Contacts of the helix formed by residues 61 - 76 (chain B) in PDB entry 3A7H
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 GLU 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B ALA* 1.3 74.8 - - - +
62B ASP* 1.3 74.8 + - + +
63B GLU* 2.3 26.3 + - - +
64B ILE* 3.3 22.0 + - + +
65B GLU* 2.9 16.3 - - - +
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Residues in contact with ASP 62 (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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61B GLU* 1.3 86.9 - - + +
63B GLU* 1.3 73.1 + - - +
65B GLU* 3.5 21.4 + - - +
66B ASP* 3.3 19.5 - - - +
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Residues in contact with GLU 63 (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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35B PHE* 3.3 50.2 - - + -
59B GLU 5.1 0.5 - - - +
60B ALA* 3.7 17.2 - - + +
61B GLU* 2.3 33.0 + - - +
62B ASP* 1.3 74.9 + - - +
64B ILE* 1.3 64.8 + - - +
66B ASP* 2.8 11.9 + - - -
67B ILE* 2.7 31.9 + - + +
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Residues in contact with ILE 64 (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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57B LEU* 4.0 46.7 - - + +
60B ALA* 4.5 4.5 - - + +
61B GLU* 3.3 26.4 + - - +
63B GLU* 1.3 75.7 - - - +
65B GLU* 1.3 68.2 + - - +
67B ILE* 3.4 10.1 - - + +
68B GLN* 2.8 32.5 + - + +
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Residues in contact with GLU 65 (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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61B GLU 2.9 26.0 - - - +
62B ASP* 3.5 20.1 - - - +
63B GLU 3.2 0.2 - - - -
64B ILE* 1.3 79.3 - - + +
66B ASP* 1.3 60.8 + - - +
68B GLN* 3.3 6.4 + - - +
69B GLN* 2.9 29.4 + - - +
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Residues in contact with ASP 66 (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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35B PHE* 4.4 15.8 - - + -
62B ASP* 3.3 18.0 - - - +
63B GLU* 2.8 14.4 + - - +
65B GLU* 1.3 71.7 - - - +
67B ILE* 1.3 62.1 + - - +
69B GLN* 3.1 6.4 + - - +
70B GLU* 2.8 34.4 + - - +
164B GLY* 5.5 7.7 - - - +
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Residues in contact with ILE 67 (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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10B LEU* 5.5 0.4 - - + -
35B PHE* 3.9 17.7 - - + -
55B ILE* 3.8 34.3 - - + -
57B LEU* 4.9 9.0 - - + -
60B ALA* 5.7 1.1 - - + -
63B GLU* 2.7 40.1 + - + +
64B ILE* 3.4 11.7 - - + +
66B ASP* 1.3 72.7 - - - +
68B GLN* 1.3 64.7 + - - +
70B GLU* 3.0 8.1 + - - +
71B ILE* 2.9 43.5 + - + +
95B LEU* 4.5 9.0 - - + -
97B ILE* 4.2 13.0 - - + -
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Residues in contact with GLN 68 (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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8B SER 5.3 4.0 - - - +
9B GLY* 4.2 24.1 + - - +
10B LEU* 3.6 33.6 + - + +
64B ILE* 2.8 28.9 + - + +
65B GLU* 3.6 6.1 - - - +
67B ILE* 1.3 73.8 - - - +
69B GLN* 1.3 54.2 + - - +
71B ILE* 3.6 1.4 + - - +
72B THR* 2.7 43.8 + - - +
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Residues in contact with GLN 69 (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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65B GLU 2.9 17.2 + - - +
66B ASP* 3.1 7.8 + - - +
68B GLN* 1.3 74.8 - - - +
70B GLU* 1.3 66.1 + - - +
72B THR* 3.3 16.5 + - - +
73B VAL* 3.0 39.8 + - + +
