Contacts of the strand formed by residues 667 - 673 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608C LEU* 4.0 27.8 - - + -
609C VAL 4.5 0.7 - - - +
610C THR* 3.5 13.9 - - + -
654C THR 5.0 1.1 - - - +
655C VAL 4.4 8.7 - - - +
656C PHE* 3.4 33.9 - - + -
657C ALA* 2.9 26.2 + - - +
666C HIS* 1.3 80.1 - - + +
668C ILE* 1.3 60.6 + - - +
669C GLY 3.8 11.9 - - - +
808C VAL* 4.1 34.8 - - + +
812C ALA* 6.0 0.2 - - + -
836C ILE* 4.4 19.1 - - + -
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Residues in contact with ILE 668 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609C VAL* 3.1 15.2 + - + +
610C THR* 4.9 1.3 - - - -
611C SER* 4.1 24.5 - - - +
618C ILE* 4.7 13.2 - - + -
621C ILE* 3.8 26.9 - - + -
635C PHE* 5.1 3.6 - - + -
637C SER* 4.6 4.7 - - - -
638C ALA 4.6 6.1 + - - -
656C PHE* 4.1 14.3 - - - +
657C ALA* 4.3 16.3 - - + +
661C VAL* 4.2 21.1 - - + -
666C HIS* 3.4 9.4 + - + +
667C ILE* 1.3 77.3 - - - +
669C GLY* 1.4 57.3 + - - +
688C ILE* 4.4 19.3 - - + -
690C TYR* 4.4 9.9 - - + +
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Residues in contact with GLY 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608C LEU* 3.3 7.1 - - - +
609C VAL* 2.9 28.5 + - - +
635C PHE* 4.4 8.7 - - - -
636C ILE 3.5 11.4 - - - -
656C PHE* 3.9 14.8 - - - -
667C ILE* 3.5 5.5 - - - +
668C ILE* 1.4 80.6 - - - +
670C ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606C LEU* 3.7 33.2 - - + -
608C LEU* 3.8 15.7 - - + +
609C VAL* 4.3 2.5 - - - -
635C PHE* 3.2 12.3 - - - -
636C ILE* 2.9 46.7 + - + +
656C PHE* 4.7 3.8 - - + -
669C GLY* 1.3 74.7 - - - +
671C VAL* 1.3 58.9 + - - +
672C VAL* 5.2 0.9 - - + -
812C ALA* 5.3 0.4 - - + -
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Residues in contact with VAL 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606C LEU* 3.8 3.1 - - - +
607C ARG* 3.1 37.6 + - + +
609C VAL* 4.7 2.9 - - + -
626C ALA* 5.0 1.6 - - + -
632C PHE* 4.0 16.8 - - + -
634C CYS 3.6 4.0 - - - -
635C PHE* 4.3 7.0 - - + +
670C ALA* 1.3 73.1 - - - +
672C VAL* 1.3 65.9 + - - +
673C ALA* 4.3 0.4 - - + -
679C THR* 4.1 10.9 + - - +
682C ALA* 3.8 16.4 - - + -
683C ALA* 3.4 42.0 - - + +
686C VAL* 4.3 14.4 - - + -
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Residues in contact with VAL 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C LEU* 3.7 33.9 - - + -
605C SER 3.6 11.2 - - - +
606C LEU* 4.6 8.1 - - + -
632C PHE* 4.1 2.4 - - - -
633C VAL* 2.7 36.2 + - + +
634C CYS* 2.9 27.2 + - - +
636C ILE* 5.4 5.6 - - + -
670C ALA 5.1 2.5 - - - +
671C VAL* 1.3 79.0 - - - +
673C ALA* 1.3 62.6 + - - +
816C ALA* 4.3 22.4 - - + -
820C THR* 5.3 2.5 - - + -
824C VAL* 5.3 4.9 - - + -
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Residues in contact with ALA 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C LEU* 3.7 10.9 - - - +
605C SER* 3.0 33.4 + - - +
631C GLY 3.3 15.9 - - - +
632C PHE* 4.2 5.4 - - - -
633C VAL* 5.0 1.6 - - - -
671C VAL* 6.2 0.2 - - + -
672C VAL* 1.3 74.6 - - - +
674C ASP* 1.3 63.1 + - - +
675C THR 3.5 2.6 + - - +
678C HIS* 4.0 24.9 - - + +
679C THR* 3.9 17.9 + - - +
682C ALA* 5.5 3.4 - - + -
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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