Contacts of the strand formed by residues 478 - 483 (chain A) in PDB entry 4KSP
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 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A LYS* 4.0 26.8 + - - -
473A GLY 3.5 4.6 - - - +
474A LYS* 3.8 23.7 + - - +
476A HIS 5.4 0.2 - - - +
477A GLY* 1.3 71.3 - - - -
479A VAL* 1.3 65.9 + - - +
516A MET* 5.2 1.0 - - - +
529A GLN* 4.7 1.0 - - - -
530A TRP* 3.4 35.2 + - + +
532A GLU* 4.5 5.9 - - - +
561B GLN* 5.3 0.4 - - - -
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Residues in contact with VAL 479 (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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456A ILE* 5.2 0.4 - - + -
472A LYS* 3.6 0.5 - - - +
473A GLY 2.8 47.4 + - - +
474A LYS 4.0 1.6 - - - +
475A TRP* 3.5 33.9 - - + +
476A HIS 5.4 0.2 - - - +
478A ASP* 1.3 80.1 - - - +
480A ALA* 1.3 60.0 + - - +
481A VAL* 3.8 20.2 - - + -
516A MET* 3.8 15.0 - - + -
527A VAL* 3.6 21.5 - - + -
528A THR 3.4 13.5 - - - +
530A TRP* 3.5 15.9 - - - -
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Residues in contact with ALA 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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470A VAL* 4.7 1.1 - - + -
471A TYR 3.5 5.6 - - - +
479A VAL* 1.3 73.8 - - - +
481A VAL* 1.3 61.6 + - - +
482A LYS 4.3 0.4 - - - -
526A ILE 4.4 0.2 - - - -
527A VAL* 3.3 5.5 - - - +
528A THR* 2.9 38.4 + - - +
529A GLN 4.0 1.9 + - - +
530A TRP* 3.8 10.9 - - + -
901A 1SU 3.3 50.7 - - + -
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Residues in contact with VAL 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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456A ILE* 4.0 25.1 - - + -
458A VAL* 4.8 7.0 - - + -
469A THR 3.3 4.3 - - - +
470A VAL* 3.3 2.5 - - - +
471A TYR* 2.9 47.0 + - + +
473A GLY* 4.5 6.5 - - - -
479A VAL* 3.8 21.1 - - + -
480A ALA* 1.3 78.9 - - - +
482A LYS* 1.3 62.3 + - - +
483A MET* 4.0 26.7 - - + -
525A ALA* 4.4 9.6 - - + -
526A ILE 3.5 4.7 - - - +
527A VAL* 4.5 9.2 - - + -
901A 1SU 4.6 1.3 - - - -
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Residues in contact with LYS 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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467A PHE* 4.4 13.6 + - - +
468A GLY* 4.6 11.0 - - - -
469A THR 3.3 7.4 - - - +
470A VAL* 4.5 14.4 - - + +
481A VAL* 1.3 71.4 - - - +
483A MET* 1.3 63.1 + - - +
484A LEU* 6.4 0.9 - - + -
500A GLU* 3.0 34.7 + - - +
525A ALA* 3.1 6.2 - - - +
526A ILE* 2.8 40.4 + - + +
593A ASP* 3.7 17.8 + - - -
594A PHE* 6.0 1.8 - - - +
595A GLY 5.7 4.2 + - - -
901A 1SU 3.4 45.3 + - + -
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Residues in contact with MET 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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456A ILE* 6.1 4.0 - - + -
458A VAL* 4.7 17.9 - - + -
468A GLY* 2.9 7.7 - - - -
469A THR* 2.7 42.3 + - - +
471A TYR* 4.5 15.9 - - + -
481A VAL* 4.0 12.6 - - + -
482A LYS* 1.3 78.2 - - - +
484A LEU* 1.3 63.4 + - - +
485A ASN* 3.8 13.1 + - - +
519A SER* 6.4 0.2 - - - -
522A PRO* 5.2 9.0 - - + -
523A GLN* 3.8 31.9 - - + +
524A LEU 3.3 11.0 - - - +
525A ALA* 3.8 18.4 - - + -
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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