164B GLY 6.1 1.3 - - - +
166B ALA 5.6 4.0 - - - +
168B GLN* 5.2 5.9 + - - +
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Residues in contact with GLU 70 (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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35B PHE* 6.1 0.9 - - - -
53B LYS* 4.6 15.1 + - - -
66B ASP* 2.8 18.8 + - - +
67B ILE* 3.7 6.0 - - - +
69B GLN* 1.3 74.0 - - - +
71B ILE* 1.3 69.7 + - + +
73B VAL* 3.3 4.7 + - - +
74B LEU* 2.9 32.7 + - + +
99B MET* 5.0 9.7 - - + +
162B ASP* 4.3 9.1 - - - +
163B PHE* 3.9 24.4 + - + +
164B GLY* 3.5 35.8 + - - +
400B ATP 5.5 2.1 + - - -
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Residues in contact with ILE 71 (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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10B LEU* 3.7 34.8 - - + -
11B PRO* 3.6 11.9 - - + +
67B ILE* 2.9 24.9 + - + +
68B GLN 3.9 3.1 - - - +
70B GLU* 1.3 80.7 - - + +
72B THR* 1.3 64.6 + - - +
74B LEU* 3.3 10.6 + - + +
75B SER* 2.9 22.0 + - - -
85B TYR* 3.5 32.5 - - + +
88B SER* 3.9 7.0 - - - +
97B ILE* 3.7 37.0 - - + -
99B MET* 6.0 1.1 - - + -
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Residues in contact with THR 72 (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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11B PRO* 3.7 26.0 - - + +
68B GLN* 2.7 30.9 + - - +
69B GLN* 3.5 23.6 + - - +
70B GLU 3.2 0.2 - - - -
71B ILE* 1.3 77.3 - - - +
73B VAL* 1.3 65.4 + - + +
75B SER* 2.7 23.1 + - - -
76B GLN* 3.3 33.3 + - + +
168B GLN* 5.6 0.9 - - - +
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Residues in contact with VAL 73 (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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69B GLN* 3.0 34.6 + - + +
70B GLU* 3.8 4.5 - - - +
72B THR* 1.3 75.8 - - - +
74B LEU* 1.4 62.7 + - - +
76B GLN* 3.3 18.7 + - - +
77B CYS* 3.5 13.3 + - - -
140B LYS* 4.3 16.1 - - + -
163B PHE* 3.5 37.7 - - + +
166B ALA* 4.0 26.5 - - + +
167B GLY 5.9 0.4 - - - +
168B GLN* 4.0 17.9 - - + +
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Residues in contact with LEU 74 (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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70B GLU* 2.9 30.3 + - + +
71B ILE* 3.7 10.5 - - + +
72B THR 3.2 0.2 - - - -
73B VAL* 1.4 76.8 - - - +
75B SER* 1.3 64.2 + - - +
77B CYS* 3.0 24.3 + - - +
82B VAL* 4.5 4.0 - - + -
83B THR* 3.5 37.2 - - - +
84B LYS* 6.1 0.2 - - - -
85B TYR* 4.0 25.7 + - + +
99B MET* 3.8 31.9 - - + -
162B ASP 6.0 0.4 - - - +
163B PHE* 4.0 28.5 - - + +
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Residues in contact with SER 75 (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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11B PRO* 3.4 28.0 - - - +
12B GLY 5.5 0.2 - - - -
71B ILE 2.9 14.6 + - - -
72B THR* 2.7 19.8 + - - -
74B LEU* 1.3 75.9 - - - +
76B GLN* 1.3 62.0 + - - +
77B CYS 3.2 5.0 + - - +
85B TYR* 3.9 22.6 - - - -
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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
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72B THR* 3.3 33.7 - - - +
73B VAL* 3.7 5.4 - - - +
74B LEU 3.1 1.0 - - - -
75B SER* 1.3 80.3 - - - +
77B CYS* 1.3 62.3 + - - +
78B ASP* 5.2 1.0 - - - +
134B TYR* 3.8 6.8 + - - -
138B GLU* 4.8 3.5 - - - +
140B LYS* 3.2 23.4 + - - +
168B GLN* 2.6 33.5 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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