Contacts of the strand formed by residues 287 - 297 (chain W) in PDB entry 6G0L
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 PRO 287 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285W HIS 3.3 9.2 - - - +
286W VAL* 1.3 102.4 - - + +
288W GLU* 1.3 59.7 + - - +
289W ARG 5.3 0.7 - - - +
290W ILE* 5.3 2.7 - - + -
309W VAL* 3.5 29.2 - - + -
310W LYS 3.4 4.9 - - - +
311W TRP* 4.0 8.5 - - + +
312W ARG* 4.2 2.1 + - - -
327W ILE* 6.4 2.0 - - + -
330W LEU* 3.6 31.4 - - + -
331W ALA* 3.8 14.7 - - + +
334W GLN* 4.1 16.3 + - + +
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Residues in contact with GLU 288 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287W PRO* 1.3 72.8 - - - +
289W ARG* 1.3 81.8 + - - +
310W LYS* 2.6 41.0 + - - +
311W TRP 3.8 20.0 - - - +
312W ARG* 3.8 29.8 - - - +
313W ARG 5.5 1.1 - - - +
334W GLN* 3.0 23.2 + - - +
441W LEU* 5.9 2.8 - - - +
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Residues in contact with ARG 289 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288W GLU* 1.3 108.0 + - - +
290W ILE* 1.3 75.2 + - - +
291W ILE* 4.2 10.8 - - + -
310W LYS* 2.7 45.8 + - + +
334W GLN* 3.5 11.6 + - - +
338W PHE* 5.9 2.0 - - - +
341W ARG* 3.8 25.5 - - - +
445W GLU* 5.9 6.5 - - - +
452W ASN* 4.9 7.9 - - - +
453W CYS* 5.3 6.5 + - - +
454W ILE* 4.0 26.1 - - - +
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Residues in contact with ILE 290 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287W PRO* 5.3 2.9 - - + -
289W ARG* 1.3 80.1 - - - +
291W ILE* 1.3 54.8 + - - +
292W ASP 3.8 2.9 - - - +
307W TYR* 3.7 21.3 - - + -
308W LEU 3.4 6.1 - - - +
309W VAL* 3.5 38.8 - - + +
327W ILE* 3.7 23.3 - - + -
334W GLN* 4.6 17.5 + - + +
335W VAL* 5.0 4.5 - - + -
338W PHE* 3.2 42.8 - - + +
341W ARG* 2.3 35.5 + - - -
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Residues in contact with ILE 291 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289W ARG* 4.2 9.0 - - + -
290W ILE* 1.3 75.7 - - - +
292W ASP* 1.3 58.2 + - - +
308W LEU* 2.7 48.6 + - + +
309W VAL 4.9 0.2 - - - -
310W LYS* 3.9 37.9 - - + +
316W TYR* 4.9 16.6 - - + +
319W ALA* 5.0 4.7 - - + -
338W PHE* 4.2 0.4 - - - -
341W ARG* 3.5 14.1 + - - +
465W THR* 5.6 5.4 - - - +
468W GLU* 3.9 20.3 - - + +
469W TYR* 4.7 17.0 - - + -
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Residues in contact with ASP 292 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290W ILE* 3.7 4.4 - - - +
291W ILE* 1.3 80.9 - - + +
293W SER* 1.3 81.7 + - - +
294W GLN* 4.6 5.0 + - - +
307W TYR* 3.5 4.2 - - - -
308W LEU* 2.9 27.6 + - + +
321W TRP* 3.9 18.5 - - + -
338W PHE* 4.0 9.2 - - - -
342W GLU* 5.6 1.5 - - - +
468W GLU* 4.0 22.3 - - - +
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Residues in contact with SER 293 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292W ASP* 1.3 87.7 + - - +
294W GLN* 1.3 59.4 + - - +
295W ARG 4.4 0.2 + - - -
305W LEU* 4.0 8.3 - - - +
306W GLN 3.5 4.9 - - - -
307W TYR* 3.1 35.0 - - - -
338W PHE* 3.5 16.2 - - - -
342W GLU* 4.1 4.7 + - - -
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Residues in contact with GLN 294 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292W ASP* 5.0 4.9 + - - +
293W SER* 1.3 72.6 - - - +
295W ARG* 1.3 82.8 + - - +
296W ALA* 3.4 12.7 + - + +
305W LEU* 4.1 4.3 - - - -
306W GLN* 2.9 36.0 + - + +
321W TRP* 3.8 28.8 - - + -
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Residues in contact with ARG 295 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293W SER 4.4 0.2 - - - -
294W GLN* 1.3 84.9 + - - +
296W ALA* 1.3 59.0 + - - +
297W SER 4.5 0.2 + - - -
303W SER* 2.6 53.3 + - - +
304W GLN 3.9 12.3 - - - -
305W LEU* 4.4 4.8 - - + +
1195W THR* 3.7 17.9 + - - +
1198W ARG* 2.4 37.9 - - - +
1199W ASP* 4.1 12.8 - - - +
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Residues in contact with ALA 296 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294W GLN* 3.4 13.1 + - + -
295W ARG* 1.3 73.7 - - - +
297W SER* 1.4 65.9 + - - +
298W LEU* 3.4 5.5 - - - +
303W SER* 3.5 4.0 - - - -
304W GLN* 3.1 29.3 + - - +
306W GLN* 4.3 20.8 - - - +
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Residues in contact with SER 297 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295W ARG 4.5 0.2 + - - -
296W ALA* 1.4 78.4 - - - +
298W LEU* 1.3 78.2 + - - +
301W GLY* 4.2 7.3 + - - -
302W THR 3.1 15.4 + - - -
303W SER* 3.8 9.2 + - - +
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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