Contacts of the helix formed by residues 79 - 97 (chain B) in PDB entry 3QNQ
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 ILE 79 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 5.0 1.3 - - + -
109A VAL* 4.7 3.1 - - + -
112A LEU* 3.2 38.4 - - + -
117A PHE* 3.7 27.6 - - + -
136A ILE* 4.6 3.4 - - + -
74B SER 3.9 7.4 - - - +
75B ALA* 3.6 27.4 - - - +
76B THR 3.4 1.1 + - - +
77B PHE 3.2 0.4 - - - -
78B ASN* 1.3 81.7 - - - +
80B MET* 1.3 71.4 + - - +
81B ALA 3.1 2.7 - - - -
82B LEU* 2.6 32.5 + - + +
83B ILE* 3.2 26.7 + - + -
141B MET* 3.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B THR* 3.8 12.4 - - + +
36B LEU* 3.4 37.7 - - + -
76B THR 3.0 9.3 + - - +
77B PHE* 3.4 18.8 - - - +
79B ILE* 1.3 76.6 - - - +
81B ALA* 1.3 57.4 + - - +
83B ILE* 3.4 6.8 + - - +
84B ALA* 2.8 29.7 + - - +
141B MET 4.1 0.2 + - - -
143B SER* 3.5 33.4 - - - +
146B LEU* 3.1 31.6 - - + -
264B LEU* 3.5 21.8 - - + -
267B MET* 4.4 9.6 - - - -
268B ASP* 4.5 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ILE 2.9 1.2 + - - -
80B MET* 1.3 74.2 - - - +
82B LEU* 1.3 58.8 + - - +
84B ALA* 3.9 8.7 - - - -
85B VAL* 2.9 28.6 + - - +
111B PHE* 4.2 8.5 - - + -
141B MET 2.9 21.1 + - - +
142B GLY 3.5 4.9 - - - +
145B GLY* 3.6 5.8 - - - -
146B LEU* 3.3 38.6 - - + +
149B ALA* 3.5 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 4.7 15.7 - - + -
108A LEU* 5.1 7.2 - - + -
112A LEU* 3.9 28.7 - - + -
136A ILE* 5.4 2.0 - - + -
79B ILE* 2.6 31.0 + - + +
81B ALA* 1.3 68.7 - - - +
83B ILE* 1.3 65.2 + - - +
85B VAL* 2.7 26.9 - - - +
86B PHE* 3.2 2.4 + - - +
108B LEU* 3.5 30.7 - - + +
111B PHE* 3.7 25.3 - - + -
112B LEU* 4.3 10.1 - - + -
141B MET* 3.7 21.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA* 4.8 5.4 - - + +
108A LEU* 4.0 17.3 - - + -
109A VAL* 3.2 30.5 - - + -
31B LEU* 3.6 41.7 - - + +
32B THR* 4.1 6.1 - - + -
35B PHE* 3.6 24.0 - - + -
75B ALA 5.1 0.7 - - - +
76B THR* 5.2 3.6 - - - +
79B ILE* 3.2 22.1 + - + +
80B MET* 3.7 7.4 - - - +
82B LEU* 1.3 74.9 - - - +
84B ALA* 1.3 63.7 + - - +
86B PHE* 2.9 20.3 + - - +
87B GLY* 3.0 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLY 4.8 5.3 - - - +
29B LEU* 3.6 29.6 - - + -
32B THR* 3.8 10.9 - - + +
80B MET 2.8 22.1 + - - +
81B ALA* 3.9 9.9 - - - -
83B ILE* 1.3 73.7 - - - +
85B VAL* 1.3 60.9 + - - +
87B GLY 4.6 0.7 - - - +
88B ILE* 3.1 31.8 + - + +
146B LEU* 4.7 8.5 - - + -
149B ALA* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA 2.9 18.3 + - - +
82B LEU* 2.7 25.5 + - - +
84B ALA* 1.3 72.6 - - - +
86B PHE* 1.3 68.7 + - - +
89B ALA* 3.3 20.6 + - - +
107B SER* 3.7 15.9 - - - +
108B LEU* 4.0 19.3 - - + -
111B PHE* 4.1 11.4 - - + -
149B ALA* 3.6 23.5 - - + +
152B ILE* 3.5 31.2 - - + -
153B ALA* 3.8 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 2.9 63.5 - + + -
101A LEU* 4.0 9.4 - - + -
105A ALA* 6.2 0.4 - - + -
108A LEU* 5.7 2.5 - - + -
31B LEU* 4.8 3.8 - - + -
82B LEU 4.3 3.8 - - - +
83B ILE* 2.9 12.5 + - - +
85B VAL* 1.3 85.9 - - + +
87B GLY* 1.3 65.7 + - - +
89B ALA* 3.8 1.2 - - - +
90B TYR* 2.9 53.0 + + + +
101B LEU* 4.3 9.6 - - + -
104B GLY* 2.7 35.3 - - - -
105B ALA* 3.8 12.8 - - + -
108B LEU* 4.5 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 5.5 2.5 - - - -
28B GLY* 3.7 19.3 - - - -
31B LEU* 3.7 21.2 - - - +
83B ILE 3.0 8.7 + - - -
84B ALA 4.0 0.2 - - - -
86B PHE* 1.3 80.6 - - - +
88B ILE* 1.3 63.4 + - - +
90B TYR* 3.3 7.3 - - - +
