Contacts of the strand formed by residues 667 - 672 (chain B) in PDB entry 2CKJ
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 ILE 667 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B LEU* 3.9 30.7 - - + -
609B VAL 4.2 2.5 - - - +
610B THR* 3.5 11.4 - - + -
654B THR 4.9 1.6 - - - +
655B VAL 4.6 6.5 - - - +
656B PHE* 3.7 23.4 - - + -
657B ALA* 2.9 33.8 + - - +
666B HIS* 1.3 80.5 - - + +
668B ILE* 1.3 54.7 + - - +
669B GLY 3.6 19.7 - - - +
808B VAL* 4.1 33.0 - - + +
809B VAL* 6.0 0.2 - - + -
812B ALA* 5.8 0.7 - - + -
836B ILE* 4.4 18.6 - - + -
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Residues in contact with ILE 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B VAL* 3.2 15.8 + - + +
610B THR 4.8 1.3 - - - -
611B SER* 4.0 21.8 - - - +
618B ILE* 4.5 13.9 - - + -
621B ILE* 3.8 27.6 - - + -
635B PHE* 5.4 2.9 - - + -
637B SER* 4.5 3.5 - - - -
638B ALA 4.4 5.4 + - - -
656B PHE* 3.8 15.9 - - - +
657B ALA* 4.2 15.5 - - + +
661B VAL* 4.4 22.2 - - + -
666B HIS 3.9 9.6 - - - +
667B ILE* 1.3 75.6 - - - +
669B GLY* 1.3 58.4 + - - +
688B ILE* 4.3 19.7 - - + -
690B TYR* 4.3 11.9 - - + +
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Residues in contact with GLY 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B LEU* 3.5 8.0 - - - +
609B VAL* 2.8 32.3 + - - +
635B PHE* 4.3 9.6 - - - -
636B ILE 3.4 13.5 - - - -
637B SER* 4.5 1.1 - - - -
656B PHE* 3.6 13.5 - - - -
667B ILE* 3.6 5.5 - - - +
668B ILE* 1.3 80.1 - - - +
670B ALA* 1.4 54.3 + - - -
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Residues in contact with ALA 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B LEU* 3.9 32.5 - - + -
607B ARG 3.8 6.5 - - - +
608B LEU* 3.9 10.3 - - + +
609B VAL* 4.0 3.0 - - - +
635B PHE* 3.4 8.5 - - - -
636B ILE* 2.9 45.0 + - + +
656B PHE* 4.7 4.7 - - + -
669B GLY* 1.4 72.5 - - - +
671B VAL* 1.3 62.7 + - - +
672B VAL* 5.7 0.2 - - + -
812B ALA* 5.5 1.1 - - + -
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Residues in contact with VAL 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B LEU* 3.8 3.6 - - - +
607B ARG* 3.0 36.5 + - + +
609B VAL* 4.7 4.5 - - + -
626B ALA* 5.3 0.9 - - + -
632B PHE* 4.3 12.3 - - + -
634B CYS 3.8 3.4 - - - -
635B PHE* 4.2 14.8 - - + -
670B ALA* 1.3 75.5 - - - +
672B VAL* 1.4 64.6 + - - +
673B ALA 4.3 0.2 - - - -
679B THR* 4.1 10.4 + - - +
682B ALA* 4.1 15.0 - - + -
683B ALA* 3.4 41.5 - - + +
686B VAL* 4.3 9.0 - - + -
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Residues in contact with VAL 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B LEU* 3.5 38.1 - - + -
605B SER 3.7 5.4 - - - +
606B LEU* 4.7 9.4 - - + -
632B PHE* 4.1 3.1 - - - -
633B VAL* 2.7 40.9 + - + +
634B CYS* 2.9 28.0 + - - +
636B ILE* 5.3 5.6 - - + -
670B ALA 5.1 2.5 - - - +
671B VAL* 1.4 75.5 - - - +
673B ALA* 1.3 61.8 + - - +
816B ALA* 4.2 22.9 - - + -
820B THR* 4.7 5.8 - - + -
824B VAL* 5.2 5.2 - - + -
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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