Contacts of the strand formed by residues 81 - 92 (chain F) in PDB entry 7GCH
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 GLN 81 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66F VAL 3.6 1.7 - - - +
67F VAL* 3.4 5.2 - - - +
68F ALA* 2.9 37.7 + - + +
79F LYS 5.1 2.8 + - - +
80F ILE* 1.3 77.2 - - - +
82F LYS* 1.3 62.4 - - - +
83F LEU* 3.8 21.5 + - + +
111F ALA 4.5 0.7 - - - +
112F ALA* 3.5 10.8 - - - -
113F SER* 2.9 53.4 + - - +
115F SER* 5.1 3.0 + - - -
118F VAL* 4.5 16.0 - - + +
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Residues in contact with LYS 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F GLN* 5.4 4.3 - - - +
65F VAL* 4.0 17.5 - - + -
66F VAL 3.7 4.0 - - - -
67F VAL* 4.1 18.2 - - + -
70F GLU* 6.1 0.9 - - - -
80F ILE* 3.1 33.3 + - + +
81F GLN* 1.3 71.8 - - - +
83F LEU* 1.3 61.4 + - - +
84F LYS* 4.4 4.6 + - - +
110F THR* 5.0 2.1 - - - +
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Residues in contact with LEU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LEU* 5.9 1.1 - - + -
65F VAL* 3.7 5.3 - - - +
66F VAL* 2.8 51.7 + - + +
68F ALA* 4.7 7.4 - - + -
81F GLN* 4.1 27.1 - - + +
82F LYS* 1.3 78.5 - - - +
84F LYS* 1.3 65.8 + - - +
108F LEU* 3.9 30.5 - - + -
110F THR* 3.0 42.4 - - + +
111F ALA 4.0 9.0 - - - +
112F ALA* 4.1 16.4 - - + -
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Residues in contact with LYS 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F THR 5.6 0.9 - - - +
64F ASP 4.8 4.0 - - - -
65F VAL* 5.3 2.2 - - + +
82F LYS 5.2 3.1 - - - +
83F LEU* 1.3 77.2 - - - +
85F ILE* 1.3 62.4 + - - +
108F LEU* 3.7 8.0 - - - +
109F SER* 3.2 41.9 + - - +
110F THR* 4.3 12.2 - - + +
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Residues in contact with ILE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 6.0 1.3 - - + -
60F VAL* 3.9 18.8 - - + -
61F THR 4.2 7.4 - - - +
62F THR* 3.6 26.6 + - + +
64F ASP* 3.3 36.7 + - + +
65F VAL 4.1 0.9 - - - +
66F VAL* 3.7 36.1 - - + +
84F LYS* 1.3 73.8 - - - +
86F ALA* 1.3 63.4 + - - +
87F LYS 3.7 9.6 - - - +
88F VAL* 3.7 30.7 - - + -
106F LEU* 4.2 14.4 - - + -
107F LYS 3.9 3.1 - - - +
108F LEU* 4.8 1.3 - - + -
109F SER* 4.5 2.3 - - - -
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Residues in contact with ALA 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F THR* 3.1 18.8 - - - +
84F LYS 3.9 1.6 + - - -
85F ILE* 1.3 72.0 - - - +
87F LYS* 1.3 61.4 + - + +
107F LYS* 2.7 24.8 + - + +
108F LEU 4.3 2.9 - - - +
109F SER* 3.8 25.1 - - - +
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Residues in contact with LYS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F THR* 4.5 0.7 - - + -
85F ILE* 3.7 2.6 - - - +
86F ALA* 1.3 83.8 - - + +
88F VAL* 1.3 84.3 + - - +
89F PHE* 3.2 48.3 + - + -
106F LEU* 3.5 5.0 - - - -
107F LYS* 3.0 32.5 + - + +
245G ASN* 5.3 1.0 + - - -
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Residues in contact with VAL 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F VAL* 3.5 21.8 - - + +
61F THR* 4.2 13.7 - - - -
62F THR* 4.0 13.0 - - + +
85F ILE* 3.7 20.6 - - + -
87F LYS* 1.3 95.8 - - - +
89F PHE* 1.3 62.4 + - - +
90F LYS* 3.7 10.3 + - + +
104F THR* 4.4 20.4 - - + +
105F LEU 3.8 2.9 - - - -
106F LEU* 4.4 5.4 - - + -
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Residues in contact with PHE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F TRP* 3.6 31.0 - + - -
87F LYS* 3.2 50.0 - - + -
88F VAL* 1.3 72.3 - - - +
90F LYS* 1.3 63.1 - - - +
104F THR* 3.2 5.1 - - - -
105F LEU* 2.8 51.6 + - + +
107F LYS* 4.0 4.7 - - + -
237G TRP* 3.6 9.5 - - + -
241G THR* 3.8 17.5 - - + -
245G ASN* 3.3 37.0 - - + -
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Residues in contact with LYS 90 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56F ALA* 3.8 19.3 - - + +
88F VAL* 3.7 11.2 + - + +
89F PHE* 1.3 73.7 - - - +
91F ASN* 1.3 71.9 + - - +
92F SER* 3.0 7.6 + - - +
94F TYR* 4.3 22.2 - - + -
104F THR* 3.3 17.5 - - - +
237G TRP* 4.1 2.1 + - - -
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Residues in contact with ASN 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F LYS* 1.3 72.2 - - - +
92F SER* 1.3 61.1 + - - +
93F LYS* 2.9 41.5 + - - +
94F TYR* 2.9 29.9 + - - +
101F ASN 4.4 5.8 - - - +
103F ILE* 3.2 35.5 + - + +
234G LEU* 4.4 11.1 - - - +
237G TRP* 2.9 60.7 + - + +
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Residues in contact with SER 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F LYS* 3.0 10.6 + - - +
91F ASN* 1.3 73.4 + - - +
93F LYS* 1.3 63.5 + - - +
94F TYR 3.2 9.8 + - - +
237G TRP* 4.9 2.0 - - - +
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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