Contacts of the strand formed by residues 501 - 510 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496K VAL 3.6 0.3 - - - +
497K TYR* 3.5 7.3 - - - -
498K SER 2.9 29.9 + - - +
499K ASP 4.3 3.6 + - - -
500K GLY* 1.3 85.4 - - - +
502K ARG* 1.3 69.6 + - - +
503K ARG* 3.4 38.4 + - + +
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Residues in contact with ARG 502 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471K GLN* 3.0 53.5 + - + +
472K GLU* 5.3 0.8 - - - +
474K LEU* 2.8 42.6 + - + -
475K LYS* 4.3 9.5 + - - +
496K VAL 3.3 5.2 - - - +
497K TYR* 3.8 26.1 + - + +
500K GLY 5.5 2.4 + - - -
501K GLN* 1.3 75.3 - - - +
503K ARG* 1.3 62.9 + - - +
504K HIS* 4.1 13.8 - - + +
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Residues in contact with ARG 503 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494K LEU 3.7 1.2 - - - +
495K SER* 3.3 3.1 - - - -
496K VAL* 2.7 39.4 + - + +
498K SER* 2.9 33.8 + - - -
499K ASP* 3.4 16.1 + - - +
501K GLN* 3.4 41.9 + - + +
502K ARG* 1.3 79.6 - - - +
504K HIS* 1.3 65.3 + - - +
505K PHE* 4.0 11.7 - - + -
542K SER* 5.6 2.5 - - - -
544K VAL* 4.1 21.1 - - + -
4L GLU* 3.8 33.0 + - + +
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Residues in contact with HIS 504 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467K ARG* 3.5 30.5 - - + +
470K ALA* 4.8 2.7 - - + -
471K GLN* 3.1 38.6 + - + -
474K LEU* 5.1 1.6 - - + -
483K ARG* 3.1 16.9 + - - -
493K VAL* 3.9 5.8 - - + -
494K LEU 3.5 3.8 - - - -
495K SER* 2.7 32.0 + - - -
502K ARG* 4.1 12.0 - - + +
503K ARG* 1.3 81.0 - - - +
505K PHE* 1.3 59.4 + - - +
2L GLU 4.5 3.3 + - - +
3L PTR 3.4 24.8 - - + -
4L GLU* 2.7 34.6 + - - +
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Residues in contact with PHE 505 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493K VAL* 3.3 5.9 - - - -
494K LEU* 2.8 54.7 + - + +
496K VAL* 4.6 4.0 - - + -
503K ARG* 4.0 20.9 - - + -
504K HIS* 1.3 74.4 - - - +
506K ILE* 1.3 63.2 + - - +
516K PHE* 3.9 18.6 - - + -
538K ILE* 3.9 20.2 - - + -
539K THR* 4.1 11.4 - - + -
542K SER* 3.5 35.2 - - - -
544K VAL* 3.8 23.6 - - + -
3L PTR 4.6 0.2 - - - -
4L GLU* 3.7 26.2 - - + -
5L ASN* 3.3 20.2 - - + +
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Residues in contact with ILE 506 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488K LYS* 4.1 16.6 - - + -
491K GLU* 3.9 37.5 - - + +
492K TYR 3.6 2.5 - - - +
493K VAL* 4.0 9.9 - - + -
504K HIS 4.2 0.8 + - - -
505K PHE* 1.3 70.7 - - - +
507K ILE* 1.3 73.3 + - - +
508K GLN* 3.3 26.9 + - - +
516K PHE* 3.8 5.8 - - - -
3L PTR 3.8 40.4 - - + -
5L ASN* 2.7 33.9 + - - +
6L VAL* 3.9 15.5 - - + -
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Residues in contact with ILE 507 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482K VAL* 4.2 13.5 - - + -
491K GLU* 3.9 6.8 - - - +
492K TYR* 2.9 39.1 + - + +
494K LEU* 4.1 19.5 - - + +
506K ILE* 1.3 75.8 - - - +
508K GLN* 1.3 66.2 + - - +
509K TYR* 3.4 4.5 + - - +
514K TYR* 3.9 26.1 - - + -
515K ARG 4.0 2.2 - - - -
516K PHE* 3.7 21.1 - - + -
524K ILE* 4.0 26.0 - - + -
527K LEU* 3.6 24.7 - - + -
528K ILE* 4.7 3.4 - - + -
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Residues in contact with GLN 508 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491K GLU* 5.1 2.6 + - - -
506K ILE* 3.6 30.6 - - - +
507K ILE* 1.3 72.0 - - - +
509K TYR* 1.3 60.8 + - - +
510K VAL* 4.0 8.1 - - + -
513K MET 3.5 0.7 - - - +
514K TYR* 3.2 6.8 - - - +
515K ARG* 2.9 55.6 + - + +
516K PHE 4.1 12.6 - - - +
5L ASN* 3.7 19.6 + - - +
6L VAL* 4.6 3.5 - - - +
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Residues in contact with TYR 509 (chain K).
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* 4.8 5.9 - - + +
468I ILE* 6.1 2.0 - - + +
1J ASP* 2.4 43.6 + - - -
3J PTR 5.9 1.3 - - - -
491K GLU* 4.8 8.6 + - - +
507K ILE 3.4 4.3 + - - +
508K GLN* 1.3 74.0 - - - +
510K VAL* 1.3 61.1 + - - +
512K ASN* 3.5 36.1 + - - +
513K MET 3.3 11.0 - - - -
514K TYR* 3.5 45.5 - + + -
522K SER 5.7 0.2 - - - -
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Residues in contact with VAL 510 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508K GLN* 4.8 6.7 - - + -
509K TYR* 1.3 76.4 - - - +
511K ASP* 1.3 79.7 + - + +
512K ASN 3.2 2.5 - - - +
513K MET* 2.9 22.9 + - + +
515K ARG* 3.6 37.2 - - + +
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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