Contacts of the strand formed by residues 479 - 484 (chain B) in PDB entry 3C4C
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 ASP 479 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511A VAL* 6.0 1.7 - - - +
558A ARG* 5.5 0.9 + - - -
562A ARG* 3.4 28.0 + - - +
473B LYS* 4.2 17.9 - - - -
474B GLY 3.6 9.0 - - - +
475B LYS* 3.3 24.8 + - - -
476B TRP 4.7 0.3 - - - +
478B GLY* 1.3 73.5 - - - -
480B VAL* 1.3 64.2 + - - +
517B MET* 3.7 13.0 - - - +
531B TRP* 3.5 30.3 + - + +
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Residues in contact with VAL 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ILE* 4.7 2.2 - - + -
473B LYS* 3.8 0.9 - - - +
474B GLY* 3.2 38.9 + - - -
475B LYS 3.7 3.6 - - - +
476B TRP* 3.7 43.3 - - + +
479B ASP* 1.3 79.9 - - - +
481B ALA* 1.3 61.6 - - - +
482B VAL* 4.2 16.4 - - + -
517B MET* 3.9 14.6 - - + -
528B VAL* 4.1 12.6 - - + -
529B THR 3.5 9.2 - - - +
531B TRP* 2.9 25.4 - - - +
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Residues in contact with ALA 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B 324 3.5 44.2 - - + +
471B VAL* 5.3 2.7 - - + -
472B TYR 3.8 6.7 - - - +
480B VAL* 1.3 76.3 - - - +
482B VAL* 1.3 62.6 + - - +
527B ILE 3.4 4.2 - - - +
528B VAL* 3.7 0.7 - - - -
529B THR* 2.9 30.3 + - - +
530B GLN 4.1 0.9 - - - +
531B TRP* 3.6 17.0 - - + -
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Residues in contact with VAL 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ILE* 4.4 23.3 - - + -
458B THR 4.9 1.1 - - - +
459B VAL* 4.4 13.2 - - + -
470B THR 3.7 0.2 - - - +
471B VAL* 3.3 4.5 - - - -
472B TYR 2.9 35.5 + - - +
474B GLY* 5.2 0.9 - - - -
480B VAL* 4.2 19.1 - - + -
481B ALA* 1.3 74.2 - - - +
483B LYS* 1.3 57.2 + - - +
484B MET* 3.5 23.3 + - + +
526B ALA* 3.5 31.0 - - + -
527B ILE 3.5 6.7 - - - +
528B VAL* 4.6 11.4 - - + -
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Residues in contact with LYS 483 (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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3B 324 3.6 61.2 + - + -
465B SER 5.0 0.2 + - - -
466B GLY* 3.6 7.4 - - - -
467B SER* 3.1 37.4 - - - +
468B PHE* 2.9 40.5 - - + -
470B THR 3.5 5.8 - - - +
471B VAL* 3.4 18.6 - - + -
482B VAL* 1.3 68.7 - - - +
484B MET* 1.3 58.9 + - - +
526B ALA* 3.2 2.5 - - - -
527B ILE* 2.9 31.3 + - + +
595B PHE* 3.5 27.3 + - - +
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Residues in contact with MET 484 (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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459B VAL* 3.9 33.4 - - + -
468B PHE* 4.6 0.2 - - - -
469B GLY* 3.7 3.3 + - - -
470B THR* 2.7 42.1 + - - +
472B TYR* 3.3 34.8 - - + -
482B VAL* 3.5 15.0 + - + +
483B LYS* 1.3 74.9 - - - +
485B LEU* 1.3 73.2 + - - +
524B GLN* 4.6 14.1 - - + -
525B LEU 3.4 9.9 - - - +
526B ALA* 4.3 8.5 - - + -
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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