Contacts of the strand formed by residues 84 - 89 (chain G) in PDB entry 2GLJ
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 GLY 84 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G THR* 4.1 5.5 + - - -
79G ASN* 3.7 8.8 - - - +
80G ASN* 2.9 41.9 + - - +
82G GLY 3.4 0.4 - - - -
83G LYS* 1.3 80.2 - - - +
85G LEU* 1.3 63.4 + - - +
291G LEU 3.5 9.2 - - - -
292G VAL* 4.7 7.2 - - - -
303G THR* 4.4 3.1 - - - +
308G LYS* 5.0 0.9 - - - -
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Residues in contact with LEU 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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46G THR* 4.2 11.6 + - - +
49G ILE* 3.4 34.5 - - + -
50G LYS* 3.3 32.5 - - - +
77G TYR* 3.9 16.2 - - + -
78G ALA 3.6 12.3 - - - +
84G GLY* 1.3 75.4 - - - +
86G ILE* 1.3 79.1 + - - +
87G MET* 4.2 12.8 - - + -
106G ILE* 5.9 0.7 - - + -
289G THR 4.0 0.5 - - - +
290G ILE* 3.7 0.9 - - - +
291G LEU* 2.8 57.8 + - + +
292G VAL* 5.6 0.8 - - - +
308G LYS* 5.1 1.5 - - - +
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Residues in contact with ILE 86 (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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77G TYR* 3.3 3.3 - - - +
78G ALA* 2.9 53.8 + - + +
85G LEU* 1.3 78.7 - - - +
87G MET* 1.3 68.2 + - - +
88G PHE* 3.6 32.3 - - + -
288G ILE* 4.9 2.2 - - + -
289G THR 3.1 11.4 - - - +
290G ILE* 4.3 12.6 - - + -
308G LYS* 3.6 17.5 - - + -
309G PHE* 3.6 40.8 - - + -
312G ASN* 4.5 5.2 - - - +
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Residues in contact with MET 87 (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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53G GLU* 3.1 45.5 - - - +
57G TYR* 4.1 13.7 - - + -
76G VAL 3.5 4.3 - - - -
77G TYR* 4.3 7.2 - - + -
85G LEU* 4.2 23.3 - - + -
86G ILE* 1.3 75.4 - - - +
88G PHE* 1.3 64.4 + - - +
274G PHE* 3.3 25.4 - - + -
277G MET* 3.2 26.4 - - + +
288G ILE* 3.1 9.2 - - - +
289G THR* 2.7 52.9 + - + +
291G LEU* 5.5 0.9 - - + -
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Residues in contact with PHE 88 (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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57G TYR* 3.1 24.3 - - - -
59G ASN* 5.9 1.3 - - - -
75G LYS* 3.5 6.8 - - - -
76G VAL* 2.8 31.5 + - + +
77G TYR* 5.3 1.1 - - - -
78G ALA* 5.3 1.8 - - + -
86G ILE* 3.6 33.9 - - + -
87G MET* 1.3 78.6 - - - +
89G LEU* 1.3 62.7 + - - +
90G ILE* 4.8 7.2 - - + -
95G LEU* 6.0 0.7 - - + -
99G PHE* 4.6 6.7 - + - -
277G MET* 3.9 1.3 - - - -
286G THR* 5.0 5.6 - - + -
287G CYS 3.7 1.3 - - - -
288G ILE* 3.0 31.2 - - + -
312G ASN* 3.4 27.6 - - - -
313G THR* 4.1 24.7 - - + -
316G ASP* 4.0 28.3 - - + +
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Residues in contact with LEU 89 (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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57G TYR* 4.7 5.6 - - - +
73G GLY* 4.8 6.5 - - - +
74G ASP 3.4 13.9 - - - +
75G LYS* 4.4 19.5 - - + -
88G PHE* 1.3 79.7 - - - +
90G ILE* 1.3 69.4 + - - +
277G MET* 4.1 10.3 - - + +
280G MET* 3.2 36.3 - - + +
281G LYS* 5.3 0.9 - - - -
282G ASN 6.1 0.7 - - - +
283G ALA* 4.0 18.9 - - + +
286G THR* 3.1 15.2 - - - +
287G CYS* 3.1 43.0 + - - +
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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