Contacts of the strand formed by residues 82 - 88 (chain E) in PDB entry 3CHB
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 82 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E LEU* 3.8 3.7 - - + +
21E ASN* 2.8 27.5 + - - -
22E ASP 2.9 18.7 + - - +
24E ILE* 4.0 28.3 - - + -
40E ILE* 6.0 0.2 - - + -
42E PHE* 4.1 11.9 - - + -
75E ALA* 5.1 2.9 - - + -
80E ALA 4.1 5.8 - - - +
81E LYS* 1.3 73.9 - - - +
83E GLU* 1.3 61.5 + - - +
84E LYS 3.9 16.2 - - - +
85E LEU* 4.2 13.5 - - + -
99E ILE* 3.9 25.1 - - + -
100E SER 3.8 10.5 - - - +
101E MET* 4.4 4.3 - - + -
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Residues in contact with GLU 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 4.5 2.8 - - - +
19E THR* 3.6 2.6 - - - +
20E LEU 2.8 26.8 + - - -
21E ASN* 3.2 26.7 + - - +
81E LYS* 3.7 3.7 + - - +
82E VAL* 1.3 71.0 - - - +
84E LYS* 1.3 85.3 + - + +
100E SER* 2.6 44.0 + - - +
102E ALA* 4.2 26.2 - - + +
103E ASN* 5.7 1.8 + - - +
26F SER* 5.9 2.1 - - - -
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Residues in contact with LYS 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 3.7 22.8 - - + +
6E THR* 4.1 11.4 + - - +
17E ILE* 3.9 20.5 - - + +
18E HIS 3.2 8.1 - - - +
19E THR* 2.8 37.4 + - - +
20E LEU* 4.6 0.4 - - - +
82E VAL* 3.9 3.1 - - - +
83E GLU* 1.3 107.3 - - - +
85E LEU* 1.3 64.9 + - - +
99E ILE* 3.5 3.3 - - - -
100E SER* 2.9 35.0 + - - +
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN 3.6 0.9 - - - +
17E ILE* 3.3 7.8 - - - +
18E HIS* 2.9 34.6 + - + +
20E LEU* 4.0 15.2 - - + +
40E ILE* 4.4 7.6 - - + -
42E PHE* 4.1 9.9 - - + -
48E PHE* 3.6 41.5 - - + -
82E VAL* 4.2 4.3 - - + -
84E LYS* 1.3 74.3 - - - +
86E CYS* 1.3 58.5 + - - +
87E VAL* 3.9 12.4 + - + +
96E ILE* 4.3 18.2 - - + -
98E ALA 3.4 14.1 - - - +
99E ILE* 3.7 31.4 - - + -
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Residues in contact with CYS 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 3.9 5.6 - - + +
8E LEU* 5.1 2.5 - - - -
9E CYS* 2.1 54.1 - - + -
12E TYR* 5.9 1.3 - - - -
15E THR* 4.0 9.2 - - - -
16E GLN 3.5 4.3 - - - -
17E ILE* 4.0 5.6 - - + -
85E LEU* 1.3 71.7 - - - +
87E VAL* 1.3 63.6 + - - +
96E ILE* 3.8 0.9 - - - -
97E ALA* 2.8 38.4 + - - -
98E ALA* 2.9 29.8 + - + +
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Residues in contact with VAL 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E THR* 3.1 8.4 - - - -
16E GLN* 2.9 48.4 + - + +
18E HIS* 3.6 24.5 - - + -
48E PHE* 3.7 28.9 - - + -
85E LEU* 3.9 16.2 - - + +
86E CYS* 1.3 81.0 - - - +
88E TRP* 1.3 63.3 + - - +
89E ASN 3.7 0.2 + - - -
94E ARG* 3.9 18.2 - - + -
95E ALA 3.1 13.0 - - - +
96E ILE* 4.4 5.8 - - + -
97E ALA* 4.3 0.7 - - - +
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Residues in contact with TRP 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GAL 3.6 62.8 - - - +
5B SIA 5.2 4.1 + - - -
12E TYR* 4.6 13.0 - + - +
13E HIS 3.8 9.8 + - - -
14E ASN* 3.1 13.7 - - + -
15E THR* 3.5 24.5 - - + +
51E GLU* 4.8 2.5 - - - -
57E HIS* 5.8 0.4 - - - -
87E VAL* 1.3 71.8 - - - +
89E ASN* 1.3 62.6 - - - +
90E ASN* 3.3 13.4 + - - +
91E LYS* 4.0 3.4 + - + -
94E ARG* 3.6 8.5 - - - +
95E ALA* 2.8 56.4 + - + +
96E ILE 3.6 7.4 - - - -
97E ALA* 3.4 35.0 - - + -
31F LEU* 3.8 15.5 - - + -
32F ALA* 4.1 17.0 - - + -
33F GLY 5.3 0.4 - - - -
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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