.5 21.7 - - + +
71B THR* 4.1 15.9 - - + +
77B LEU* 3.1 32.4 + - + +
78B LEU 3.8 3.6 - - - +
80B THR* 1.3 76.6 - - + +
82B ALA* 1.3 59.4 + - - +
84B LEU* 3.9 9.9 - - + +
85B CYS* 3.0 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 5.1 3.3 + - - +
68B LEU* 3.8 23.1 - - + -
78B LEU* 3.2 17.6 + - + +
79B LEU* 3.8 7.6 - - - +
80B THR 3.1 0.4 - - - -
81B VAL* 1.3 78.1 - - - +
83B PHE* 1.3 66.1 - - - +
85B CYS* 4.1 2.8 - - - +
86B SER* 3.4 22.5 + - - -
303B GLY* 3.4 26.7 - - - +
304B LEU* 4.4 3.4 - - + -
307B PHE* 4.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU 3.3 11.4 + - - +
80B THR* 2.9 11.8 + - + +
82B ALA* 1.3 80.6 - - - +
84B LEU* 1.3 64.3 + - + +
87B ALA* 2.7 54.4 + - + +
296B GLY 3.9 11.7 - - - -
297B ALA* 4.1 15.5 - - + -
300B GLY* 3.2 35.9 - - - +
301B LEU* 4.0 7.4 - - + -
304B LEU* 4.4 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 2.7 41.9 + - + +
81B VAL* 4.3 7.4 - - + +
83B PHE* 1.3 86.5 - - + +
85B CYS* 1.3 60.5 + - - +
87B ALA* 3.9 5.4 - - + -
88B VAL* 2.8 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 3.9 25.4 - - + -
67B ALA* 4.4 22.4 - - - -
68B LEU* 6.3 0.2 - - - -
81B VAL* 3.0 29.3 + - - +
82B ALA* 4.1 3.6 - - - +
84B LEU* 1.3 76.0 - - - +
86B SER* 1.3 58.4 + - - +
88B VAL* 4.3 5.1 - - - +
89B LEU* 3.3 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 3.2 7.1 + - - -
82B ALA 3.4 9.7 + - - -
83B PHE 3.3 1.9 + - - -
84B LEU 3.1 0.4 - - - -
85B CYS* 1.3 77.5 - - - +
87B ALA* 1.3 54.2 + - - +
88B VAL 3.2 0.2 - - - -
89B LEU* 3.0 2.9 + - - +
90B ALA* 2.6 36.4 + - - +
141B GLY* 2.4 35.4 + - - -
299B GLY* 3.0 26.9 - - - -
303B GLY* 3.1 15.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 2.7 37.4 + - + +
84B LEU* 3.5 11.0 - - + +
86B SER* 1.3 70.9 - - - +
88B VAL* 1.3 57.7 + - + +
91B MET* 2.9 40.5 + - + +
296B GLY* 3.1 32.9 - - - +
300B GLY 3.6 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 2.8 32.0 + - + +
85B CYS* 4.3 4.7 - - - +
87B ALA* 1.3 72.3 - - + +
89B LEU* 1.3 64.4 + - + +
91B MET* 3.2 21.2 + - + +
92B PHE* 2.9 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.4 29.6 - - + -
64B ARG* 4.3 10.3 - - + -
85B CYS* 3.3 21.0 + - + +
86B SER 3.0 4.1 + - - +
88B VAL* 1.3 82.8 - - + +
90B ALA* 1.3 63.0 + - - +
92B PHE* 3.4 13.6 + - + +
93B GLY 3.1 15.8 + - - -
137B GLY* 3.5 36.0 - - - +
140B GLY 4.1 9.6 - - - +
141B GLY* 4.1 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B SER 2.6 21.0 + - - +
87B ALA 3.6 4.3 - - - +
89B LEU* 1.3 72.8 - - - +
91B MET* 1.3 56.9 + - - +
93B GLY* 2.9 16.8 + - - -
94B TYR* 3.0 24.0 + - + -
137B GLY 4.2 2.8 + - - -
138B THR* 4.4 10.2 - - - +
141B GLY* 6.3 0.4 - - - -
143B MET* 4.2 9.0 - - + -
295B GLY 3.4 24.5 - - - +
299B GLY* 3.6 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA* 2.9 30.0 + - + +
88B VAL* 3.5 23.3 - - + +
90B ALA* 1.3 75.4 - - - +
92B PHE* 1.3 56.7 + - - +
94B TYR* 3.5 1.1 + - - +
95B PHE* 2.8 33.2 + - - +
292B VAL* 3.0 41.5 - - + +
293B LEU* 4.2 22.9 - - - +
296B GLY* 3.4 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 2.9 19.4 + - + +
89B LEU* 3.6 16.8 - - + +
