Contacts of the strand formed by residues 492 - 498 (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 TYR 492 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464G ALA 3.8 0.7 + - - -
466G PRO* 3.6 22.3 - - + +
486G HIS* 3.0 39.3 + + - -
455I LEU* 3.7 20.7 - - + +
461I TYR* 3.8 11.2 - + - -
482I VAL* 4.4 3.8 - - + -
483I ARG 3.5 9.2 - - - +
484I GLU* 3.1 29.0 + - - -
490I GLY 4.5 2.9 - - - -
491I GLU* 1.3 77.9 - - - +
493I VAL* 1.3 63.7 + - - +
506I ILE* 3.6 7.3 - - - +
507I ILE* 2.9 40.4 + - + +
514I TYR* 4.4 19.1 - + - -
524I ILE* 3.4 31.6 - - + -
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Residues in contact with VAL 493 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481I LEU 3.9 0.2 - - - +
482I VAL* 3.2 7.4 - - - +
483I ARG* 2.8 53.7 + - + +
485I SER* 3.5 32.5 - - - +
492I TYR* 1.3 79.0 - - - +
494I LEU* 1.3 65.9 + - - +
495I SER* 3.5 22.3 + - - +
504I HIS* 4.0 4.9 - - + -
505I PHE 3.2 9.6 - - - +
506I ILE* 4.0 2.7 - - + -
507I ILE* 4.3 5.2 - - - -
3J PTR 3.6 26.2 - - + +
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Residues in contact with LEU 494 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480I PHE* 4.0 28.0 - - + -
481I LEU 3.5 14.8 - - - +
482I VAL* 4.0 13.2 - - + -
493I VAL* 1.3 71.6 - - - +
495I SER* 1.3 60.3 + - - +
496I VAL* 3.7 7.9 - - + -
504I HIS* 3.5 1.2 - - - -
505I PHE* 2.8 44.3 + - + +
507I ILE* 4.2 6.3 - - + +
516I PHE* 3.5 35.2 - - + -
528I ILE* 4.1 8.1 - - + -
538I ILE* 3.6 33.0 - - + -
546I LEU* 4.0 9.9 - - + -
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Residues in contact with SER 495 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470I ALA* 4.5 0.9 - - - -
474I LEU* 3.7 19.4 - - - +
480I PHE* 3.2 4.0 - - - -
481I LEU* 2.9 46.1 + - - +
483I ARG* 2.9 21.1 + - - -
493I VAL* 3.5 5.1 - - - +
494I LEU* 1.3 71.2 - - - +
496I VAL* 1.3 62.8 + - - +
503I ARG 3.4 4.5 - - - -
504I HIS* 2.7 28.4 + - - -
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Residues in contact with VAL 496 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474I LEU* 3.8 6.7 - - - +
478I GLY* 4.3 9.6 - - - -
479I ASP 3.1 20.4 - - - +
480I PHE* 3.9 4.3 - - + -
494I LEU* 3.7 24.2 - - + -
495I SER* 1.3 80.2 - - - +
497I TYR* 1.3 71.8 + - - +
498I SER* 3.9 2.8 + - - +
501I GLN 3.6 0.3 - - - +
502I ARG* 3.3 3.8 - - - +
503I ARG* 2.7 36.4 + - + +
505I PHE* 4.5 7.9 - - + -
544I VAL* 3.7 29.8 - - + -
546I LEU* 3.8 17.0 - - + -
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Residues in contact with TYR 497 (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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474I LEU* 3.4 30.5 - - + +
475I LYS 3.5 21.0 + - - +
476I LYS* 3.3 33.2 - - - +
477I GLN* 3.6 5.2 - - - -
478I GLY 2.8 28.2 + - - -
479I ASP* 3.0 8.3 + - + -
496I VAL* 1.3 72.3 - - - +
498I SER* 1.3 65.5 + - - +
499I ASP 5.0 0.4 - - - -
500I GLY* 3.4 39.9 + - - -
501I GLN 3.4 4.7 - - - -
502I ARG* 3.6 37.1 + - - +
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Residues in contact with SER 498 (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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477I GLN* 3.4 17.5 + - - -
478I GLY* 5.3 0.7 - - - -
496I VAL* 3.9 2.4 + - - -
497I TYR* 1.3 77.1 - - - +
499I ASP* 1.3 77.6 + - - +
500I GLY 3.3 1.8 - - - -
501I GLN 2.9 12.5 + - - +
503I ARG* 2.9 29.0 + - - -
542I SER 5.2 1.2 + - - -
543I GLY 5.2 0.7 + - - -
544I VAL* 3.7 41.1 - - - +
545I VAL 5.1 1.4 + - - -
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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