Contacts of the helix formed by residues 71 - 81 (chain B) in PDB entry 3C6Q
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 VAL 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B ILE* 3.9 8.7 - - + -
47B LEU* 3.7 22.4 - - + -
50B LEU* 4.7 2.9 - - + -
63B ILE* 4.2 15.0 - - + -
65B PRO* 3.6 22.0 - - + -
67B ASP 3.3 13.0 - - - +
68B PRO 3.3 21.8 - - - +
70B ALA* 1.3 76.1 - - - +
72B ILE* 1.3 68.6 + - - +
74B THR* 3.0 7.4 + - - -
75B ILE* 2.9 41.2 + - + +
92B SER* 3.7 11.2 - - - +
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Residues in contact with ILE 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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68B PRO 3.5 17.3 - - - +
69B THR* 3.1 29.6 + - + +
71B VAL* 1.3 78.3 - - - +
73B PRO* 1.3 69.6 - - + +
75B ILE* 3.3 2.3 + - - +
76B LYS* 2.9 27.3 + - + +
92B SER* 4.0 6.7 - - - +
94B ASP* 3.5 39.0 - - + +
95B SER* 4.0 14.6 - - - +
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Residues in contact with PRO 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 THR 3.9 2.7 - - - +
70B ALA* 3.1 20.2 - - - +
71B VAL 3.4 0.9 - - - -
72B ILE* 1.3 96.1 - - + +
74B THR* 1.3 62.7 + - - +
76B LYS* 3.2 12.1 + - + +
77B LYS* 3.0 22.1 + - - +
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Residues in contact with THR 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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47B LEU* 3.8 25.9 - - - +
50B LEU* 3.6 37.2 - - + -
51B GLU* 4.3 17.1 + - + +
54B ILE* 3.9 17.0 - - + +
70B ALA 4.4 3.1 + - - -
71B VAL 3.0 8.8 + - - -
73B PRO* 1.3 78.8 - - - +
75B ILE* 1.3 63.6 + - - +
77B LYS* 3.0 18.8 + - + +
78B ALA 3.1 9.4 + - - -
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Residues in contact with ILE 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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50B LEU* 4.3 15.9 - - + -
63B ILE* 4.2 18.4 - - + -
71B VAL* 2.9 29.8 + - + +
72B ILE 3.6 6.7 - - - +
74B THR* 1.3 76.6 - - - +
76B LYS* 1.3 63.0 + - - +
78B ALA* 3.1 16.6 + - - +
79B LEU* 3.1 24.7 + - + +
85B VAL* 4.0 27.4 - - + -
87B THR* 5.0 4.7 - - + -
95B SER* 3.2 44.4 - - - +
97B ARG 4.2 1.6 - - - +
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Residues in contact with LYS 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 ILE* 2.9 19.2 + - + +
73B PRO* 3.2 14.3 + - + +
75B ILE* 1.3 77.1 - - - +
77B LYS* 1.3 61.8 + - - +
79B LEU* 3.4 14.0 + - + +
80B GLU* 3.3 34.8 + - + +
95B SER 4.6 4.3 - - - +
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Residues in contact with LYS 77 (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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51B GLU* 4.4 21.5 + - - +
54B ILE* 4.6 10.3 - - + -
73B PRO 3.0 12.2 + - - +
74B THR* 3.0 14.3 + - - +
76B LYS* 1.3 77.6 - - - +
78B ALA* 1.3 61.2 + - - +
80B GLU* 3.2 18.1 + - + +
81B MET* 3.3 35.8 + - + +
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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
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50B LEU* 6.3 0.9 - - + -
54B ILE* 3.8 29.6 - - + +
61B ILE* 4.5 7.0 - - + -
74B THR 3.1 5.6 + - - +
75B ILE* 3.1 10.6 + - - +
77B LYS* 1.3 73.8 - - - +
79B LEU* 1.3 64.7 + - - +
81B MET* 3.1 10.9 + - - +
83B ILE* 2.9 40.9 + - + +
85B VAL* 4.2 14.1 - - + -
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Residues in contact with LEU 79 (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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75B ILE* 3.1 25.5 + - + +
76B LYS* 3.5 11.4 - - + +
78B ALA* 1.3 77.1 - - - +
80B GLU* 1.3 58.4 + - + +
82B GLY* 3.0 19.1 + - - -
83B ILE 3.4 16.8 - - - +
85B VAL* 3.8 14.1 - - + +
96B GLY* 3.6 35.4 - - - +
98B TYR* 3.7 37.7 + - + +
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Residues in contact with GLU 80 (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 LYS* 3.3 23.6 + - + +
77B LYS* 3.2 14.9 + - + +
78B ALA 3.2 0.6 - - - -
79B LEU* 1.3 78.8 - - + +
81B MET* 1.3 67.3 + - + +
82B GLY 3.2 1.1 + - - -
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Residues in contact with MET 81 (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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54B ILE* 4.4 19.1 - - + -
77B LYS* 3.3 31.8 + - + +
78B ALA* 3.1 9.6 + - - +
80B GLU* 1.3 85.0 - - + +
82B GLY* 1.3 61.1 + - - +
83B ILE* 3.3 15.9 + - + +
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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