Contacts of the strand formed by residues 668 - 677 (chain C) in PDB entry 2VKX
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 GLU 668 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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640C ALA* 3.5 6.6 - - - +
641C LEU* 2.8 39.5 + - + +
667C ALA* 1.3 74.0 - - - +
669C TYR* 1.3 61.1 + - - +
689C PHE 3.4 4.9 - - - -
690C ARG* 3.6 25.0 + - + +
540E VAL* 3.0 37.2 - - + +
541E GLY* 6.3 1.0 - - - -
592E GLU* 2.7 29.4 - - - +
607F GLU* 2.4 38.3 - - - +
622F ILE* 4.4 0.2 - - - +
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Residues in contact with TYR 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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638C TYR* 4.8 6.3 - + + -
639C ARG* 3.1 24.7 - - - +
640C ALA* 3.3 25.1 - - + -
641C LEU* 4.2 3.0 - - - +
646C LYS* 4.9 11.3 + - - -
663C LEU* 3.7 40.9 - - + +
664C ASP* 2.9 43.9 + - - -
667C ALA* 3.6 29.2 - - + -
668C GLU* 1.3 74.0 - - - +
670C GLU* 1.3 64.8 + - - +
671C VAL* 6.0 0.2 - - + -
688C VAL* 3.3 9.7 - - - +
689C PHE* 2.8 54.6 + + + +
691C THR* 4.4 1.3 - - + -
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Residues in contact with GLU 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C TYR* 3.1 5.4 - - - -
639C ARG* 2.8 69.3 + - + +
641C LEU* 3.7 17.8 - - + +
645C TRP* 4.0 4.9 - - + -
669C TYR* 1.3 78.2 - - - +
671C VAL* 1.3 63.8 + - - +
672C TYR* 3.1 43.9 + - + -
686C HIS* 5.0 1.6 - - - +
687C PHE 3.3 8.5 - - - +
688C VAL* 4.3 15.9 - - + +
1697C SO4 4.8 0.2 + - - -
594E LYS* 5.1 3.0 + - - -
605F LYS* 4.5 10.9 + - - -
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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* 4.5 6.0 - - + +
619C VAL* 4.7 15.7 - - + -
636C VAL* 4.5 8.5 - - + -
637C ARG 3.4 7.2 - - - +
638C TYR* 3.7 8.1 - - + -
658C VAL* 5.4 2.5 - - + -
660C LEU* 3.5 31.9 - - + -
670C GLU* 1.3 75.7 - - - +
672C TYR* 1.3 76.4 + - - +
673C VAL* 3.9 22.2 - - + -
686C HIS* 3.3 2.3 - - - -
687C PHE* 2.7 45.3 + - + +
689C PHE* 4.2 11.9 - - + -
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Residues in contact with TYR 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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635C LEU 3.6 1.8 - - - +
636C VAL* 3.3 5.2 - - - +
637C ARG* 2.7 50.6 + - + +
645C TRP* 3.4 31.5 - + + -
670C GLU* 3.1 40.1 + - + -
671C VAL* 1.3 94.9 - - - +
673C VAL* 1.3 64.6 + - - +
674C VAL* 5.6 1.1 - - + -
684C ALA* 4.0 15.3 - - + -
685C ALA 3.2 3.6 - - - +
686C HIS* 3.0 47.2 + + - -
594E LYS* 5.7 1.0 + - - -
605F LYS* 5.0 4.3 + - - -
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Residues in contact with VAL 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 PRO* 4.0 22.7 - - + +
606C LEU* 3.8 30.7 - - + -
619C VAL* 5.4 2.0 - - + -
621C LEU* 4.2 15.3 - - + -
634C TYR* 4.3 21.1 - - + -
635C LEU 3.5 4.5 - - - +
636C VAL* 4.3 14.6 - - + -
658C VAL* 5.4 2.5 - - + -
671C VAL* 3.9 11.9 - - + -
672C TYR* 1.3 79.9 - - - +
674C VAL* 1.3 66.5 + - - +
683C LYS 4.1 1.2 - - - +
684C ALA* 3.5 1.6 - - - -
685C ALA* 2.8 38.0 + - + +
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Residues in contact with VAL 674 (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 PRO* 5.0 0.2 - - - -
633C HIS 3.8 0.2 - - - +
634C TYR* 3.3 4.5 - - - -
635C LEU* 2.8 50.0 + - + +
637C ARG* 6.2 2.2 - - - +
672C TYR* 5.6 1.3 - - + -
673C VAL* 1.3 77.3 - - - +
675C ALA* 1.3 74.5 + - - +
676C GLU 3.8 0.3 + - - -
681C LYS* 3.8 20.9 - - + -
682C SER* 3.4 25.6 - - - +
684C ALA* 3.5 35.4 - - + +
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Residues in contact with ALA 675 (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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601C PRO* 3.4 7.4 - - + +
602C SER 3.6 18.6 - - - +
604C PRO* 4.0 14.4 - - + +
631C ILE* 4.1 13.9 - - + -
633C HIS 3.9 3.4 - - - -
634C TYR* 4.0 16.4 - - + -
674C VAL* 1.3 73.2 - - - +
676C GLU* 1.3 59.9 + - - +
681C LYS* 3.5 1.6 - - - -
682C SER* 2.9 41.1 + - - +
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Residues in contact with GLU 676 (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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601C PRO* 4.3 0.4 - - - -
631C ILE* 3.3 10.2 - - - +
632C ARG* 2.5 70.3 + - + -
633C HIS* 2.9 32.9 + - - +
635C LEU* 3.7 27.4 - - + +
674C VAL 4.8 0.2 - - - +
675C ALA* 1.3 76.4 - - - +
677C ASN* 1.3 62.6 + - - +
680C GLY 3.5 11.4 - - - +
681C LYS* 3.9 18.0 - - + +
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Residues in contact with ASN 677 (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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599C ARG 3.1 19.6 + - - -
601C PRO* 3.2 12.3 - - + +
626C ASP 2.8 26.0 + - - +
629C SER* 4.0 12.6 - - - +
630C PRO 3.0 26.0 - - - +
631C ILE* 4.3 2.7 - - + -
632C ARG* 4.0 12.1 + - - +
676C GLU* 1.3 78.3 - - - +
678C GLN* 1.3 66.5 + - - +
679C GLN* 2.8 18.3 + - - +
680C GLY* 2.9 29.4 + - - +
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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