Contacts of the strand formed by residues 501 - 510 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519C THR* 3.6 23.3 + - - +
496G VAL 3.5 0.7 - - - +
497G TYR* 3.4 5.9 - - - -
498G SER 2.8 37.3 + - - +
499G ASP* 3.8 10.2 - - - +
500G GLY* 1.3 84.6 - - - +
502G ARG* 1.3 65.8 + - - +
503G ARG* 3.7 22.7 + - + +
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Residues in contact with ARG 502 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526C GLN* 4.3 6.9 - - - +
471G GLN* 2.9 55.6 + - - +
474G LEU* 2.9 38.0 + - + -
475G LYS* 3.5 19.6 - - - +
496G VAL 3.5 4.5 - - - +
497G TYR* 3.8 26.2 + - + -
500G GLY 5.6 2.0 + - - -
501G GLN* 1.3 73.4 - - - +
503G ARG* 1.3 63.1 + - - +
504G HIS* 3.9 25.5 - - + +
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Residues in contact with ARG 503 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494G LEU 3.7 1.6 - - - +
495G SER* 3.3 3.6 - - - -
496G VAL* 2.8 35.7 + - + +
498G SER* 4.4 27.1 + - - -
499G ASP* 5.5 4.8 + - - +
501G GLN* 4.1 22.1 + - + +
502G ARG* 1.3 78.1 - - - +
504G HIS* 1.3 64.8 + - - +
505G PHE* 3.9 14.6 - - + -
541G LYS* 6.1 1.0 - - - +
542G SER* 3.4 28.3 + - - +
544G VAL* 3.8 21.5 - - - +
4H GLU* 2.8 43.8 + - - +
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Residues in contact with HIS 504 (chain G).
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* 3.4 42.0 + - + +
470G ALA* 4.7 7.4 - - + -
471G GLN* 5.8 1.8 - - - -
474G LEU* 5.0 1.6 - - + -
483G ARG* 3.1 16.3 + - - -
493G VAL* 3.9 5.8 - - + -
494G LEU 3.5 4.3 - - - -
495G SER* 2.8 32.3 + - - -
502G ARG* 3.9 30.3 + - + +
503G ARG* 1.3 76.7 - - - +
505G PHE* 1.3 56.2 + - - +
2H GLU 4.4 4.0 + - - +
3H PTR 3.4 26.0 - - + -
4H GLU* 2.8 34.3 + - - +
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Residues in contact with PHE 505 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493G VAL* 3.3 5.4 - - - +
494G LEU* 2.8 51.2 + - + +
496G VAL* 4.5 14.8 - - + -
503G ARG* 3.9 23.6 - - + -
504G HIS* 1.3 74.2 - - - +
506G ILE* 1.3 64.6 + - - +
507G ILE 3.4 0.2 + - - -
516G PHE* 4.2 17.7 - - + -
538G ILE* 4.1 16.4 - - + -
539G THR* 4.4 5.8 - - + -
542G SER* 3.7 32.5 - - - -
544G VAL* 4.1 18.4 - - + -
4H GLU* 3.4 39.5 - - + +
5H ASN* 4.2 11.9 - - + -
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Residues in contact with ILE 506 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488G LYS* 4.0 19.3 - - + -
491G GLU* 3.8 32.5 - - + +
492G TYR 3.6 10.5 - - - +
493G VAL* 4.1 5.6 - - + -
505G PHE* 1.3 72.2 - - - +
507G ILE* 1.3 69.2 + - - +
508G GLN* 3.4 9.2 + - + +
516G PHE* 3.9 3.6 - - - -
3H PTR 3.8 30.3 - - + -
4H GLU 3.0 10.5 + - - +
5H ASN* 3.0 41.2 + - - +
6H VAL* 3.8 26.7 - - + +
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Residues in contact with ILE 507 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482G VAL* 4.0 29.4 - - + -
491G GLU* 4.3 5.4 - - - +
492G TYR* 2.9 27.7 + - + +
493G VAL 4.0 2.0 - - - -
494G LEU* 3.9 23.1 - - + +
506G ILE* 1.3 72.9 - - - +
508G GLN* 1.3 63.1 + - - +
509G TYR* 3.5 2.4 + - - +
514G TYR* 4.1 14.1 - - + -
515G ARG 3.9 3.8 - - - +
516G PHE* 3.7 18.8 - - + -
524G ILE* 4.1 29.8 - - + -
527G LEU* 3.7 25.8 - - + -
528G ILE* 4.5 5.2 - - + -
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Residues in contact with GLN 508 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491G GLU* 5.0 0.9 - - - -
506G ILE* 3.4 11.4 + - + +
507G ILE* 1.3 72.6 - - - +
509G TYR* 1.3 59.4 + - - +
510G VAL* 4.0 8.5 - - + -
513G MET 3.4 0.9 - - - +
514G TYR* 3.1 6.6 - - - +
515G ARG* 2.9 74.7 + - + +
516G PHE 3.6 5.2 + - - +
5H ASN* 3.1 48.6 + - - +
6H VAL* 3.8 19.2 - - + +
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Residues in contact with TYR 509 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491G GLU* 4.8 8.9 + - - +
507G ILE 3.5 2.8 + - - +
508G GLN* 1.3 72.9 - - - +
510G VAL* 1.3 63.7 + - - +
511G ASP 5.8 0.2 - - - -
512G ASN* 3.4 39.1 + - - +
513G MET 3.2 10.1 - - - -
514G TYR* 3.5 46.4 - + + -
522G SER 5.4 0.2 - - - -
467K ARG* 4.9 5.5 - - + +
468K ILE* 6.3 1.3 - - + -
1L ASP* 2.5 39.3 + - - -
3L PTR 6.1 0.4 - - - -
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Residues in contact with VAL 510 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508G GLN* 4.0 8.0 - - + +
509G TYR* 1.3 85.3 - - - +
511G ASP* 1.3 80.3 + - + +
512G ASN 3.2 1.3 - - - -
513G MET* 2.9 23.8 + - - +
515G ARG* 3.8 45.5 + - - +
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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