91B ARG* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 3.9 19.3 - - + +
25B ILE* 3.5 53.4 - - + +
28B GLY* 3.7 6.7 - - - -
29B LEU* 4.5 9.0 - - + -
84B ALA* 3.1 21.3 + - + +
86B PHE 3.2 0.2 + - - -
87B GLY* 1.3 73.7 - - - +
89B ALA* 1.3 62.8 + - - +
91B ARG* 3.3 1.4 + - - +
92B LEU* 3.0 23.2 + - + +
149B ALA* 5.1 0.9 - - + -
150B MET* 3.8 23.8 - - + +
153B ALA* 4.1 17.7 - - + -
154B ILE* 4.4 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL 3.3 8.4 + - - +
86B PHE 3.2 3.2 + - - +
88B ILE* 1.3 77.5 - - - +
90B TYR* 1.3 54.0 + - - +
92B LEU* 3.3 3.0 + - - -
93B GLY 2.7 30.5 + - - -
103B SER* 2.8 20.3 + - - +
104B GLY* 3.9 0.7 - - - -
107B SER* 3.2 28.9 - - - +
153B ALA* 4.0 7.1 - - + +
157B THR* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 2.5 30.0 + + - -
101A LEU* 3.8 36.6 - - + +
182A ARG* 5.7 2.4 + - - -
443A ZDM 6.1 0.2 - - - -
86B PHE* 2.9 43.8 + + + +
87B GLY* 3.3 6.1 - - - +
89B ALA* 1.3 76.8 - - - +
91B ARG* 1.3 58.5 + - + +
93B GLY* 3.0 2.8 + - - -
94B GLU* 2.9 53.8 + - - +
100B ALA* 3.3 38.4 - - + +
101B LEU* 3.5 12.3 - - - -
103B SER* 3.7 6.3 + - - -
104B GLY* 3.7 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ZDM 2.9 69.3 + - - +
23B LEU* 4.1 15.0 - - - +
24B ALA* 4.0 22.7 - - - +
27B ASP* 3.2 27.2 + - + -
28B GLY* 4.5 4.0 - - - +
87B GLY 2.9 15.9 + - - +
88B ILE 3.8 3.4 - - - +
90B TYR* 1.3 75.1 - - + +
92B LEU* 1.3 65.2 + - - +
93B GLY 2.7 5.3 + - - -
94B GLU* 3.0 19.2 + - - +
95B TYR* 2.9 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 4.0 11.2 - - + +
21B HIS* 4.1 13.7 - - + -
24B ALA* 3.7 21.3 - - + +
88B ILE* 3.0 17.8 + - + +
89B ALA* 3.5 3.8 - - - +
91B ARG* 1.3 76.8 - - - +
93B GLY* 1.3 62.8 + - - +
95B TYR* 3.5 13.1 - - + +
96B TYR* 3.3 46.4 + - + +
153B ALA 4.8 0.4 - - - +
154B ILE* 4.3 17.5 - - + +
157B THR* 3.8 25.9 - - + +
158B GLU* 4.0 21.3 - - - +
----------------------------------------------------------
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 ALA 2.7 14.7 + - - -
90B TYR 3.2 6.3 - - - -
91B ARG 2.7 1.4 - - - -
92B LEU* 1.3 74.7 - - - +
94B GLU* 1.3 64.9 + - - +
95B TYR 3.0 0.9 - - - -
96B TYR 2.9 13.7 + - - -
97B LYS 3.2 7.3 + - - -
98B VAL* 3.4 26.2 + - - +
100B ALA* 4.6 2.0 - - - -
103B SER* 3.5 12.6 - - - -
157B THR* 4.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ARG* 5.6 4.4 + - - -
443A ZDM 4.0 12.6 + - - +
444A CIT 5.3 4.3 - - - +
90B TYR* 2.9 42.5 + - + +
91B ARG* 3.6 27.8 + - - +
93B GLY* 1.3 69.6 - - - +
95B TYR* 1.3 64.6 + - - +
97B LYS* 3.1 14.1 + - - +
98B VAL 5.0 3.4 - - - -
100B ALA* 3.9 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU 5.1 3.4 + - - -
20B ARG* 2.5 63.0 + - + +
23B LEU* 4.1 16.4 - - + -
91B ARG* 2.9 32.9 + - - +
92B LEU* 3.5 16.4 - - + +
93B GLY 3.0 0.2 + - - -
94B GLU* 1.3 79.2 - - - +
96B TYR* 1.3 82.7 + + - +
97B LYS* 3.0 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 3.2 32.1 + - - -
21B HIS* 4.3 0.3 + - - -
92B LEU* 3.3 47.3 + - + +
93B GLY 2.9 8.6 + - - +
95B TYR* 1.3 86.5 - + - +
97B LYS* 1.3 69.9 + - - +
98B VAL* 3.2 4.8 + - + +
157B THR* 5.3 0.7 - - + -
158B GLU* 2.6 34.6 + - - -
161B ARG* 3.3 58.0 + - + -
165B GLN* 3.5 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU 3.1 11.8 + - - +
95B TYR 3.0 9.9 + - - +
96B TYR* 1.3 81.2 - - - +
98B VAL* 1.3 62.3 + - - +
165B GLN* 5.6 0.2 + - - -
----------------------------------------------------------
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