Contacts of the strand formed by residues 82 - 86 (chain H) in PDB entry 6BCH
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 ALA 82 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H ILE 3.9 0.3 - - - +
55H GLY* 3.3 3.1 - - - -
56H LEU* 2.8 41.6 + - + +
57H HIS 3.9 3.8 - - - +
58H ASN* 3.4 12.0 + - - +
61H VAL* 3.6 33.2 - - + -
64H LEU* 3.8 13.4 - - + +
77H THR 3.3 6.5 - - - +
78H SER* 4.6 0.2 - - - +
81H ASP* 1.3 73.8 - - - +
83H ARG* 1.3 62.5 + - - +
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Residues in contact with ARG 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H ARG* 3.0 48.1 - - + +
54H ILE 3.2 6.5 - - - +
55H GLY* 4.2 10.2 - - - -
64H LEU* 3.5 6.5 - - - +
75H ILE 3.5 1.7 - - - +
76H ILE* 3.2 6.4 - - - +
77H THR* 2.9 47.7 + - - +
81H ASP* 3.2 33.4 + - - +
82H ALA* 1.3 79.3 - - - +
84H ILE* 1.3 60.1 + - - +
85H ARG* 5.7 1.8 - - + -
8J T 5.1 6.4 + - - +
9J C 3.5 12.4 - - - +
10J C 3.5 10.5 - - - +
17K A 4.3 6.9 + - - +
18K G 2.4 31.5 + - - -
19K G 3.0 12.5 + - - -
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Residues in contact with ILE 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H ARG* 3.4 5.4 - - - +
54H ILE* 2.9 62.3 + - + +
64H LEU* 3.6 34.4 - - + +
67H ILE* 4.1 18.6 - - + -
68H ARG* 4.3 8.3 - - + +
73H ALA 4.2 4.7 - - - +
74H GLY* 4.1 13.2 - - - -
75H ILE 3.3 8.3 - - - +
76H ILE* 4.2 6.5 - - + -
83H ARG* 1.3 74.3 - - - +
85H ARG* 1.3 64.2 + - - +
86H PHE* 3.8 30.3 - - + -
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Residues in contact with ARG 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H PHE 3.5 7.0 - - - +
53H ARG* 4.2 17.3 - - + +
74H GLY* 3.5 5.0 - - - -
75H ILE* 2.9 66.7 + - + +
77H THR* 3.2 36.2 + - - +
83H ARG* 5.6 2.2 - - + -
84H ILE* 1.3 76.0 - - - +
86H PHE* 1.3 64.5 + - - +
87H GLU* 3.8 28.1 + - + +
6J G 3.4 30.9 + - - +
7J C 3.5 38.8 + - - +
8J T 4.1 14.1 - - - +
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Residues in contact with PHE 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H ARG* 3.6 0.9 - - - -
52H PHE* 2.9 65.1 + + + +
54H ILE* 5.7 0.4 - - + -
67H ILE* 5.0 2.0 - - + -
71H LEU* 3.9 22.9 - - + -
73H ALA* 3.6 22.9 - - + -
74H GLY* 3.6 18.8 - - - -
84H ILE* 3.8 31.4 - - + -
85H ARG* 1.3 75.5 - - - +
87H GLU* 1.3 61.9 + - - +
91H GLU* 3.8 25.8 - - + -
92H LEU* 3.2 23.2 - - + +
94H VAL* 5.5 0.9 - - + -
95H VAL* 3.4 21.8 - - + -
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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