Contacts of the helix formed by residues 76 - 96 (chain B) in PDB entry 6FI8
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 GLY 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PRO 5.6 2.9 - - - -
71B ILE* 3.8 5.5 - - - +
72B ASP 3.0 10.6 + - - -
73B PRO* 3.6 9.2 + - - -
74B SER 3.4 2.2 - - - -
75B PHE* 1.3 92.8 - - - +
77B VAL* 1.3 65.3 + - - +
78B MET* 3.1 5.0 + - - -
79B LYS 3.3 11.1 + - - -
80B PHE 3.6 1.9 + - - -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 5.2 0.7 - - - +
73A PRO* 3.6 36.3 + - + +
19B TYR* 3.8 39.2 + - + +
21B ILE* 3.8 18.6 - - + -
71B ILE* 3.6 29.2 - - + +
73B PRO* 6.0 0.4 - - - +
76B GLY* 1.3 72.9 - - - -
78B MET* 1.3 64.2 + - + +
80B PHE* 3.4 4.3 + - - +
81B ILE* 3.1 27.7 + - + +
113B ILE* 4.3 9.0 - - + -
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Residues in contact with MET 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.9 24.7 - - + -
73A PRO* 3.7 11.2 + - - +
74A SER* 3.6 21.3 - - - -
76B GLY* 3.1 2.1 - - - -
77B VAL* 1.3 76.9 - - - +
79B LYS* 1.3 59.6 + - - +
81B ILE* 3.8 7.2 - - + +
82B LYS* 2.8 32.7 + - - +
111B CYS* 4.5 8.1 - - - -
113B ILE* 3.5 31.4 - - - -
35D T 3.7 26.0 - - - +
36D A 3.4 35.4 - - - +
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.1 4.7 - - - +
75B PHE* 3.7 51.7 - - + +
76B GLY* 3.3 7.2 + - - +
78B MET* 1.3 79.0 - - - +
80B PHE* 1.3 57.2 + - - +
82B LYS* 4.0 8.0 - - + +
83B THR* 2.6 39.4 + - - +
27D C 6.0 0.9 - - - -
28D T 5.1 15.6 + - - -
36D A 5.6 0.4 + - - -
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 4.2 18.2 - - + -
23B TRP* 5.3 1.6 - + - -
44B ILE* 4.2 21.3 - - + -
47B VAL* 4.2 22.4 - - + -
48B ALA* 4.2 12.8 - - + -
51B LEU* 4.2 8.7 - - + -
53B VAL* 3.8 40.2 - - + -
55B ILE* 4.9 4.3 - - + -
67B ILE* 4.4 22.0 - - + -
69B ALA* 4.7 0.4 - - + -
71B ILE* 3.8 24.7 - - + -
75B PHE* 3.9 3.7 - - + -
76B GLY 3.6 5.3 + - - +
77B VAL 3.4 7.5 + - - +
78B MET 3.2 0.4 - - - -
79B LYS* 1.3 77.0 - - - +
81B ILE* 1.3 63.4 + - + +
83B THR* 3.2 1.6 + - - -
84B ALA* 2.8 37.4 + - + +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 3.6 40.2 - - + -
23B TRP* 4.4 7.6 - - + -
77B VAL* 3.1 16.2 + - + +
78B MET* 3.8 10.5 - - + +
80B PHE* 1.3 79.4 - - + +
82B LYS* 1.3 58.4 + - - +
84B ALA* 4.5 3.8 - - - -
85B LYS* 2.9 54.6 + - + +
111B CYS* 3.9 14.4 - - - -
113B ILE* 3.6 32.3 - - + -
35D T 4.1 8.3 - - - +
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B MET 2.8 21.9 + - - +
79B LYS* 4.0 8.5 - - + +
81B ILE* 1.3 74.0 - - - +
83B THR* 1.3 62.9 + - - +
86B GLY* 2.8 27.9 + - - -
26D G 3.7 7.9 - - - +
27D C 2.9 35.0 + - - -
28D T 3.2 26.0 + - - -
29D T 3.7 11.4 + - + +
33D G 3.7 0.6 - - - +
34D C 3.2 27.8 - - + +
35D T 3.5 37.4 + - - +
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Residues in contact with THR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 3.8 16.8 - - + +
51B LEU* 3.7 20.5 - - + +
79B LYS* 2.6 31.1 + - - +
80B PHE 3.8 2.2 - - - -
82B LYS* 1.3 79.3 - - - +
84B ALA* 1.3 60.1 + - - +
87B ARG* 2.9 46.1 + - - +
28D T 4.8 5.6 - - - +
29D T 3.7 29.4 - - + +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 3.9 22.7 - - + -
43B ILE* 5.1 0.9 - - - +
44B ILE* 4.3 14.6 - - + +
47B VAL* 3.9 14.0 - - + +
80B PHE* 2.8 41.3 + - + +
81B ILE* 4.0 1.3 - - - +
83B THR* 1.3 73.4 - - - +
85B LYS* 1.3 52.3 + - - +
88B SER* 2.6 37.2 + - - -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 3.5 39.9 - - + +
81B ILE* 2.9 29.8 + - + +
84B ALA* 1.3 74.8 - - - +
86B GLY* 1.3 66.0 + - - +
88B SER* 3.1 5.2 + - - -
89B SER* 2.9 21.1 + - - -
107B TRP* 3.2 32.1 + - + +
108B THR* 2.9 25.9 + - - -
110B SER 3.0 23.4 + - - +
111B CYS* 4.6 0.6 - - + +
34D C 3.5 13.2 - - - +
35D T 2.6 28.7 + - - +
