Contacts of the strand formed by residues 485 - 493 (chain B) in PDB entry 2C11
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 ILE 485 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B TRP* 3.6 18.6 - - + -
352B VAL* 3.8 29.6 - - + -
359B LEU* 4.5 5.6 - - + -
360B VAL* 4.4 12.3 - - + -
363B ILE* 4.4 7.2 - - + -
477B THR* 4.6 3.4 - - + -
478B VAL 3.5 8.7 - - - +
479B PHE* 3.9 13.5 - - + -
483B GLY 4.5 1.8 - - - +
484B ALA* 1.3 77.0 - - - +
486B GLU* 1.3 69.4 + - - +
487B ILE* 4.3 13.0 + - + -
603B TYR* 5.5 0.9 - - + -
703B PHE 4.0 0.3 - - - +
704B PHE* 3.4 6.2 - - - -
705B LEU* 2.8 67.5 + - + +
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Residues in contact with GLU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B GLN* 5.6 0.5 + - - -
476B ASP 3.8 0.2 - - - +
477B THR* 3.5 4.3 - - - +
478B VAL* 2.7 52.8 + - + +
480B HIS* 3.1 27.4 + - - +
485B ILE* 1.3 74.1 - - - +
487B ILE* 1.3 67.8 + - - +
488B ARG* 3.1 50.6 + - + +
703B PHE 3.6 5.2 - - - +
704B PHE* 3.4 30.3 - - + -
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Residues in contact with ILE 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ILE* 4.0 21.3 - - + -
476B ASP 3.5 3.4 - - - +
477B THR* 3.6 29.2 - - + +
485B ILE* 4.3 11.2 - - + +
486B GLU* 1.3 83.9 - - - +
488B ARG* 1.3 69.5 + - - +
526B PHE* 3.8 32.8 - - + -
702B GLY* 3.1 4.7 - - - -
703B PHE* 3.0 68.4 + - + +
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Residues in contact with ARG 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A ARG* 5.1 11.1 - - - +
474B VAL 4.1 0.4 - - - -
475B TRP* 3.8 1.6 - - - -
476B ASP* 2.8 39.8 + - + +
478B VAL* 5.1 2.9 - - + -
486B GLU* 3.1 36.7 + - + +
487B ILE* 1.3 88.4 - - - +
489B PHE* 1.3 64.3 + - - +
490B TYR* 3.8 31.9 + - + +
526B PHE* 5.6 0.6 - - - -
608B LEU* 2.8 39.7 - - - +
700B GLY* 3.2 26.2 + - - -
701B VAL 3.2 10.8 - - - +
702B GLY* 4.4 0.7 - - - -
704B PHE* 4.4 4.6 - - - -
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Residues in contact with PHE 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B TYR* 3.6 38.4 - + - -
474B VAL 3.0 7.4 - - - +
475B TRP* 3.4 30.1 - + + -
488B ARG* 1.3 76.4 - - - +
490B TYR* 1.3 72.6 + - - +
491B ALA* 4.4 6.3 - - + -
522B HIS* 4.6 17.9 - - + -
523B SER 5.0 1.1 - - - -
524B ALA* 3.9 28.3 - - + -
526B PHE* 4.4 11.0 - + + -
680B ALA* 4.3 11.2 - - + -
682B PHE* 4.6 6.3 - + - -
699B ASN 3.9 1.2 - - - +
700B GLY* 3.6 0.9 - - - -
701B VAL* 3.0 57.7 + - + -
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Residues in contact with TYR 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A LEU* 3.6 39.1 - - + +
472B ASP 3.7 1.6 - - - +
473B TYR* 3.4 7.3 - - - -
474B VAL* 3.0 46.6 + - + +
476B ASP* 4.3 9.4 + - + -
488B ARG* 3.8 41.5 + - + +
489B PHE* 1.3 84.5 - - - +
491B ALA* 1.3 61.7 + - - +
492B THR 3.9 0.2 - - - -
696B THR* 3.6 43.5 - - + -
699B ASN 4.0 5.2 - - - +
700B GLY* 3.4 24.7 - - - -
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Residues in contact with ALA 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471B PAQ 5.0 7.6 - - + +
472B ASP 4.0 3.1 - - - -
473B TYR* 4.7 7.2 - - + -
489B PHE* 4.4 10.0 - - + -
490B TYR* 1.3 74.3 - - - +
492B THR* 1.3 60.2 + - - +
522B HIS* 4.0 33.0 - - + +
682B PHE* 4.5 14.3 - - + -
684B HIS* 6.0 0.4 - - + +
694B THR* 4.0 18.0 - - + +
695B VAL 4.0 6.4 - - - +
696B THR* 5.3 0.2 - - - -
699B ASN* 4.4 10.5 + - - +
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Residues in contact with THR 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A PRO* 5.9 0.7 - - + -
441A ARG* 3.5 3.6 - - - -
442A ARG* 3.3 34.8 + - + +
471B PAQ 2.9 9.8 - - - +
472B ASP* 2.7 46.9 + - + +
474B VAL* 3.9 21.3 - - + -
491B ALA* 1.3 73.0 - - - +
493B GLY* 1.3 65.1 + - - +
694B THR* 2.7 25.7 + - - -
696B THR* 4.0 17.0 - - + -
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Residues in contact with GLY 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A ARG 3.4 1.1 - - - -
443A HIS* 4.2 1.3 - - - -
472B ASP* 3.3 16.2 - - - -
492B THR* 1.3 85.3 + - - +
494B TYR* 1.3 61.4 + - - -
692B PRO 3.9 0.3 - - - +
693B ASN* 2.9 47.2 + - - -
694B THR* 2.9 10.1 + - - -
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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