Contacts of the helix formed by residues 64 - 85 (chain B) in PDB entry 1Q4U
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 HIS 64 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.8 26.0 - - + -
31A ASP* 2.6 43.0 + - - -
36A PHE* 4.6 1.6 - - - -
70A ALA* 3.4 35.8 - - + +
73A GLU* 4.4 1.3 - - + -
74A MET 4.3 1.6 - - - -
370A 4CA 3.5 24.3 - + - -
56B LEU 2.8 19.3 + - - +
57B ARG* 3.8 3.3 - - - +
58B GLN* 3.8 13.7 - - + -
62B LEU 3.2 2.8 + - - -
63B VAL* 1.3 71.6 - - - +
65B GLY* 1.3 68.0 + - - +
66B GLY* 2.9 24.2 + - - -
67B ALA* 2.8 17.9 + - - +
68B TYR* 3.4 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 3.7 15.7 - - - -
370A 4CA 3.6 16.8 - - - +
63B VAL 3.5 2.6 + - - -
64B HIS* 1.3 74.4 + - - +
66B GLY* 1.3 62.9 + - - +
67B ALA 3.0 1.0 + - - -
68B TYR* 3.0 18.1 + - - +
69B CYS* 3.2 15.2 + - - -
100B PHE* 3.5 26.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.7 2.0 - - - -
66A GLY 4.1 3.1 - - - +
69A CYS 4.6 0.9 - - - -
70A ALA* 3.6 29.2 - - - -
73A GLU* 4.2 4.0 - - - +
64B HIS* 2.9 18.1 + - - -
65B GLY* 1.3 75.8 - - - +
67B ALA* 1.3 55.3 + - - +
69B CYS* 3.4 9.9 + - - +
70B ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.3 10.2 - - + +
36B PHE* 3.6 7.1 - - + -
56B LEU* 3.7 42.4 - - + +
63B VAL* 3.9 8.3 - - + -
64B HIS* 2.8 18.3 + - - +
66B GLY* 1.3 74.5 - - - +
68B TYR* 1.3 63.5 + - - +
70B ALA* 3.3 4.5 + - - -
71B LEU* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A 4CA 4.9 5.0 + - - -
63B VAL* 3.6 29.0 + - + +
64B HIS 3.4 12.3 - - - -
65B GLY* 3.0 11.7 + - - +
67B ALA* 1.3 77.3 - - - +
69B CYS* 1.3 64.6 + - - +
71B LEU* 3.3 3.0 + - - +
72B ALA* 3.0 25.8 + - - +
98B THR* 4.3 9.0 - - + -
100B PHE* 3.6 25.1 - + + -
102B ARG 4.2 2.1 + - - -
103B PRO* 4.0 5.9 - - + +
104B VAL* 3.4 35.6 + - + +
109B VAL* 4.2 21.8 - - + -
129B LEU* 3.8 28.5 - - + +
137B CYS* 4.3 20.0 - - + -
138B ALA* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY* 4.6 0.7 - - - -
69A CYS* 3.5 37.2 - - + -
96A ASN* 3.9 17.3 - - - -
65B GLY 3.2 16.6 + - - -
66B GLY* 3.5 9.6 - - - +
68B TYR* 1.3 79.3 - - - +
70B ALA* 1.3 57.7 + - - +
72B ALA* 3.7 0.9 - - - +
73B GLU* 2.8 25.6 + - - +
96B ASN* 3.0 14.2 + - - +
98B THR* 3.7 32.3 - - - -
100B PHE* 4.1 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 6.5 0.2 - - + -
64A HIS* 3.5 18.6 - - + +
66A GLY* 3.7 25.4 - - - -
30B LEU* 4.4 9.4 - - + -
36B PHE* 3.5 14.9 - - + -
66B GLY 2.9 17.6 + - - +
67B ALA* 3.8 5.6 - - - +
69B CYS* 1.3 75.3 - - - +
71B LEU* 1.3 64.6 + - - +
73B GLU* 4.2 0.4 - - - -
74B MET* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 3.5 36.5 - - + -
