Contacts of the strand formed by residues 477 - 481 (chain A) in PDB entry 1CK7
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 GLY 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A PHE 3.3 0.8 - - - -
476A ASP* 1.3 83.5 - - - +
478A ILE* 1.3 67.9 + - - +
488A PHE* 3.0 30.3 + - - +
520A ILE* 5.0 0.2 - - - -
522A ALA* 4.6 2.7 - - - -
523A VAL* 4.2 18.4 - - - -
619A ALA* 4.4 4.0 - - - -
995A CL 4.0 13.7 - - - -
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Residues in contact with ILE 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A PHE* 3.1 42.0 - - + +
477A GLY* 1.3 77.8 - - - +
479A ALA* 1.3 58.7 + - - +
485A ILE* 4.6 3.6 - - + -
486A PHE 3.5 4.7 - - - +
487A PHE* 3.3 39.9 - - + -
523A VAL* 4.6 0.2 - - - +
619A ALA* 3.8 22.4 - - + +
620A VAL 3.5 8.3 - - - +
621A VAL* 4.2 9.4 - - + -
632A PHE* 3.9 36.1 - - + -
653A ILE* 4.8 3.4 - - + -
657A TRP* 5.5 0.2 - - + -
995A CL 4.0 3.0 - - - +
996A NA 2.7 24.3 - - - -
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Residues in contact with ALA 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A ILE* 1.3 82.8 - - - +
480A GLN* 1.3 64.9 + - - +
481A ILE* 4.1 1.4 - - + +
485A ILE* 4.5 1.8 - - - -
486A PHE* 2.7 43.4 + - - +
523A VAL* 4.0 26.0 - - + +
524A TYR* 4.4 4.7 - - - +
620A VAL 4.9 0.2 - - - +
621A VAL* 3.8 12.1 - - + -
996A NA 3.1 15.3 - - - -
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Residues in contact with GLN 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A ALA* 1.3 79.2 - - - +
481A ILE* 1.3 64.7 + - - +
483A GLY* 3.9 22.8 - - - -
484A GLU 3.1 11.4 - - - +
485A ILE* 3.1 26.4 - - + +
524A TYR 4.9 0.3 - - - -
525A GLU* 4.2 18.1 + - - +
621A VAL* 3.7 11.9 - - + +
622A ASP 5.0 2.2 - - - +
623A LEU* 2.9 34.9 - - - +
624A GLN* 3.0 28.6 + - - +
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Residues in contact with ILE 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A ALA 4.1 4.5 - - - +
480A GLN* 1.3 81.1 + - - +
482A ARG* 1.3 71.8 + - + +
483A GLY* 2.6 18.5 + - - -
484A GLU 2.7 11.7 + - - -
486A PHE* 3.6 47.8 - - + -
488A PHE* 4.5 2.0 - - + -
513A TRP* 3.9 23.6 - - + -
523A VAL* 4.7 8.3 - - + -
524A TYR 5.4 2.7 - - - +
525A GLU* 2.5 30.2 - - + +
530A GLU 6.1 0.2 - - - +
532A ALA* 4.6 19.3 - - + +
534A PHE* 4.5 13.9 - - + -
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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