Contacts of the strand formed by residues 287 - 292 (chain T) 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 CYS 287 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89T LEU* 3.2 33.3 + - - -
100T LYS* 3.1 33.7 - - + +
277T MET* 3.1 26.6 - - - +
280T MET* 3.7 30.1 - - - -
283T ALA* 4.7 1.3 - - - -
285T LYS 4.0 4.9 - - - +
286T THR* 1.3 72.5 - - - +
288T ILE* 1.3 68.5 + - - +
463T LEU* 6.0 1.3 - - - +
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Residues in contact with ILE 288 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86T ILE* 4.8 3.4 - - + -
87T MET 3.1 9.0 - - - +
88T PHE* 3.0 50.7 - - + -
89T LEU 4.4 0.7 - - - +
99T PHE* 3.7 28.0 - - + -
100T LYS 3.0 5.3 + - - +
101T ILE* 3.1 29.4 - - + +
102T LEU* 2.9 25.6 + - - +
277T MET* 3.4 3.1 - - - -
286T THR* 4.8 1.8 - - + -
287T CYS* 1.3 82.1 - - - +
289T THR* 1.3 61.1 + - - +
290T ILE* 5.2 0.4 - - + -
309T PHE* 3.7 30.1 - - + -
313T THR* 4.7 1.3 - - - +
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Residues in contact with THR 289 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85T LEU 3.9 0.2 - - - +
86T ILE* 3.1 6.5 - - - +
87T MET* 2.8 57.2 + - + -
102T LEU* 3.3 19.0 - - + +
273T SER* 4.0 13.8 + - - +
274T PHE* 5.1 1.1 - - - -
277T MET* 3.1 36.5 - - - +
288T ILE* 1.3 72.5 - - - +
290T ILE* 1.3 63.7 + - - +
291T LEU* 4.1 23.3 - - + -
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Residues in contact with ILE 290 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85T LEU 3.8 4.0 - - - +
86T ILE* 4.3 14.6 - - + +
101T ILE* 3.5 23.1 - - + -
102T LEU 2.7 11.6 + - - +
103T GLY* 3.4 7.3 - - - -
104T ALA 3.1 17.1 + - - -
288T ILE* 4.7 1.1 - - + +
289T THR* 1.3 76.4 - - - +
291T LEU* 1.3 77.7 + - - +
292T VAL* 3.9 24.2 - - + +
308T LYS* 6.6 0.4 - - + -
309T PHE* 3.4 43.5 - - + -
338T MET* 5.0 0.9 - - - -
423T LEU* 3.8 19.7 - - + -
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Residues in contact with LEU 291 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45T VAL* 5.8 0.2 - - + -
49T ILE* 4.0 27.1 - - + -
84T GLY* 3.5 3.8 - - - -
85T LEU* 2.8 57.0 + - + +
87T MET* 5.5 0.7 - - + -
103T GLY 5.2 0.2 - - - -
104T ALA* 3.1 17.0 - - + +
106T ILE* 3.9 22.5 - - + +
270T ALA* 3.9 32.8 - - + +
273T SER* 4.4 2.0 - - - +
274T PHE* 5.1 4.5 - - + -
289T THR* 4.1 18.2 - - + -
290T ILE* 1.3 85.6 - - - +
292T VAL* 1.3 63.1 + - - +
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Residues in contact with VAL 292 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83T LYS 4.8 0.4 - - - -
84T GLY* 4.8 7.9 - - - -
85T LEU 5.6 0.7 - - - +
104T ALA 3.1 8.8 + - - +
105T HIS* 2.9 7.6 - - + -
106T ILE* 2.7 35.7 + - - -
290T ILE* 3.9 20.2 - - + -
291T LEU* 1.3 77.3 - - - +
293T ASP* 1.3 63.5 + - - +
295T GLU* 5.9 0.9 - - + -
303T THR 3.6 9.9 - - - +
304T GLY* 4.1 15.5 - - - +
306T GLN* 3.9 24.5 - - - +
308T LYS* 6.3 0.4 - - + -
419T ILE* 4.3 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