48B ALA* 4.1 24.7 - - + +
49B SER* 4.6 3.1 - - - +
50B VAL* 4.2 22.0 - - + -
67B ALA 3.0 16.5 + - - +
68B TYR* 3.3 4.0 + - - +
70B ALA* 1.3 76.4 - - - +
72B ALA* 1.3 65.1 + - - +
74B MET* 4.0 3.7 - - + -
75B LEU* 2.9 28.8 + - - +
109B VAL* 4.2 16.2 - - + +
111B ALA* 3.9 26.5 - - + +
129B LEU* 4.0 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR 3.0 18.0 + - - +
69B CYS 3.7 2.7 - - - +
71B LEU* 1.3 81.0 - - - +
73B GLU* 1.3 62.6 + - - +
75B LEU* 4.0 1.3 - - - +
76B ALA* 3.0 28.2 + - - +
127B VAL* 4.0 24.2 - - + +
129B LEU* 4.6 3.8 - - + +
140B SER* 3.5 35.0 - - - +
142B MET* 3.8 2.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY* 3.4 22.6 - - - -
66A GLY 4.2 8.3 - - - +
100A PHE* 3.5 13.1 - - - -
371A 4CA 3.4 34.9 - - + +
69B CYS 2.8 17.7 + - - +
70B ALA* 3.7 7.6 - - - +
72B ALA* 1.3 77.4 - - - +
74B MET* 1.3 61.6 + - - +
77B THR* 2.6 32.7 + - - -
93B GLY* 3.9 7.5 - - - -
96B ASN* 3.0 25.2 + - - +
142B MET* 3.4 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A 4CA 3.5 34.3 - - + +
15B LEU* 4.2 14.6 - - + -
31B ASP* 3.3 26.9 - - + +
36B PHE* 3.6 36.1 - - + -
38B ILE* 3.8 35.7 - - + -
48B ALA* 4.7 3.1 - - + -
70B ALA 3.0 16.0 + - - +
71B LEU* 4.1 8.7 - - + +
73B GLU* 1.3 75.9 - - - +
75B LEU* 1.3 59.4 + - - +
78B GLU* 2.7 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.2 12.1 - - + -
41B MET* 4.3 2.5 - - + -
46B ALA* 3.5 39.7 - - + +
47B THR* 3.9 17.3 - - - +
48B ALA* 4.0 13.5 - - + +
71B LEU* 2.9 19.8 + - + +
72B ALA* 4.0 2.9 - - - +
74B MET* 1.3 83.0 - - - +
76B ALA* 1.3 62.0 + - - +
78B GLU* 4.1 0.6 - - - +
79B ALA* 3.0 26.9 + - - +
111B ALA* 3.9 26.9 - - + +
113B ALA* 3.7 22.7 - - + +
127B VAL* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA 3.0 20.9 + - - +
73B GLU 4.4 0.7 - - - +
75B LEU* 1.3 74.6 - - - +
77B THR* 1.3 60.7 + - - +
79B ALA* 3.6 1.4 + - - +
80B THR* 2.8 27.7 + - - -
113B ALA* 4.8 2.8 - - - +
125B TRP* 3.6 30.4 + - + -
127B VAL* 4.5 3.8 - - + -
142B MET* 3.5 30.5 - - + -
144B ILE* 4.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A 4CA 3.6 31.4 - - + +
73B GLU* 2.6 26.9 + - - +
74B MET 3.9 0.7 - - - -
76B ALA* 1.3 74.9 - - - +
78B GLU* 1.3 61.4 + - - +
80B THR* 2.9 7.5 + - - -
81B VAL* 2.9 29.0 + - + +
91B ALA 3.4 31.2 - - - +
92B VAL* 4.1 7.6 - - - +
93B GLY* 4.1 6.7 + - - +
144B ILE* 3.7 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 2.8 32.8 + - - -
60A TRP* 2.9 23.9 + - - -
371A 4CA 2.7 33.1 + - + +
15B LEU* 3.8 11.7 - - + -
16B PRO* 3.4 24.4 - - + +
38B ILE* 4.3 9.4 - - + -
41B MET* 4.2 0.2 - - - -
74B MET* 2.7 26.4 + - + +
75B LEU 4.3 0.9 - - - +
77B THR* 1.3 74.1 - - - +
