Contacts of the strand formed by residues 77 - 85 (chain G) in PDB entry 6X0A
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 TRP 77 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2G PRO* 3.4 26.5 - - + +
4G ILE* 3.3 28.1 - - + +
73G LEU* 4.4 0.7 - - - +
74G ALA* 3.0 37.6 + - + +
75G GLU* 3.3 30.5 - - + -
76G GLY* 1.3 81.8 - - - +
78G ILE* 1.3 64.3 + - - +
79G GLU* 2.8 41.7 + - + +
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Residues in contact with ILE 78 (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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2G PRO 3.0 10.1 + - - +
3G ILE* 3.4 12.7 - - + +
4G ILE* 3.0 28.8 + - - +
42G LEU* 3.1 55.6 - - + +
43G ALA* 3.5 12.1 - - + +
46G PRO* 4.7 3.8 - - + -
71G TYR* 3.9 26.7 - - + -
72G ARG 4.0 3.4 - - - +
73G LEU* 4.0 17.7 - - + -
74G ALA 4.9 0.2 - - - +
77G TRP* 1.3 76.5 - - - +
79G GLU* 1.3 61.5 + - - +
80G ILE* 4.2 10.1 - - + -
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Residues in contact with GLU 79 (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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4G ILE* 3.3 15.9 - - + +
71G TYR* 3.2 6.0 - - - +
72G ARG* 2.9 72.5 + - + +
74G ALA* 3.3 17.3 - - + +
77G TRP* 2.8 39.5 + - + +
78G ILE* 1.3 70.3 - - - +
80G ILE* 1.3 63.0 + - - +
81G VAL* 3.4 8.1 + - + +
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Residues in contact with ILE 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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3G ILE* 3.6 23.3 - - + -
4G ILE 2.8 11.8 + - - +
5G ARG* 3.2 10.1 - - + +
6G SER 2.8 26.9 + - - -
9G ALA* 3.7 4.1 - - + +
13G LEU* 6.3 0.2 - - + -
39G ILE* 3.7 29.6 - - + -
42G LEU* 3.8 15.0 - - + -
69G ILE* 4.2 14.6 - - + -
70G LEU 4.4 1.8 - - - +
71G TYR* 3.7 20.6 - - + -
78G ILE* 4.2 5.2 - - + -
79G GLU* 1.3 70.3 - - - +
81G VAL* 1.3 59.9 + - - +
83G ILE* 3.8 29.6 - - + -
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Residues in contact with VAL 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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6G SER* 3.2 28.8 + - - +
8G ALA* 4.5 0.2 - - - +
9G ALA* 3.3 5.6 + - - +
70G LEU* 2.9 18.2 + - + +
71G TYR* 4.4 6.3 - - - -
72G ARG* 4.4 16.2 - - + +
79G GLU* 3.8 20.0 - - + +
80G ILE* 1.3 73.2 - - - +
82G ARG* 1.3 78.7 + - + +
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Residues in contact with ARG 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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8G ALA* 4.1 22.5 - - + +
9G ALA* 3.8 4.5 - - - -
12G ASP* 2.7 50.6 + - - +
69G ILE 3.7 0.5 - - - -
70G LEU* 2.8 40.5 + - + +
80G ILE* 3.8 0.9 - - - +
81G VAL* 1.3 92.8 - - + +
83G ILE* 1.3 68.3 + - - +
84G VAL* 3.4 28.4 - - + +
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Residues in contact with ILE 83 (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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9G ALA* 3.8 21.5 - - + +
12G ASP* 2.8 30.4 + - + +
13G LEU* 4.0 24.5 - - + -
16G ILE* 3.5 29.7 - - + +
35G ILE* 5.0 8.3 - - + -
39G ILE* 5.1 1.3 - - + -
64G ILE* 6.0 0.9 - - + -
67G TYR* 4.6 10.6 - - + -
68G LEU 3.0 15.3 - - - +
69G ILE* 4.3 19.3 - - + -
80G ILE* 3.8 22.7 - - + -
82G ARG* 1.3 81.9 - - - +
84G VAL* 1.3 60.0 + - - +
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Residues in contact with VAL 84 (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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67G TYR* 3.4 6.1 - - - -
68G LEU* 2.7 40.2 + - + +
70G LEU* 4.4 13.9 - - + +
82G ARG* 3.4 46.1 - - + +
83G ILE* 1.3 74.8 - - - +
85G HIS* 1.3 85.0 + - + +
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Residues in contact with HIS 85 (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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66G ASN* 3.7 25.6 - - + +
67G TYR* 3.4 48.6 - + + +
68G LEU* 4.4 3.1 - - - +
84G VAL* 1.3 91.6 - - + +
86G GLY* 1.3 94.2 + - - +
87G ALA 5.4 0.2 - - - -
88G ARG* 3.5 49.7 + - + +
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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