Contacts of the strand formed by residues 63 - 69 (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 SER 63 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F LYS* 4.0 40.8 + - - +
61F THR* 3.2 10.5 + - - -
62F THR* 1.3 74.8 + - - +
64F ASP* 1.3 68.1 + - - +
65F VAL* 3.9 9.4 - - - +
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Residues in contact with ASP 64 (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 0.9 - - + -
34F GLN 3.3 8.1 - - - +
35F ASP* 3.7 20.1 - - - +
36F LYS* 6.0 0.3 - - - +
41F PHE* 3.2 32.5 - - + -
59F GLY 4.4 2.3 - - - +
60F VAL* 3.5 8.9 - - + -
61F THR* 3.3 35.9 + - - +
62F THR 3.8 6.9 - - - +
63F SER* 1.3 86.0 - - - +
65F VAL* 1.3 66.2 + - - +
84F LYS* 4.7 1.2 - - - -
85F ILE* 3.3 20.9 + - + +
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Residues in contact with VAL 65 (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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32F SER 3.8 0.9 - - - +
33F LEU* 3.9 2.9 - - - +
34F GLN* 2.8 40.1 + - + +
35F ASP 4.5 10.8 - - - +
36F LYS* 5.0 3.1 - - - +
63F SER 3.9 9.4 - - - +
64F ASP* 1.3 80.4 - - - +
66F VAL* 1.3 68.6 - - - +
67F VAL* 3.8 19.0 + - + -
82F LYS* 4.0 20.6 - - + -
83F LEU 3.7 8.5 - - - +
84F LYS* 5.5 2.0 - - + -
85F ILE* 4.2 2.6 - - - +
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Residues in contact with VAL 66 (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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31F VAL* 4.2 19.1 - - + -
32F SER 4.0 3.6 - - - -
33F LEU* 5.2 5.6 - - + +
46F LEU* 5.6 1.1 - - + -
52F VAL* 3.8 19.3 - - + -
65F VAL* 1.3 72.6 - - - +
67F VAL* 1.3 59.6 + - - +
68F ALA* 5.1 0.4 - - + -
81F GLN 3.6 1.0 - - - +
82F LYS* 3.7 2.1 - - - -
83F LEU* 2.8 48.6 + - + +
85F ILE* 3.7 22.8 - - + +
106F LEU* 3.8 17.7 - - + -
108F LEU* 3.5 31.6 - - + -
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Residues in contact with VAL 67 (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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30F GLN 4.8 0.2 - - - +
31F VAL* 3.5 5.4 - - - -
32F SER* 2.9 38.9 + - - +
34F GLN* 3.7 23.3 - - + +
65F VAL* 3.8 21.3 - - + -
66F VAL* 1.3 73.1 - - - +
68F ALA* 1.3 64.2 + - - +
70F GLU* 3.2 41.1 + - + +
80F ILE* 5.2 5.4 - - + -
81F GLN 3.4 3.1 - - - +
82F LYS* 4.1 23.1 - - + -
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Residues in contact with ALA 68 (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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30F GLN 5.1 0.2 - - - -
31F VAL* 4.0 20.0 - - + +
46F LEU* 4.4 2.9 - - + -
66F VAL* 4.1 0.8 - - + -
67F VAL* 1.3 76.8 - - - +
69F GLY* 1.3 63.9 + - - +
70F GLU 3.5 2.2 + - - -
79F LYS 4.8 0.2 - - - +
80F ILE* 3.3 7.6 - - - +
81F GLN* 2.9 44.3 + - + +
83F LEU* 4.7 12.1 - - + -
118F VAL* 4.1 24.7 - - + +
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Residues in contact with GLY 69 (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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28F PRO 5.5 1.6 + - - -
30F GLN 4.9 5.0 + - - -
68F ALA* 1.3 76.5 - - - +
70F GLU* 1.3 58.2 + - - +
71F PHE 4.1 1.0 + - - -
78F GLU* 4.4 8.0 - - - +
79F LYS 4.9 4.7 - - - +
80F ILE* 4.4 11.4 - - - +
117F THR* 4.1 18.8 + - - -
118F VAL* 3.6 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