Contacts of the strand formed by residues 479 - 485 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473A LYS* 4.3 20.8 + - - -
474A GLY 3.4 4.0 - - - +
475A LYS* 3.0 28.4 + - - +
476A TRP 4.3 0.2 - - - +
478A GLY* 1.3 74.5 - - - -
480A VAL* 1.3 68.7 + - - +
517A MET* 5.2 2.4 - - - +
529A THR 4.6 0.2 - - - +
530A GLN* 5.0 1.6 - - - -
531A TRP* 3.7 29.7 + - + +
533A GLU* 4.7 4.7 - - - +
510B HIS* 5.6 2.6 + - - -
511B VAL* 6.0 1.6 - - - +
562B ARG* 4.0 26.7 + - - +
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Residues in contact with VAL 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A ILE* 4.9 2.5 - - + -
473A LYS* 4.0 0.5 - - - +
474A GLY 2.7 44.1 + - - +
475A LYS 4.6 0.2 - - - -
476A TRP* 3.7 38.4 - - + +
479A ASP* 1.3 83.4 - - - +
481A ALA* 1.3 60.5 + - - +
482A VAL* 4.0 13.7 - - + -
517A MET* 4.3 8.7 - - + -
528A VAL* 3.5 26.0 - - + -
529A THR 3.2 17.3 - - - +
531A TRP* 3.5 20.7 - - - +
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Residues in contact with ALA 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A 324 3.4 46.8 - - + +
471A VAL* 4.7 0.4 - - + -
472A TYR 3.2 8.5 - - - +
480A VAL* 1.3 74.8 - - - +
482A VAL* 1.3 65.2 + - - +
527A ILE 3.5 0.9 - - - +
528A VAL* 3.4 6.9 - - - +
529A THR* 3.1 29.1 + - - +
530A GLN 3.8 0.7 - - - +
531A TRP* 3.6 13.7 - - + -
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Residues in contact with VAL 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A 324 3.9 2.0 - - - -
457A ILE* 3.9 31.9 - - + -
459A VAL* 5.0 6.1 - - + -
470A THR 3.3 5.4 - - - +
472A TYR* 2.9 38.9 + - + +
473A LYS 4.9 7.6 - - - +
474A GLY* 5.0 0.2 - - - -
480A VAL* 4.0 12.6 - - + -
481A ALA* 1.3 81.1 - - - +
483A LYS* 1.3 56.9 + - - +
484A MET* 3.5 18.9 + - - +
520A SER* 5.2 0.4 - - - +
526A ALA* 3.7 27.6 - - + -
527A ILE 3.4 4.7 - - - +
528A VAL* 4.5 11.0 - - + -
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Residues in contact with LYS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A 324 3.4 61.0 + - + -
468A PHE* 3.4 30.2 - - + +
469A GLY* 4.4 15.7 - - - +
470A THR 3.3 5.8 - - - -
471A VAL* 4.1 14.6 - - + +
482A VAL* 1.3 68.8 - - - +
484A MET* 1.3 59.8 + - - +
485A LEU* 3.6 11.3 + - + +
526A ALA* 3.3 3.2 - - - -
527A ILE* 3.1 40.8 + - + +
594A ASP* 3.0 27.9 + - - +
595A PHE 5.3 1.4 + - - -
596A GLY 5.8 1.6 + - - -
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Residues in contact with MET 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A VAL* 4.9 16.2 - - + -
469A GLY* 3.7 0.8 - - - -
470A THR* 2.8 38.4 + - - +
472A TYR* 3.6 34.5 - - + +
482A VAL* 3.9 20.0 - - - +
483A LYS* 1.3 71.6 - - - +
485A LEU* 1.3 66.9 + - - +
523A PRO* 6.5 1.1 - - - -
524A GLN* 3.2 38.4 - - + +
525A LEU 3.5 10.5 - - - +
526A ALA* 4.0 5.6 - - - -
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Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A PHE* 4.2 13.2 - - + +
469A GLY* 4.5 0.4 - - - -
483A LYS* 3.7 22.4 - - + +
484A MET* 1.3 78.1 - - - +
486A ASN* 1.3 63.5 + - - +
487A VAL* 3.0 18.2 + - + +
498A PHE* 4.2 27.1 - - + -
524A GLN* 3.3 17.0 + - - -
525A LEU* 3.1 33.7 + - + +
526A ALA* 4.4 1.6 - - - -
527A ILE* 4.2 21.8 - - + -
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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