Contacts of the strand formed by residues 84 - 89 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46V THR* 4.0 6.1 + - - -
79V ASN* 3.7 8.0 - - - +
80V ASN* 2.9 40.5 + - - +
82V GLY 3.4 0.2 - - - -
83V LYS* 1.3 81.2 - - - +
85V LEU* 1.3 62.5 + - - +
106V ILE* 4.9 0.2 - - - -
291V LEU 3.5 10.1 - - - -
292V VAL* 4.7 7.2 - - - -
303V THR* 4.5 3.8 - - - +
306V GLN* 6.3 0.2 - - - -
308V LYS* 5.0 0.7 - - - -
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Residues in contact with LEU 85 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46V THR* 4.2 11.4 - - - +
49V ILE* 3.3 34.8 - - + -
50V LYS* 3.3 32.1 - - - +
77V TYR* 3.9 15.9 - - + -
78V ALA 3.6 12.8 - - - +
84V GLY* 1.3 75.3 - - - +
86V ILE* 1.3 78.2 + - - +
87V MET* 4.3 12.8 - - + -
106V ILE* 5.4 0.6 - - + +
289V THR 4.0 0.2 - - - +
290V ILE* 3.6 1.3 - - - +
291V LEU* 2.8 58.5 + - + +
292V VAL* 5.7 0.6 - - - +
308V LYS* 5.1 1.9 - - - +
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Residues in contact with ILE 86 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76V VAL 4.1 0.2 - - - +
77V TYR* 3.3 3.6 - - - -
78V ALA* 2.9 53.3 + - + +
85V LEU* 1.3 79.1 - - - +
87V MET* 1.3 66.5 + - - +
88V PHE* 3.6 31.5 - - + -
288V ILE* 4.9 2.5 - - + -
289V THR 3.1 11.9 - - - +
290V ILE* 4.3 12.8 - - + -
308V LYS* 3.7 17.5 - - + -
309V PHE* 3.6 41.1 - - + +
312V ASN* 4.4 4.9 - - - +
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Residues in contact with MET 87 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53V GLU* 3.1 39.0 - - - +
57V TYR* 4.1 13.2 - - + -
76V VAL 3.5 4.3 - - - +
77V TYR* 4.3 7.6 - - + -
85V LEU* 4.3 22.7 - - + -
86V ILE* 1.3 77.0 - - - +
88V PHE* 1.3 64.4 + - - +
274V PHE* 3.3 30.7 - - + -
277V MET* 3.2 18.3 - - + +
288V ILE* 3.1 8.7 - - - +
289V THR* 2.7 61.9 + - + +
291V LEU* 5.4 0.7 - - + -
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Residues in contact with PHE 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57V TYR* 3.1 24.8 + - - -
59V ASN* 5.9 1.1 - - - -
75V LYS* 3.5 0.5 - - - -
76V VAL* 2.8 36.8 + - + +
77V TYR* 5.3 1.1 - - - -
78V ALA* 5.3 1.8 - - + -
86V ILE* 3.6 34.1 - - + -
87V MET* 1.3 77.6 - - - +
89V LEU* 1.3 62.8 + - - +
90V ILE* 4.8 7.0 - - + -
95V LEU* 6.1 1.6 - - + -
99V PHE* 4.6 5.6 - + - -
277V MET* 3.9 1.1 - - - -
286V THR* 5.0 5.4 - - + -
287V CYS 3.7 1.3 - - - -
288V ILE* 3.0 31.6 - - + -
312V ASN* 3.5 27.1 - - - -
313V THR* 4.1 25.8 - - + -
316V ASP* 4.0 27.6 - - + +
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Residues in contact with LEU 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57V TYR* 4.7 4.7 - - - +
73V GLY* 4.8 6.7 - - - -
74V ASP 3.4 14.8 - - - +
75V LYS* 4.4 18.8 - - + -
88V PHE* 1.3 79.0 - - - +
90V ILE* 1.3 68.6 + - - +
277V MET* 4.2 10.8 - - + +
280V MET* 3.2 36.8 - - + +
281V LYS* 5.3 0.9 - - - -
282V ASN 6.1 0.7 - - - +
283V ALA* 4.0 18.4 - - + +
286V THR* 3.1 15.5 - - - +
287V CYS* 3.2 41.4 + - - +
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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