Contacts of the helix formed by residues 68 - 87 (chain B) in PDB entry 1EQB
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 CYS 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LYS* 3.7 19.5 - - - -
55B TYR 3.8 2.5 - - - -
56B ALA* 3.7 26.7 - - - -
63B ARG* 3.7 16.2 - - + -
65B PHE* 3.7 20.9 - - - +
67B GLY* 1.3 77.0 - - - +
69B GLU* 1.3 60.3 + - - +
70B TYR 3.4 1.8 - - - -
71B VAL* 3.4 17.0 - - + -
72B ASP* 2.8 39.1 + - - +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 3.8 16.3 - - - +
29A HIS* 4.3 8.3 - - - -
67B GLY* 3.0 34.9 + - - -
68B CYS* 1.3 84.2 + - - +
70B TYR* 1.3 82.9 + - + +
72B ASP* 3.7 5.4 - - - +
73B ILE* 3.5 23.7 + - - +
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 3.6 17.6 - - - +
21A GLN* 3.5 52.3 + - + -
22A GLU* 3.9 23.7 + - + +
25A ARG* 3.7 35.7 - - + -
68B CYS 3.4 0.2 - - - -
69B GLU* 1.3 95.0 + - + +
71B VAL* 1.3 66.0 + - - +
72B ASP 3.0 1.8 - - - -
73B ILE* 3.2 16.4 + - + +
74B VAL* 3.1 25.8 + - - +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 4.2 17.2 + - + +
51B LEU* 4.8 7.0 - - + -
54B LYS* 4.0 28.9 - - + -
56B ALA* 4.1 10.5 - - + -
63B ARG* 3.9 1.7 + - - +
67B GLY 4.8 0.4 - - - +
68B CYS* 3.4 39.3 - - + -
70B TYR* 1.3 76.3 - - - +
72B ASP* 1.3 64.1 + - - +
74B VAL* 3.4 6.0 + - - -
75B GLU* 2.9 25.1 + - - +
266B MET* 3.2 35.9 - - + +
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PRO* 3.2 20.1 - - + +
61B GLY* 2.7 27.8 + - - -
63B ARG* 2.6 35.6 + - - +
68B CYS* 2.8 29.7 + - - +
69B GLU* 3.7 8.2 - - - +
70B TYR 3.0 0.2 - - - -
71B VAL* 1.3 76.5 - - - +
73B ILE* 1.3 65.3 + - + +
75B GLU 3.6 0.2 + - - -
76B GLN* 3.1 24.3 + - - +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 5.1 2.2 - - + +
17A GLN* 6.2 0.9 - - - +
18A ALA* 3.5 20.0 - - + -
21A GLN* 4.4 9.0 - - - +
69B GLU 3.5 17.9 + - - +
70B TYR* 3.2 25.0 + - + +
72B ASP* 1.3 78.7 - - + +
74B VAL* 1.3 62.6 + - - +
76B GLN* 3.2 7.5 + - - +
77B LEU* 3.0 33.6 + - + +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.1 11.9 - - + -
18A ALA* 4.0 18.8 - - + -
19A MET 4.9 0.9 - - - +
51B LEU* 4.3 16.8 - - + -
70B TYR 3.1 16.7 + - - +
71B VAL* 3.5 12.6 - - - +
73B ILE* 1.3 77.4 - - - +
75B GLU* 1.3 62.6 + - - +
77B LEU* 3.2 11.9 + - - +
78B ALA* 3.2 19.6 + - - +
266B MET* 4.4 10.8 - - + +
269B ILE 4.4 2.0 - - - +
270B ALA* 3.6 39.5 - - + +
273B ALA* 4.3 1.4 - - - +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 3.8 5.0 - - - -
60B PRO* 3.3 21.6 - - + +
63B ARG* 2.7 33.3 + - - +
71B VAL 2.9 16.7 + - - +
72B ASP 4.0 2.2 - - - +
74B VAL* 1.3 76.9 - - - +
76B GLN* 1.3 57.8 + - - +
78B ALA* 3.3 2.8 + - - +
79B ILE* 3.0 44.0 + - + +
93B VAL* 3.7 15.2 + - + +
94B GLN* 2.7 36.1 + - - +
266B MET* 4.1 13.7 - - + +
269B ILE* 4.0 13.0 - - + -
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Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PRO* 3.7 22.5 - - + +
72B ASP 3.1 19.3 + - - +
73B ILE* 3.5 7.2 - - - +
74B VAL 3.2 0.2 - - - -
75B GLU* 1.3 72.9 - - - +
77B LEU* 1.3 61.8 + - - +
79B ILE* 3.2 17.4 + - - +
80B ASP* 2.8 70.2 + - - +
83B LYS* 6.0 0.4 - - - +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 3.6 24.2 - - + +
15A LEU* 3.7 45.5 - - + +
18A ALA* 5.4 0.2 - - + -
73B ILE* 3.0 28.5 + - + +
74B VAL* 3.4 9.4 - - - +
76B GLN* 1.3 77.1 - - - +
78B ALA* 1.3 56.0 + - - +
80B ASP* 3.5 5.5 + - + +
81B ARG* 2.5 65.4 + - - +
273B ALA* 4.3 7.2 - - + -
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL 3.2 3.6 + - - +
75B GLU 3.7 7.0 - - - +
76B GLN 3.2 0.2 - - - -
77B LEU* 1.3 79.4 - - - +
79B ILE* 1.3 58.8 + - - +
81B ARG* 4.4 0.9 - - - -
82B ALA* 3.0 31.2 + - - +
93B VAL* 3.9 14.1 - - + +
