Contacts of the strand formed by residues 287 - 292 (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 CYS 287 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G LEU* 3.1 32.1 + - - -
100G LYS* 3.1 33.7 - - + +
277G MET* 3.1 26.5 - - - +
280G MET* 3.7 31.0 - - + -
283G ALA* 4.8 0.7 - - - -
285G LYS 4.0 5.2 - - - +
286G THR* 1.3 72.6 - - - +
288G ILE* 1.3 68.3 + - - +
463G LEU* 6.0 1.3 - - - +
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Residues in contact with ILE 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ILE* 4.9 2.5 - - + -
87G MET 3.1 13.5 - - - +
88G PHE* 3.0 47.3 - - + -
89G LEU 4.4 0.2 - - - +
99G PHE* 3.7 27.4 - - + -
100G LYS 3.0 5.6 + - - +
101G ILE* 3.1 28.3 - - + +
102G LEU* 2.9 25.5 + - - +
277G MET* 3.4 2.7 - - - -
286G THR* 4.8 1.6 - - + -
287G CYS* 1.3 81.5 - - - +
289G THR* 1.3 61.4 + - - +
290G ILE* 5.2 0.7 - - + -
309G PHE* 3.8 28.9 - - + -
313G THR* 4.7 1.3 - - + +
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Residues in contact with THR 289 (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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85G LEU 4.0 0.5 - - - +
86G ILE* 3.1 5.4 - - - +
87G MET* 2.7 57.2 + - + +
102G LEU* 3.3 18.7 - - + +
273G SER* 4.1 13.6 + - - +
274G PHE* 5.1 1.1 - - - -
277G MET* 3.0 36.5 - - - +
288G ILE* 1.3 73.1 + - - +
290G ILE* 1.3 65.1 + - - +
291G LEU* 4.1 24.2 - - + -
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Residues in contact with ILE 290 (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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85G LEU 3.8 4.7 - - - +
86G ILE* 4.3 13.0 - - + +
101G ILE* 3.5 24.2 - - + -
102G LEU 2.7 12.0 + - - +
103G GLY* 3.5 7.4 - - - -
104G ALA 3.1 17.3 + - - +
288G ILE* 4.8 1.1 - - + +
289G THR* 1.3 76.3 - - - +
291G LEU* 1.3 77.5 + - - +
292G VAL* 3.9 24.2 - - + +
308G LYS* 6.5 0.4 - - + -
309G PHE* 3.3 45.3 - - + -
338G MET* 5.0 1.1 - - - -
423G LEU* 3.8 18.8 - - + -
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Residues in contact with LEU 291 (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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49G ILE* 4.0 27.8 - - + -
84G GLY* 3.5 4.3 - - - -
85G LEU* 2.8 56.1 + - + +
87G MET* 5.5 0.9 - - + -
103G GLY 5.2 0.2 - - - -
104G ALA* 3.1 16.8 - - + +
106G ILE* 3.9 22.5 - - + +
270G ALA* 3.9 31.6 - - + +
273G SER* 4.4 1.8 - - - +
274G PHE* 5.1 4.3 - - + -
289G THR* 4.1 18.8 - - + -
290G ILE* 1.3 91.5 - - - +
292G VAL* 1.3 62.3 + - - +
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Residues in contact with VAL 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G LYS 4.8 0.9 - - - -
84G GLY* 4.7 7.9 - - - -
85G LEU 5.6 0.7 - - - +
104G ALA 3.2 7.6 + - - +
105G HIS* 2.9 7.3 - - + -
106G ILE* 2.7 34.9 + - - +
290G ILE* 3.9 20.9 - - + -
291G LEU* 1.3 76.6 - - - +
293G ASP* 1.3 63.8 + - - +
295G GLU* 5.9 0.7 - - + -
303G THR 3.6 10.1 - - - +
304G GLY* 4.2 15.7 - - - +
306G GLN* 4.0 24.5 - - - +
308G LYS* 6.3 0.4 - - + -
419G ILE* 4.3 22.7 - - + -
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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