Contacts of the strand formed by residues 287 - 292 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89S LEU* 3.1 39.2 + - - -
100S LYS* 3.1 34.8 - - + +
277S MET* 3.1 18.5 - - - +
280S MET* 3.7 31.2 - - - -
283S ALA* 4.7 1.3 - - - -
285S LYS 3.9 5.6 - - - +
286S THR* 1.3 72.8 - - - +
288S ILE* 1.3 68.7 + - - +
463S LEU* 6.0 1.3 - - - +
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Residues in contact with ILE 288 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86S ILE* 4.9 2.9 - - + -
87S MET 3.1 8.5 - - - +
88S PHE* 3.0 50.7 - - + -
89S LEU 4.4 0.2 - - - +
99S PHE* 3.6 28.5 - - + -
100S LYS 3.0 6.1 + - - +
101S ILE* 3.2 27.7 - - + +
102S LEU* 2.8 25.7 + - - +
277S MET* 3.4 3.1 - - - -
286S THR* 4.8 1.8 - - + -
287S CYS* 1.3 81.3 - - - +
289S THR* 1.3 62.2 + - - +
290S ILE* 5.2 0.7 - - + -
309S PHE* 3.7 29.8 - - + -
313S THR* 4.7 1.3 - - - +
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Residues in contact with THR 289 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86S ILE* 3.1 6.1 - - - +
87S MET* 2.7 57.4 + - + +
102S LEU* 3.3 19.0 - - + +
273S SER* 4.0 13.1 + - - +
274S PHE* 5.1 0.9 - - - -
277S MET* 3.1 38.1 - - - +
288S ILE* 1.3 72.8 - - - +
290S ILE* 1.3 63.1 + - - +
291S LEU* 4.2 24.7 - - + -
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Residues in contact with ILE 290 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85S LEU 3.8 4.0 - - - +
86S ILE* 4.3 14.8 - - + +
101S ILE* 3.4 24.5 - - + -
102S LEU 2.7 11.4 + - - +
103S GLY* 3.5 7.9 - - - -
104S ALA 3.1 17.1 + - - -
288S ILE* 4.8 1.6 - - + +
289S THR* 1.3 76.4 - - - +
291S LEU* 1.3 79.8 + - - +
292S VAL* 3.9 23.3 - - + -
308S LYS* 6.5 0.2 - - + -
309S PHE* 3.4 45.1 - - + -
338S MET* 5.0 0.9 - - - -
423S LEU* 3.8 19.5 - - + -
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Residues in contact with LEU 291 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S ILE* 4.0 27.4 - - + -
84S GLY* 3.5 4.0 - - - -
85S LEU* 2.8 56.5 + - + +
87S MET* 5.5 0.9 - - + -
103S GLY 5.2 0.2 - - - -
104S ALA* 3.2 15.7 - - + +
106S ILE* 3.9 22.8 - - + +
270S ALA* 3.9 31.9 - - + +
273S SER* 4.4 2.2 - - - +
274S PHE* 5.1 4.0 - - + -
289S THR* 4.2 17.9 - - + -
290S ILE* 1.3 94.3 - - - +
292S VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 292 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S LYS 4.8 0.7 - - - -
84S GLY* 4.8 7.2 - - - -
85S LEU 5.6 0.7 - - - +
104S ALA 3.2 8.6 + - - +
105S HIS* 2.9 8.2 - - + -
106S ILE* 2.7 32.2 + - - -
290S ILE* 3.9 21.1 - - + -
291S LEU* 1.3 77.1 - - - +
293S ASP* 1.3 64.4 + - - +
295S GLU* 5.9 1.1 - - + -
303S THR 3.6 9.9 - - - +
304S GLY* 4.2 15.5 - - - +
306S GLN* 4.0 24.5 - - - +
308S LYS* 6.3 0.4 - - + -
419S ILE* 4.3 22.2 - - + -
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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