79B ALA* 1.3 62.5 + - - +
81B VAL* 3.2 16.9 + - - +
82B ALA 2.9 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B MET* 3.7 24.6 - - + +
42B THR 4.8 4.4 - - - +
43B PRO* 5.1 0.5 - - - +
46B ALA* 4.0 12.1 - - + -
75B LEU 3.0 19.4 + - - +
76B ALA 3.9 1.6 - - - +
77B THR 3.2 0.2 - - - -
78B GLU* 1.3 78.4 - - - +
80B THR* 1.3 61.6 + - - +
82B ALA* 3.6 11.3 - - - +
83B VAL* 4.0 11.1 + - - +
113B ALA* 5.9 0.2 - - + -
123B TRP* 4.4 0.2 - - - -
125B TRP* 3.7 33.5 - - + -
----------------------------------------------------------
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 ALA 2.8 18.4 + - - -
77B THR 2.9 8.1 + - - -
79B ALA* 1.3 73.2 - - - +
81B VAL* 1.3 67.2 + - - +
83B VAL* 2.9 13.5 + - - +
84B VAL* 3.0 16.4 + - + +
91B ALA* 3.7 17.3 - - + -
123B TRP* 3.7 31.8 - - + -
125B TRP* 2.9 19.4 + - - -
144B ILE* 3.8 14.7 - - + +
146B VAL* 3.9 15.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
59A ARG* 4.7 0.7 - - - +
60A TRP* 4.1 15.3 - - + +
371A 4CA 5.7 0.2 - - + -
16B PRO* 5.1 0.2 - - + -
18B VAL* 3.9 27.6 - - + -
77B THR* 2.9 22.1 + - + +
78B GLU* 3.5 29.6 - - - +
80B THR* 1.3 76.2 - - - +
82B ALA* 1.3 64.8 + - - +
84B VAL* 4.2 8.7 - - - -
85B HIS* 2.9 34.4 + - + +
91B ALA* 4.0 24.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
16B PRO* 3.9 17.5 - - + -
18B VAL* 4.4 9.9 - - - +
41B MET* 3.9 21.5 - - + -
42B THR 6.4 0.7 - - - -
78B GLU 2.9 16.7 + - - +
79B ALA 3.6 8.5 - - - +
80B THR 3.1 0.4 - - - -
81B VAL* 1.3 78.2 - - - +
83B VAL* 1.4 61.3 + - + +
85B HIS* 4.9 0.7 + - - +
86B GLU* 5.3 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO* 3.8 37.9 - - + -
79B ALA 4.1 7.2 - - - +
80B THR 2.9 7.3 + - - +
82B ALA* 1.4 79.1 - - + +
84B VAL* 1.3 68.6 + - + +
85B HIS 3.5 0.7 - - - -
86B GLU* 3.7 12.5 - - - +
87B LYS* 3.5 40.0 - - - +
123B TRP* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 3.0 22.5 + - + +
81B VAL* 4.2 2.2 - - - -
83B VAL* 1.3 80.9 - - + +
85B HIS* 1.3 66.8 + - - +
86B GLU 3.2 2.5 - - - -
87B LYS* 2.9 20.7 + - + +
89B MET* 3.2 43.5 + - + +
91B ALA* 4.0 23.8 - - + +
123B TRP* 3.9 28.9 - - + +
146B VAL* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 4.2 22.1 - + - -
18B VAL* 3.3 48.1 + - + +
19B ALA* 4.1 8.4 - - + +
81B VAL* 2.9 32.8 + - + +
82B ALA 5.3 0.2 - - - +
83B VAL 3.5 0.4 - - - -
84B VAL* 1.3 73.4 - - - +
86B GLU* 1.3 61.0 + - + +
87B LYS 3.0 5.4 + - - -
88B GLY 3.1 3.1 + - - -
89B MET 3.6 9.6 + - - -
90B MET* 5.9 0.4 - - - -
149B ARG* 2.6 61.4 + - - -
----------------------------------------------------------
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