Contacts of the strand formed by residues 84 - 89 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46P THR* 4.0 6.2 + - - -
79P ASN* 3.7 7.6 - - - +
80P ASN* 2.9 41.7 + - - +
82P GLY 3.4 0.2 - - - -
83P LYS* 1.3 80.5 - - - +
85P LEU* 1.3 63.6 + - - +
106P ILE* 4.9 0.2 - - - -
291P LEU 3.5 9.4 - - - -
292P VAL* 4.7 7.0 - - - -
303P THR* 4.4 3.3 - - - +
308P LYS* 5.0 0.7 - - - -
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Residues in contact with LEU 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P THR* 4.2 11.4 - - - +
49P ILE* 3.4 35.0 - - + -
50P LYS* 3.3 32.8 - - - +
77P TYR* 3.9 15.9 - - + -
78P ALA 3.6 13.2 - - - +
84P GLY* 1.3 74.6 - - - +
86P ILE* 1.3 79.4 + - - +
87P MET* 4.2 13.2 - - + -
106P ILE* 5.4 0.9 - - + +
289P THR 3.9 0.5 - - - +
290P ILE* 3.6 1.5 - - - +
291P LEU* 2.7 57.7 + - + +
292P VAL* 5.6 1.0 - - - +
308P LYS* 5.1 1.7 - - - +
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Residues in contact with ILE 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76P VAL 4.1 0.3 - - - +
77P TYR* 3.2 2.9 - - - +
78P ALA* 2.9 54.3 + - + +
85P LEU* 1.3 78.1 - - - +
87P MET* 1.3 68.6 + - - +
88P PHE* 3.5 33.0 - - + -
288P ILE* 4.8 3.1 - - + -
289P THR 3.1 11.2 - - - +
290P ILE* 4.3 13.9 - - + -
308P LYS* 3.7 17.0 - - + -
309P PHE* 3.6 40.8 - - + +
312P ASN* 4.5 4.7 - - - +
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Residues in contact with MET 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P GLU* 3.2 44.4 - - - +
57P TYR* 4.1 15.0 - - + -
76P VAL 3.5 4.0 - - - +
77P TYR* 4.3 7.9 - - + -
85P LEU* 4.2 22.4 - - + -
86P ILE* 1.3 77.0 - - - +
88P PHE* 1.3 63.0 + - - +
274P PHE* 3.3 24.9 - - + -
277P MET* 3.2 17.4 - - + +
288P ILE* 3.1 9.2 - - - +
289P THR* 2.8 61.2 + - + +
291P LEU* 5.5 0.9 - - + -
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Residues in contact with PHE 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P TYR* 3.1 24.8 - - - -
59P ASN* 5.9 0.9 - - - -
75P LYS* 3.5 6.6 - - - -
76P VAL* 2.8 32.1 + - + +
77P TYR* 5.3 0.9 - - - -
78P ALA* 5.3 1.8 - - + -
86P ILE* 3.5 34.8 - - + -
87P MET* 1.3 78.0 - - - +
89P LEU* 1.3 62.3 + - - +
90P ILE* 4.8 7.0 - - + -
95P LEU* 6.1 0.9 - - + -
99P PHE* 4.6 6.5 - + - -
277P MET* 3.9 1.1 - - - -
286P THR* 5.0 4.7 - - + -
287P CYS 3.7 1.1 - - - -
288P ILE* 3.1 32.5 - - + -
312P ASN* 3.5 27.6 - - - -
313P THR* 4.1 25.1 - - + -
316P ASP* 4.0 27.6 - - + +
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Residues in contact with LEU 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P TYR* 4.8 5.2 - - - +
73P GLY* 4.8 7.0 - - - -
74P ASP 3.4 14.6 - - - +
75P LYS* 4.5 19.3 - - + -
88P PHE* 1.3 80.3 - - - +
90P ILE* 1.3 68.2 + - - +
277P MET* 4.2 10.5 - - + +
280P MET* 3.2 36.6 - - + +
281P LYS* 5.3 1.1 - - - -
282P ASN 6.1 0.9 - - - +
283P ALA* 4.0 18.6 - - + +
286P THR* 3.1 15.3 - - - +
287P CYS* 3.1 42.1 + - - +
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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