Contacts of the strand formed by residues 479 - 484 (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 ASP 479 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473K LEU 4.2 0.9 - - - +
474K LEU* 3.7 16.0 - - + +
475K LYS* 3.0 12.9 + - - +
476K LYS* 2.9 42.9 + - - +
477K GLN 3.3 0.2 - - - -
478K GLY* 1.3 75.5 - - - +
480K PHE* 1.3 60.1 + - - +
496K VAL* 3.1 7.8 - - - +
497K TYR* 2.9 29.3 + - + -
548K ASN* 3.0 32.4 + - - +
550K ILE* 3.7 18.0 - - + +
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Residues in contact with PHE 480 (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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460K TRP* 4.0 19.8 - + + +
474K LEU* 3.8 5.3 - - - +
478K GLY 3.5 11.4 - - - +
479K ASP* 1.3 76.3 - - - +
481K LEU* 1.3 66.5 + - - +
482K VAL* 5.4 0.4 - - + -
494K LEU* 4.0 14.8 - - + -
495K SER 3.2 11.0 - - - +
496K VAL* 3.8 15.5 - - + -
528K ILE* 3.7 27.6 - - + -
532K TYR* 3.9 16.8 - + - -
546K LEU* 3.8 27.8 - - + -
548K ASN 3.0 18.5 + - - -
549K PRO* 3.3 35.6 - - + +
550K ILE* 3.0 26.4 + - - +
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Residues in contact with LEU 481 (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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460K TRP 3.4 13.9 - - - +
462K HIS* 3.6 19.1 - - + +
465K ILE* 4.2 6.1 - - + -
470K ALA* 4.0 25.4 - - + -
473K LEU* 4.0 37.7 - - + -
474K LEU* 4.0 15.5 - - + -
480K PHE* 1.3 79.3 - - - +
482K VAL* 1.3 77.5 + - - +
483K ARG* 4.2 8.5 - - - -
494K LEU* 3.6 5.7 - - - +
495K SER* 2.9 40.6 + - - +
550K ILE* 4.3 3.6 - - + +
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Residues in contact with VAL 482 (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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455K LEU* 5.0 0.2 - - + -
460K TRP* 2.9 39.5 + - + -
461K TYR* 3.6 18.4 - - + -
462K HIS* 2.9 29.3 + - - +
480K PHE* 5.4 0.7 - - + -
481K LEU* 1.3 79.7 - - - +
483K ARG* 1.3 70.7 + - - +
492K TYR* 4.4 8.3 - - + -
493K VAL 3.2 12.1 - - - +
494K LEU* 4.1 6.7 - - + -
507K ILE* 4.2 16.8 - - + -
524K ILE* 4.5 4.9 - - + -
528K ILE* 3.9 23.6 - - + -
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Residues in contact with ARG 483 (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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461K TYR* 4.6 1.3 - - - -
462K HIS* 4.9 0.2 - - + -
463K GLY 3.2 15.3 - - - +
465K ILE* 3.5 29.7 + - + +
466K PRO* 4.5 1.0 - - - +
467K ARG* 3.7 19.6 - - - +
470K ALA* 3.8 21.9 - - - +
481K LEU* 4.2 5.4 - - + -
482K VAL* 1.3 78.5 - - - +
484K GLU* 1.3 65.0 + - - +
486K HIS* 4.7 0.6 + - - +
492K TYR* 3.5 7.1 - - - +
493K VAL* 2.8 56.8 + - + +
495K SER* 3.0 14.9 + - - +
504K HIS* 3.1 28.1 + - - -
3L PTR 2.8 43.2 + - - -
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Residues in contact with GLU 484 (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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464I ALA* 4.0 23.2 - - - +
486I HIS* 5.1 8.2 + - + +
461K TYR* 3.4 25.8 + - - +
463K GLY* 2.8 15.8 + - - +
464K ALA* 3.4 33.1 + - + +
465K ILE 4.2 8.3 - - - +
483K ARG* 1.3 76.7 + - - +
485K SER* 1.3 66.6 + - - +
486K HIS* 3.7 11.8 + - - -
490K GLY 6.4 0.2 - - - +
491K GLU 3.8 6.7 - - - +
492K TYR* 4.4 12.1 - - + +
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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