269B ILE* 3.8 25.8 - - + +
272B LYS* 4.7 3.8 - - + -
273B ALA* 3.8 28.7 - - + +
276B LEU* 3.5 5.7 - - + +
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 5.6 4.5 - - + -
60B PRO* 4.6 13.2 - - + -
75B GLU* 3.0 41.6 + - + +
76B GLN* 3.2 19.7 + - - +
78B ALA* 1.3 77.0 - - - +
80B ASP* 1.3 63.6 + - - +
82B ALA* 3.4 3.8 + - - +
83B LYS* 3.1 42.1 + - + +
91B ALA* 3.9 28.9 - - + +
92B ASN* 5.5 0.7 - - - -
93B VAL* 3.7 21.5 - - + +
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLN* 2.8 53.7 + - - +
77B LEU* 4.1 5.7 - - + +
79B ILE* 1.3 73.0 - - - +
81B ARG* 1.3 63.3 + - + +
83B LYS* 3.2 20.9 + - - +
84B GLU* 3.0 24.1 + - - +
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 2.4 43.4 + - - -
14A GLU* 3.4 23.8 + - - -
15A LEU* 4.3 4.8 - - - +
77B LEU* 2.5 49.2 + - - +
78B ALA* 4.1 3.4 - - - +
80B ASP* 1.3 76.9 - - + +
82B ALA* 1.3 58.3 + - - +
84B GLU* 3.7 2.2 - - - +
85B LEU* 2.8 34.1 + - - +
273B ALA* 3.2 26.1 + - - +
276B LEU* 3.9 15.9 - - + -
277B LYS* 3.8 21.5 - - - +
280B MET* 3.7 26.1 - - + +
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Residues in contact with ALA 82 (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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78B ALA 3.0 19.6 + - - +
79B ILE* 3.5 5.2 - - - +
81B ARG* 1.3 77.4 - - - +
83B LYS* 1.3 62.1 + - - +
85B LEU* 4.8 1.1 - - - -
86B PHE* 3.3 30.6 + - - +
91B ALA* 4.0 14.1 - - + -
238B LEU* 4.4 14.6 - - + -
240B LEU* 4.2 11.7 - - + +
276B LEU* 3.5 22.3 - - + +
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Residues in contact with LYS 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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76B GLN* 6.0 0.4 - - - +
79B ILE* 3.1 22.0 + - + +
80B ASP* 3.2 25.1 + - - +
82B ALA* 1.3 77.5 - - - +
84B GLU* 1.3 57.3 + - - +
87B GLY* 2.7 28.4 + - - -
88B ALA* 3.1 25.2 + - - +
89B ASP* 3.4 37.4 + - - +
90B TYR* 3.6 7.6 - - - +
91B ALA* 3.6 15.7 - - + +
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP 3.0 16.1 + - - +
81B ARG* 3.9 5.4 - - - +
83B LYS* 1.3 76.5 - - - +
85B LEU* 1.3 64.8 + - - +
86B PHE 3.4 0.3 + - - -
87B GLY* 3.8 6.2 + - - -
280B MET* 4.2 19.5 - - + +
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Residues in contact with LEU 85 (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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81B ARG 2.8 17.4 + - - +
82B ALA* 4.1 3.1 - - - +
84B GLU* 1.3 78.9 - - - +
86B PHE* 1.3 76.0 + - + +
209B ALA* 4.1 32.6 - - + +
215B ASN* 5.5 0.7 + - - -
231B LEU* 4.5 1.1 - - + -
276B LEU* 3.9 25.8 - - + +
279B ALA* 3.6 43.1 - - + +
280B MET* 4.1 22.2 - - + +
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Residues in contact with PHE 86 (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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82B ALA* 3.3 20.9 + - - +
84B GLU 3.3 0.2 - - - -
85B LEU* 1.3 98.7 - - + +
87B GLY* 1.3 60.9 + - - +
88B ALA* 4.7 2.7 - - + +
201B MET* 3.4 26.7 - - + -
205B ALA* 3.5 26.9 - - + -
208B VAL* 4.2 13.9 - - + -
209B ALA* 4.1 17.9 - - + -
215B ASN* 3.2 24.4 + - - +
217B VAL* 3.8 13.9 - - + +
225B THR* 5.3 0.9 - - + -
231B LEU* 4.1 22.2 - - + -
238B LEU* 4.9 5.8 - - + -
240B LEU* 3.6 29.6 - - + -
276B LEU* 4.7 5.2 - - + -
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Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS 2.7 15.5 + - - -
84B GLU* 3.8 5.7 + - - -
85B LEU 3.7 1.4 - - - -
86B PHE* 1.3 75.2 - - - +
88B ALA* 1.3 60.7 + - - -
217B VAL* 4.2 1.1 - - - +
242B LYS* 3.1 35.2 + - - +
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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