Contacts of the strand formed by residues 77 - 82 (chain G) in PDB entry 6I53
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 77 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G SER* 4.9 4.7 - - - -
22G CYS 3.3 16.4 - - - -
23G ALA* 4.1 9.9 - - - -
34G MET* 4.0 10.4 - - - +
71G ARG* 3.7 8.7 + - - +
72G ASP* 3.2 39.2 + - - +
75G LYS* 4.4 10.4 - - - +
76G ASN* 1.3 79.5 - - - +
78G VAL* 1.3 67.4 + - - +
79G ASP* 4.6 6.4 + - - -
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Residues in contact with VAL 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G SER* 3.6 0.9 - - - -
22G CYS* 3.0 42.3 + - + -
34G MET* 3.8 31.6 - - + +
35G ALA 5.3 0.2 - - - +
36G TRP* 3.6 22.9 - - + +
69G ILE* 3.8 18.8 - - + -
70G SER 3.7 5.4 - - - -
71G ARG* 3.7 21.3 - - + +
77G SER* 1.3 76.9 - - - +
79G ASP* 1.3 72.6 + - - +
95G CYS* 3.8 9.6 - - - -
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Residues in contact with ASP 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ARG* 2.7 37.0 + - + +
20G VAL 3.6 5.4 - - - +
21G SER* 3.0 23.2 + - - -
36G TRP* 3.5 2.7 + - - -
69G ILE* 3.3 12.5 - - - +
70G SER* 2.7 48.6 + - - +
71G ARG 5.7 0.7 - - - -
72G ASP* 5.6 4.3 - - - +
77G SER* 4.6 6.8 + - - -
78G VAL* 1.3 84.8 + - - +
80G LEU* 1.3 62.1 + - - +
81G GLN 4.2 0.4 - - - -
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Residues in contact with LEU 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G ARG* 4.8 1.5 - - - +
20G VAL* 2.9 31.8 + - + +
36G TRP* 3.5 45.1 - - + +
48G LEU* 4.1 19.5 - - + -
49G ALA* 4.0 24.0 - - + -
67G PHE* 3.9 27.6 - - + -
68G THR 3.8 1.1 - - - -
69G ILE* 4.3 9.2 - - - +
79G ASP* 1.3 75.4 - - - +
81G GLN* 1.3 58.9 + - - +
82G LEU* 3.0 29.6 + - + +
93G TYR* 4.9 4.7 - - + -
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Residues in contact with GLN 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G SER* 4.1 14.8 + - - -
18G LEU 3.4 19.7 + - - -
19G ARG* 3.0 39.6 + - - +
66G ARG 4.0 1.8 - - - +
67G PHE* 3.4 9.5 - - - -
68G THR* 2.9 45.7 + - + +
79G ASP 4.2 0.2 - - - -
80G LEU* 1.3 67.4 - - - +
82G LEU* 1.3 70.3 + - - +
83G ASP* 3.5 9.7 + - + +
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Residues in contact with LEU 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G SER* 3.4 6.9 - - - -
18G LEU* 2.8 62.1 + - + +
20G VAL* 3.7 18.6 - - + -
67G PHE* 3.6 19.5 - - + -
80G LEU* 3.0 41.1 + - + +
81G GLN* 1.3 73.4 + - - +
83G ASP* 1.3 59.7 + - - +
85G LEU* 3.7 27.8 - - + -
93G TYR* 3.6 24.2 - - + -
119G VAL* 3.9 4.9 - - + -
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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