Contacts of the strand formed by residues 83 - 88 (chain B) in PDB entry 5GKI
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 ARG 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLY 4.2 6.7 - - - +
82B SER* 1.3 77.2 - - - +
84B VAL* 1.3 60.9 + - - +
85B ARG 4.4 0.2 + - - -
95B VAL 3.7 0.9 - - - +
96B SER* 3.3 1.6 - - - -
97B ILE* 2.8 41.6 + - + +
99B ARG* 4.2 25.7 - - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 3.6 25.0 - - + +
58B VAL* 4.0 28.0 - - + -
62B GLY* 4.4 11.7 - - - +
64B PHE* 3.9 21.8 - - + -
82B SER 4.6 1.6 - - - +
83B ARG* 1.3 79.5 - - - +
85B ARG* 1.3 65.8 + - - +
94B LEU* 4.1 17.9 - - + -
95B VAL 3.2 16.8 - - - +
96B SER* 4.0 13.7 - - - +
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.5 4.0 - - - -
84B VAL* 1.3 77.1 - - - +
86B LEU* 1.3 62.6 + - - +
87B GLU* 2.3 43.5 + - + -
89B ARG* 5.9 0.2 - - - +
93B VAL 3.7 1.0 - - - +
94B LEU* 4.0 5.2 - - - -
95B VAL* 2.9 47.6 + - + +
97B ILE* 4.1 22.8 - - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 4.3 11.2 - - + -
18B VAL* 3.9 42.8 - - + +
21B VAL* 4.0 27.1 - - + -
22B ASN* 4.5 14.6 + - - +
25B LEU* 4.8 2.4 - - - +
85B ARG* 1.3 75.7 - - - +
87B GLU* 1.3 67.0 + - - +
88B LEU* 4.4 3.1 + - + +
92B PRO* 3.9 12.8 - - + -
93B VAL 3.4 33.4 - - - +
94B LEU* 4.0 13.6 - - + +
109B LEU* 5.0 4.7 - - + -
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ARG* 2.3 55.5 + - + +
86B LEU* 1.3 79.6 - - - +
88B LEU* 1.3 65.5 + - - +
89B ARG* 2.8 41.2 + - + +
91B ASN 3.9 0.3 - - - +
92B PRO* 3.5 1.4 - - - +
93B VAL* 2.7 46.3 + - + +
95B VAL* 4.4 5.4 - - + -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR* 4.1 25.4 - - + +
18B VAL* 3.7 28.9 - - + -
86B LEU* 4.3 3.8 + - + -
87B GLU* 1.3 73.8 - - - +
89B ARG* 1.3 67.1 + - - +
92B PRO* 4.1 28.5 - - + -
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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