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Residues in contact with GLY 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS 2.8 17.1 + - - -
85B LYS* 1.3 75.4 - - - +
87B ARG* 1.3 60.9 + - - +
89B SER* 3.5 2.6 + - - -
90B ARG* 3.1 22.9 + - - +
29D T 3.2 35.9 + - - -
33D G 4.0 2.4 - - - +
34D C 3.6 13.0 - - - -
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 4.0 9.9 - - + -
46B GLU* 4.5 11.0 + - - +
47B VAL* 3.6 34.1 - - + +
50B GLU* 2.9 42.8 + - - -
51B LEU* 5.2 0.2 - - - +
83B THR* 2.9 31.3 + - - +
86B GLY* 1.3 69.7 - - - +
88B SER* 1.3 61.8 + - - +
90B ARG* 3.1 1.4 + - - +
91B ILE* 2.9 48.2 + - + +
29D T 2.6 61.7 + - - +
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 5.2 0.5 - - - -
40B LEU* 3.7 25.1 - - - +
43B ILE* 4.0 23.4 - - - +
44B ILE* 5.0 1.3 - - - -
84B ALA 2.6 24.8 + - - -
85B LYS* 3.1 5.4 + - - -
87B ARG* 1.3 78.6 - - - +
89B SER* 1.3 59.1 + - - +
92B LEU* 3.0 40.0 + - - +
106B LEU* 4.4 0.4 - - - -
107B TRP* 3.1 15.9 + - - -
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LYS 2.9 19.8 + - - -
86B GLY 3.7 2.0 - - - -
88B SER* 1.3 79.3 + - - +
90B ARG* 1.3 61.3 + - - +
93B ARG* 3.2 33.4 + - - +
106B LEU* 3.4 17.6 - - - +
107B TRP* 3.8 7.2 - - - -
33D G 3.0 17.8 + - - -
34D C 2.5 29.4 + - - -
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLY 3.1 14.9 + - - +
87B ARG 3.1 7.2 + - - +
89B SER* 1.3 76.9 - - - +
91B ILE* 1.3 63.8 + - + +
93B ARG* 4.1 1.9 - - - +
94B GLN* 3.2 65.9 + - - +
29D T 3.6 34.8 - - - +
30D T 2.9 30.6 + - - -
31D T 4.0 16.0 + - - -
32D A 3.3 47.5 + - - -
33D G 3.7 9.7 + - - -
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Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 4.0 8.5 - - - +
43B ILE* 3.7 29.8 - - + -
46B GLU* 5.5 3.8 - - - +
87B ARG* 2.9 43.7 + - + +
90B ARG* 1.3 79.4 - - + +
92B LEU* 1.3 65.6 + - - +
94B GLN* 2.9 26.0 + - - +
95B GLU* 3.0 41.9 + - + +
29D T 5.5 2.9 - - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 5.9 0.2 - - + -
36B VAL* 4.2 12.6 - - + +
39B ARG* 3.6 27.8 - - + -
40B LEU* 4.0 36.1 - - + +
43B ILE* 4.1 7.4 - - + -
88B SER* 3.0 22.4 + - - +
91B ILE* 1.3 76.7 - - - +
93B ARG* 1.3 57.3 + - - +
95B GLU* 4.4 1.1 - - - +
96B PHE* 2.8 61.1 + - + +
99B LEU* 3.9 14.5 - - + +
106B LEU* 3.7 20.0 - - + -
107B TRP* 5.0 0.2 - - + -
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Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B SER* 3.2 34.7 + - - +
90B ARG 4.2 0.4 - - - +
91B ILE 3.2 0.8 - - - -
92B LEU* 1.3 75.6 - - - +
94B GLN* 1.3 62.5 + - - +
96B PHE 3.7 10.9 - - - +
97B ASN* 5.0 0.7 - - - -
99B LEU* 3.0 33.3 + - + +
100B LYS* 3.4 38.3 + - + +
103B LEU 3.0 24.0 + - - -
104B PRO 3.3 22.7 + - - -
105B THR* 3.8 4.9 - - - +
106B LEU* 4.0 14.1 - - + +
33D G 2.5 44.6 + - - +
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Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ARG* 3.2 62.6 + - - +
91B ILE* 2.9 19.7 + - - +
93B ARG* 1.3 79.5 - - - +
95B GLU* 1.3 63.9 + - + +
96B PHE 5.0 0.9 - - - -
97B ASN* 5.4 0.3 + - - -
30D T 4.9 0.8 + - - -
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 3.0 52.3 + - - +
91B ILE* 3.0 30.5 + - + +
92B LEU* 3.3 0.5 + - - +
94B GLN* 1.3 81.1 - - + +
96B PHE* 1.3 80.2 + - + +
97B ASN 4.1 1.0 + - - -
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA* 3.7 25.4 - - + -
36B VAL* 3.6 38.1 - - + -
39B ARG* 4.3 7.0 - - + -
92B LEU* 2.8 54.6 + - + +
93B ARG 3.7 6.1 - - - +
94B GLN 5.0 0.7 - - - -
95B GLU* 1.3 96.0 - - + +
97B ASN* 1.3 65.8 + - - +
98B HIS* 3.2 23.3 - + + -
99B LEU* 3.1 19.5 + - + +
100B LYS 3.5 6.1 + - - -
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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) + - + + + + + -
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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