Contacts of the strand formed by residues 287 - 292 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M LEU* 3.2 32.4 + - - -
100M LYS* 3.1 33.4 - - + +
277M MET* 3.1 25.7 - - - +
280M MET* 3.6 30.5 - - + -
283M ALA* 4.7 1.1 - - - -
285M LYS 4.0 5.8 - - - +
286M THR* 1.3 73.2 - - - +
288M ILE* 1.3 68.7 + - - +
463M LEU* 6.1 1.1 - - - +
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Residues in contact with ILE 288 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M ILE* 4.9 2.9 - - + -
87M MET 3.1 9.0 - - - +
88M PHE* 3.1 50.0 - - + -
89M LEU 4.4 0.7 - - - +
99M PHE* 3.6 27.8 - - + -
100M LYS 3.0 5.3 + - - +
101M ILE* 3.1 28.9 - - + +
102M LEU* 2.9 24.9 + - - +
277M MET* 3.4 2.5 - - - -
286M THR* 4.8 1.8 - - + -
287M CYS* 1.3 81.5 - - - +
289M THR* 1.3 61.4 + - - +
290M ILE* 5.2 0.7 - - + -
309M PHE* 3.8 29.6 - - + -
313M THR* 4.7 2.0 - - - +
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Residues in contact with THR 289 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M LEU 4.0 0.2 - - - +
86M ILE* 3.1 5.9 - - - +
87M MET* 2.7 58.3 + - + +
102M LEU* 3.3 18.4 - - + +
273M SER* 4.1 13.9 + - - +
274M PHE* 5.1 0.9 - - - -
277M MET* 3.0 36.6 - - - +
288M ILE* 1.3 72.6 + - - +
290M ILE* 1.3 62.7 + - - +
291M LEU* 4.1 23.3 - - + -
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Residues in contact with ILE 290 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M LEU 3.8 3.8 - - - +
86M ILE* 4.3 13.9 - - + +
101M ILE* 3.5 25.1 - - + -
102M LEU 2.7 11.3 + - - +
103M GLY* 3.5 6.8 - - - -
104M ALA 3.2 17.4 + - - +
288M ILE 4.8 1.1 - - - +
289M THR* 1.3 76.7 - - - +
291M LEU* 1.3 78.4 + - - +
292M VAL* 4.0 23.3 - - + +
308M LYS* 6.6 0.4 - - + -
309M PHE* 3.4 43.5 - - + -
338M MET* 4.9 1.1 - - - -
423M LEU* 3.8 19.1 - - + -
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Residues in contact with LEU 291 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M ILE* 4.0 28.5 - - + -
84M GLY* 3.5 3.8 - - - -
85M LEU* 2.8 57.2 + - + +
87M MET* 5.5 0.4 - - + -
103M GLY 5.2 0.2 - - - -
104M ALA* 3.1 17.5 - - + +
106M ILE* 3.9 21.8 - - + +
270M ALA* 3.9 30.7 - - + +
273M SER* 4.4 2.0 - - - +
274M PHE* 5.1 4.5 - - + -
289M THR* 4.1 19.3 - - + -
290M ILE* 1.3 91.1 - - - +
292M VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 292 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83M LYS 4.8 0.7 - - - -
84M GLY* 4.8 7.0 - - - -
85M LEU 5.7 0.7 - - - +
104M ALA 3.2 8.6 + - - +
105M HIS* 2.9 8.2 - - + -
106M ILE* 2.7 35.4 + - - +
290M ILE* 4.0 20.4 - - + -
291M LEU* 1.3 77.9 - - - +
293M ASP* 1.3 63.8 + - - +
295M GLU* 5.9 0.7 - - + -
303M THR 3.6 9.4 - - - +
304M GLY* 4.2 15.5 - - - +
306M GLN* 4.0 24.5 - - - +
308M LYS* 6.3 0.4 - - + -
419M ILE* 4.3 21.5 - - + -
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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