Contacts of the helix formed by residues 67 - 82 (chain B) in PDB entry 5H1C
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 SER 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B GLY 4.3 0.6 - - - -
66B ILE* 1.3 80.7 - - - +
68B GLU* 1.3 65.5 + - - +
69B ALA* 3.9 7.6 + - - +
70B LYS* 3.0 51.5 + - - +
71B ALA 3.4 0.3 + - - -
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Residues in contact with GLU 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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57B LYS* 3.0 23.8 + - - +
61B ILE* 3.5 43.6 - - + +
66B ILE* 3.9 0.6 + - - +
67B SER* 1.3 73.7 - - - +
69B ALA* 1.3 57.6 + - - +
71B ALA* 2.9 16.6 + - - -
72B ASP* 2.9 14.0 + - - -
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Residues in contact with ALA 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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67B SER* 3.2 8.6 + - - +
68B GLU* 1.3 75.7 - - - +
70B LYS* 1.3 66.3 + - - +
72B ASP* 2.9 26.3 + - + +
73B LYS* 3.0 22.0 + - - +
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Residues in contact with LYS 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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37B ASP* 4.5 22.2 + - - +
40B LYS* 5.1 3.2 - - - +
65B GLY 3.5 20.1 + - - +
66B ILE* 4.2 13.5 - - + -
67B SER* 3.0 37.5 + - - +
69B ALA* 1.3 78.7 - - + +
71B ALA* 1.3 56.3 + - - +
73B LYS* 3.0 19.5 + - + +
74B ILE* 2.9 39.4 + - + +
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Residues in contact with ALA 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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57B LYS* 3.1 33.7 - - + +
60B LEU* 3.5 25.6 - - + -
61B ILE* 5.1 1.8 - - + -
66B ILE* 4.7 1.3 - - + +
67B SER 3.4 2.7 + - - +
68B GLU* 2.9 7.0 + - - +
70B LYS* 1.3 78.5 - - - +
72B ASP* 1.3 59.0 + - - +
74B ILE* 3.7 10.5 - - - +
75B LEU* 2.9 39.2 + - + +
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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
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57B LYS* 4.1 8.7 + - - -
68B GLU* 2.9 17.0 + - - +
69B ALA* 2.9 20.3 + - + +
71B ALA* 1.3 77.5 - - - +
73B LYS* 1.3 62.1 + - + +
75B LEU* 4.2 4.2 - - - +
76B ALA* 2.9 26.0 + - - +
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Residues in contact with LYS 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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31B CYS* 5.4 10.3 - - - +
32B GLY 5.4 7.8 + - - +
33B ILE* 5.1 13.2 - - + -
69B ALA* 3.0 21.4 + - - +
70B LYS* 3.0 19.2 + - + +
72B ASP* 1.3 76.8 - - + +
74B ILE* 1.3 64.0 + - + +
76B ALA* 3.1 8.4 + - - +
77B GLU* 2.9 29.4 + - + +
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Residues in contact with ILE 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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28B LEU* 5.1 6.6 - - + +
33B ILE* 4.6 22.2 - - + -
41B LEU* 4.2 31.6 - - + -
52B VAL* 3.5 28.0 - - + +
60B LEU* 4.1 23.1 - - + -
66B ILE* 5.2 3.1 - - + -
70B LYS* 2.9 32.4 + - + +
71B ALA* 3.8 9.2 - - - +
73B LYS* 1.3 76.3 - - + +
75B LEU* 1.3 59.1 + - - +
77B GLU* 3.0 10.6 + - - +
78B ALA* 2.9 23.9 + - - +
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Residues in contact with LEU 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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196A ASN* 5.4 3.1 - - - +
52B VAL* 4.0 22.9 - - + +
53B ALA* 5.5 1.8 - - - +
55B ALA 4.4 10.3 - - - +
57B LYS* 4.2 33.0 - - + +
60B LEU* 4.4 16.4 - - + -
71B ALA* 2.9 26.0 + - + +
72B ASP* 4.3 4.0 - - - +
74B ILE* 1.3 75.1 - - - +
76B ALA* 1.3 60.8 + - - +
78B ALA* 3.1 7.7 + - + +
79B ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 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 ASP 2.9 20.6 + - - +
73B LYS* 3.1 8.5 + - - +
75B LEU* 1.3 76.5 - - - +
77B GLU* 1.3 63.6 + - - +
79B ALA* 3.5 7.5 + - - +
80B LYS* 2.9 24.3 + - - +
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Residues in contact with GLU 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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28B LEU* 3.6 22.3 - - + +
30B GLN* 5.0 5.3 - - - +
31B CYS* 3.1 40.3 - - + +
33B ILE* 4.4 15.9 - - + -
73B LYS* 2.9 19.9 + - + +
74B ILE* 3.3 8.3 - - - +
76B ALA* 1.3 81.8 - - - +
78B ALA* 1.3 59.5 + - - +
79B ALA 3.2 0.4 - - - -
80B LYS* 2.9 38.5 + - - +
81B LEU* 2.9 20.6 + - - +
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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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28B LEU* 4.6 1.1 - - + +
49B VAL* 4.5 13.0 - - - +
52B VAL* 4.3 9.9 - - + +
53B ALA* 3.7 34.4 - - + +
74B ILE 2.9 12.0 + - - +
75B LEU* 3.1 14.1 + - + +
77B GLU* 1.3 76.4 - - - +
79B ALA* 1.3 57.3 + - - +
81B LEU* 4.1 0.2 - - - -
82B VAL* 2.9 35.5 + - - +
84B MET* 6.0 0.4 - - - -
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Residues in contact with ALA 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 LEU 2.9 15.4 + - - +
76B ALA* 3.7 8.1 - - - +
78B ALA* 1.3 75.2 - - - +
80B LYS* 1.3 63.5 + - - +
82B VAL 3.3 19.9 - - - +
83B PRO* 4.4 3.1 - - - +
84B MET* 5.4 6.3 - - + +
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Residues in contact with LYS 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 ALA 2.9 16.2 + - - +
77B GLU* 2.9 33.6 + - - +
79B ALA* 1.3 79.3 - - - +
81B LEU* 1.3 66.0 + - + +
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Residues in contact with LEU 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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23B GLN* 4.0 20.4 + - - +
27B ARG* 4.1 24.9 - - + +
28B LEU* 3.8 17.5 - - + -
49B VAL* 3.6 37.9 - - + -
77B GLU* 2.9 12.9 + - - +
80B LYS* 1.3 91.1 - - + +
82B VAL* 1.3 61.8 + - - +
83B PRO* 3.6 9.0 - - - +
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Residues in contact with VAL 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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23B GLN* 3.9 11.2 - - - +
49B VAL* 4.7 2.7 - - + -
50B GLU* 3.6 37.9 - - + +
53B ALA* 4.4 7.0 - - + -
54B TYR* 4.1 15.7 - - + +
78B ALA 2.9 20.7 + - - +
79B ALA* 3.3 14.8 - - - +
81B LEU* 1.3 81.6 - - + +
83B PRO* 1.3 79.5 - - + +
84B MET* 3.6 20.5 + - - +
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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