Contacts of the strand formed by residues 501 - 510 (chain I) in PDB entry 6KC4
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 GLN 501 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496I VAL 3.6 0.3 - - - +
497I TYR* 3.4 4.9 - - - -
498I SER 2.9 28.8 + - - +
499I ASP 3.8 3.1 + - - +
500I GLY* 1.3 89.3 + - - +
502I ARG* 1.3 72.4 + - - +
503I ARG* 3.4 33.6 + - + +
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Residues in contact with ARG 502 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471I GLN* 3.2 43.8 + - + +
472I GLU* 5.3 1.8 - - - +
474I LEU* 3.0 45.9 + - + -
475I LYS* 4.4 8.7 - - - +
496I VAL 3.3 5.4 - - - +
497I TYR* 3.6 24.6 + - + -
500I GLY 4.9 4.6 + - - -
501I GLN* 1.3 78.0 + - - +
503I ARG* 1.3 61.8 + - - +
504I HIS* 4.0 24.1 + - + +
4J GLU* 5.3 0.5 - - - +
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Residues in contact with ARG 503 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494I LEU 3.8 1.4 - - - +
495I SER* 3.4 3.1 - - - -
496I VAL* 2.7 39.5 + - + +
498I SER* 2.9 42.6 + - - -
499I ASP* 3.4 17.5 + - - +
501I GLN* 3.4 25.3 - - + +
502I ARG* 1.3 78.8 - - - +
504I HIS* 1.3 63.0 + - - +
505I PHE* 4.2 11.3 - - + -
542I SER* 5.5 2.7 - - - +
544I VAL* 4.3 11.4 - - + -
4J GLU* 3.8 37.9 + - + +
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Residues in contact with HIS 504 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467I ARG* 3.5 43.5 - - + +
470I ALA* 4.7 7.4 - - + -
471I GLN* 5.4 2.6 - - - +
474I LEU* 5.1 1.3 - - + -
483I ARG* 3.1 16.4 + - - -
493I VAL* 4.0 2.2 - - + -
494I LEU 3.5 3.1 - - - -
495I SER* 2.7 33.3 + - - -
502I ARG* 4.0 29.0 + - + +
503I ARG* 1.3 78.3 - - - +
505I PHE* 1.3 58.6 + - - +
2J GLU 4.5 2.7 + - - +
3J PTR 3.4 25.5 - - + -
4J GLU* 2.8 35.9 + - - +
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Residues in contact with PHE 505 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493I VAL* 3.2 6.5 - - - +
494I LEU* 2.8 54.0 + - + +
496I VAL* 4.5 4.7 - - + -
503I ARG* 4.2 17.7 - - + -
504I HIS* 1.3 75.2 - - - +
506I ILE* 1.3 62.5 + - - +
516I PHE* 4.0 18.6 - - + -
538I ILE* 3.8 23.6 - - + -
539I THR* 4.0 11.9 - - + -
542I SER* 3.4 35.9 - - - -
544I VAL* 3.8 24.7 - - + -
3J PTR 4.4 0.2 - - - -
4J GLU* 3.7 27.4 - - + -
5J ASN* 3.4 18.2 - - + +
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Residues in contact with ILE 506 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485I SER* 4.3 0.2 - - - +
488I LYS* 4.2 14.4 - - + +
491I GLU* 3.2 31.2 - - + +
492I TYR 3.6 11.0 - - - +
493I VAL* 4.0 5.4 - - + -
504I HIS 4.3 0.6 + - - -
505I PHE* 1.3 73.2 - - - +
507I ILE* 1.3 75.2 + - - +
508I GLN* 3.4 18.0 + - - +
516I PHE* 3.7 6.2 - - - -
3J PTR 3.7 39.4 - - + -
5J ASN* 2.8 28.6 + - - +
6J VAL* 3.6 28.9 - - + -
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Residues in contact with ILE 507 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482I VAL* 4.3 13.7 - - + -
491I GLU* 4.9 3.8 - - - +
492I TYR* 2.9 43.5 + - + +
494I LEU* 4.2 15.3 - - + +
506I ILE* 1.3 76.8 - - - +
508I GLN* 1.3 65.8 + - - +
509I TYR* 3.6 4.2 + - - +
514I TYR* 3.9 26.5 - - + -
515I ARG 3.9 3.8 - - - +
516I PHE* 3.6 24.2 - - + -
524I ILE* 4.0 23.3 - - + -
527I LEU* 3.7 23.8 - - + -
528I ILE* 4.8 2.2 - - + -
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Residues in contact with GLN 508 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491I GLU* 4.9 4.2 + - - -
506I ILE* 4.1 21.9 - - - +
507I ILE* 1.3 74.0 - - - +
509I TYR* 1.3 60.9 + - - +
510I VAL* 4.1 11.8 - - + +
513I MET 3.6 0.3 - - - +
514I TYR* 3.2 6.1 - - - +
515I ARG* 2.9 54.3 + - + +
516I PHE 4.1 13.0 - - - +
5J ASN* 3.8 28.4 + - - +
6J VAL* 4.3 4.7 - - - +
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Residues in contact with TYR 509 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467G ARG* 5.0 5.3 - - + +
468G ILE* 6.5 0.4 - - + -
1H ASP* 2.6 39.3 + - - -
3H PTR 6.0 0.9 - - - -
491I GLU* 6.3 1.2 - - - -
507I ILE 3.6 3.2 + - - +
508I GLN* 1.3 74.8 - - - +
510I VAL* 1.3 64.3 + - - +
511I ASP 5.9 0.2 - - - -
512I ASN* 3.5 39.4 + - - +
513I MET 3.3 11.2 - - - -
514I TYR* 3.6 45.1 - + + -
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Residues in contact with VAL 510 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508I GLN* 4.1 14.8 - - + +
509I TYR* 1.3 84.6 - - - +
511I ASP* 1.3 90.4 + - - +
512I ASN 3.2 1.3 - - - -
513I MET* 2.9 25.4 + - - +
515I ARG* 4.9 13.8 - - - +
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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