90B ALA 3.3 0.2 - - - -
91B MET* 1.3 76.7 - - - +
93B GLY* 1.3 56.9 + - - +
95B PHE* 3.7 7.8 - + - +
96B LEU* 3.2 55.4 + - + +
133B PHE* 3.6 42.0 - + + -
136B LEU* 6.0 0.2 - - + -
137B GLY* 4.9 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU 3.1 9.2 + - - -
90B ALA 2.9 10.0 + - - -
92B PHE* 1.3 76.4 - - - +
94B TYR* 1.3 64.0 + - - -
95B PHE 3.0 1.8 + - - -
96B LEU* 3.4 10.2 + - - +
97B VAL* 3.4 18.9 + - - +
133B PHE 5.0 0.2 - - - -
134B GLY* 3.8 27.0 - - - -
138B THR* 4.6 3.1 - - - -
353B PRO* 4.5 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA 3.0 29.3 + - - +
91B MET 4.0 2.9 - - - +
93B GLY* 1.3 73.8 - - - +
95B PHE* 1.3 62.3 + - - +
97B VAL* 3.4 5.8 + - - +
98B ARG* 3.0 28.9 + - + +
138B THR* 4.3 6.5 - - + -
143B MET* 3.5 18.0 - - + +
291B TRP* 3.5 26.9 - + + -
292B VAL* 3.9 17.7 - - + +
294B MET* 5.0 1.1 - - + -
295B GLY* 3.3 37.0 - - - -
298B ILE* 4.1 4.0 - - - +
350B SER* 2.3 50.1 + - - -
351B GLY 4.8 1.3 - - - -
352B ALA* 3.3 28.3 - - + +
353B PRO* 4.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B MET 2.8 20.7 + - - +
92B PHE* 3.7 8.7 - + - +
93B GLY 3.0 0.2 - - - -
94B TYR* 1.3 74.1 - - - +
96B LEU* 1.3 82.4 + - + +
97B VAL 2.9 5.5 + - - -
98B ARG* 3.8 1.5 - - - +
99B LYS* 3.0 41.3 + - + +
100B TYR* 4.3 20.6 - + - -
288B ILE* 4.3 17.7 - - + -
292B VAL* 3.5 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 3.2 59.2 + - + +
93B GLY 3.4 4.9 + - - +
95B PHE* 1.3 92.5 - - + +
97B VAL* 1.3 59.4 + - - +
99B LYS 4.2 0.4 - - - -
100B TYR* 3.4 38.6 + - + +
129B PRO* 5.5 1.8 - - + +
130B VAL* 3.3 47.8 - - + +
133B PHE* 5.1 7.2 - - + -
134B GLY* 4.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLY 3.4 14.3 + - - +
94B TYR* 3.6 8.1 - - - +
95B PHE 2.9 2.0 + - - -
96B LEU* 1.3 75.4 - - - +
98B ARG* 1.3 73.6 + - + +
99B LYS 3.1 1.6 - - - -
101B ALA 3.0 46.3 + - - +
102B PRO* 3.2 8.8 - - + +
104B ALA 3.6 16.2 - - - +
105B GLY* 3.5 25.1 - - - +
130B VAL* 3.8 15.7 - - + +
351B GLY 4.9 2.2 - - - +
353B PRO* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 3.0 20.1 + - - +
95B PHE 4.0 0.7 - - - +
97B VAL* 1.3 86.1 - - + +
99B LYS* 1.3 59.6 + - - +
102B PRO* 3.1 51.2 + - - +
105B GLY* 6.0 0.8 - - - -
286B GLY* 4.6 7.4 + - - -
288B ILE* 3.4 31.4 - - + +
291B TRP* 3.0 69.0 - - + +
292B VAL* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 3.0 31.9 + - + +
98B ARG* 1.3 80.3 - - - +
100B TYR* 1.3 96.9 + - + +
102B PRO* 5.6 0.9 - - - -
126B ARG* 4.7 2.3 + - - -
288B ILE* 4.0 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 4.3 13.5 - + - -
96B LEU* 3.4 36.4 + - + +
99B LYS* 1.3 113.3 - - + +
101B ALA* 1.3 63.5 + - - +
102B PRO* 4.0 3.8 - - - -
123B ARG* 3.8 2.6 + - - -
126B ARG* 2.4 47.8 + - + +
130B VAL* 3.8 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU 3.8 2.0 + - - -
97B VAL* 3.0 21.5 + - - +
100B TYR* 1.3 81.9 - - - +
102B PRO* 1.3 67.9 - - - +
103B GLU* 3.2 5.2 - - - +
104B ALA* 3.2 18.1 + - + +
123B ARG* 4.6 2.9 - - - +
126B ARG* 3.9 17.3 - - + +
127B VAL* 4.4 7.9 - - + -
130B VAL* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il