Contacts of the strand formed by residues 571 - 580 (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 THR 571 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641A LEU* 4.4 20.0 - - + +
539C ALA* 3.5 4.9 - - - -
540C VAL* 2.8 43.1 + - + +
569C GLU 4.4 0.2 + - - -
570C THR* 1.3 77.5 - - - +
572C TYR* 1.3 61.8 + - - +
592C GLU* 3.6 19.7 - - + +
593C PHE 3.4 11.4 - - - +
594C LYS* 4.0 17.7 - - - +
622D ILE* 4.1 14.6 - - + +
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Residues in contact with TYR 572 (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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537C TRP* 4.2 7.2 - + + -
538C ARG* 3.4 9.2 - - - -
539C ALA* 3.2 30.3 - - + -
540C VAL* 4.0 3.4 - - - -
566C LEU* 3.5 26.5 - - + -
567C LYS* 2.9 33.5 + - - +
570C THR* 3.5 35.3 - - + +
571C THR* 1.3 73.0 - - - +
573C ALA* 1.3 61.9 + - - +
592C GLU* 3.4 8.1 - - - +
593C PHE* 2.8 55.7 + + + +
595C THR* 4.0 10.5 - - + -
1696C SO4 2.9 34.4 + - - -
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Residues in contact with ALA 573 (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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537C TRP* 3.0 25.6 - - - +
538C ARG* 3.0 19.9 + - + +
540C VAL* 4.5 10.3 - - + -
545C TRP* 3.9 14.3 - - + -
572C TYR* 1.3 76.0 - - - +
574C VAL* 1.3 60.3 + - - +
590C ALA* 4.4 17.0 - - + -
591C SER 3.4 8.1 - - - +
592C GLU* 5.0 4.5 - - + -
593C PHE* 4.7 0.2 - - - -
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Residues in contact with VAL 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C ILE* 3.8 16.9 - - + +
508C VAL* 4.5 10.5 - - + -
517C VAL* 4.7 15.0 - - + -
535C ALA* 5.2 0.2 - - + -
536C GLU 3.1 18.6 - - - +
537C TRP* 3.9 12.6 - - + -
545C TRP* 5.0 0.2 - - - -
563C ILE* 4.4 14.8 - - + -
573C ALA* 1.3 74.6 - - - +
575C ARG* 1.3 68.6 + - - +
576C LEU* 4.7 9.2 - - + -
590C ALA* 3.4 1.8 - - - -
591C SER* 2.8 46.3 + - - +
593C PHE* 4.2 15.9 - - + -
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Residues in contact with ARG 575 (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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505C ILE* 4.1 2.7 - - - -
534C LYS 3.9 0.3 - - - +
535C ALA* 3.7 0.2 - - - -
536C GLU* 2.7 66.7 + - + +
545C TRP* 3.3 52.5 - - + +
574C VAL* 1.3 77.7 - - - +
576C LEU* 1.3 65.5 + - - +
587C ILE* 3.9 34.0 - - + +
588C SER* 3.8 24.0 - - - +
589C ALA 4.2 2.7 - - - +
590C ALA* 4.3 7.4 - - - +
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Residues in contact with LEU 576 (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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503C PRO* 3.4 18.1 - - + +
505C ILE* 4.2 16.6 - - + -
517C VAL* 4.4 8.5 - - + -
519C PHE* 3.3 50.5 - - + -
533C TYR* 5.4 6.7 - - + -
534C LYS 3.3 4.7 - - - +
535C ALA* 3.3 35.9 - - + +
550C TYR* 5.9 0.4 - - + -
561C VAL* 4.8 9.2 - - + -
574C VAL* 4.7 7.4 - - + -
575C ARG* 1.3 76.5 - - - +
577C ALA* 1.3 61.5 + - - +
587C ILE* 3.1 5.2 - - - -
588C SER* 2.9 33.0 + - - +
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Residues in contact with ALA 577 (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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503C PRO* 3.9 10.3 - - - -
533C TYR* 3.4 5.2 - - - -
534C LYS* 2.8 41.6 + - + +
576C LEU* 1.3 75.4 - - - +
578C ALA* 1.3 59.4 + - - +
584C LEU* 3.7 23.1 - - + -
585C GLY 4.4 1.8 - - - +
586C GLU 4.2 4.3 - - - -
587C ILE* 3.5 27.4 - - + +
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Residues in contact with ALA 578 (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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500C PRO* 3.6 26.5 - - + +
501C SER 4.4 1.9 + - - +
503C PRO* 3.8 8.8 - - + +
522C PRO* 4.0 13.0 - - + -
530C ILE* 4.0 6.1 - - + -
532C LYS 3.9 3.4 - - - -
533C TYR* 3.8 22.9 - - + -
577C ALA* 1.3 73.7 - - - +
579C LEU* 1.3 55.8 + - - +
584C LEU* 3.5 2.3 - - - +
585C GLY* 2.7 34.4 + - - +
586C GLU 4.9 1.6 + - - -
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Residues in contact with LEU 579 (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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500C PRO* 4.2 1.8 - - - -
530C ILE* 3.5 2.8 - - - +
531C LEU* 2.8 29.9 + - + -
532C LYS* 2.9 33.6 + - + +
549C TRP* 3.6 34.5 - - + -
577C ALA 4.2 0.2 + - - -
578C ALA* 1.3 75.3 - - - +
580C ASN* 1.3 68.4 + - - +
583C GLY* 3.1 11.4 - - - -
584C LEU* 3.0 39.0 - - + +
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Residues in contact with ASN 580 (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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498C ASP 2.6 24.0 + - - +
500C PRO* 3.1 25.4 - - + +
525C THR 3.3 14.2 + - - +
526C GLY* 4.5 0.2 - - - -
528C VAL* 3.3 12.5 - - + +
529C PRO 3.3 23.3 - - - +
530C ILE* 4.4 1.1 - - - -
531C LEU* 4.3 9.7 - - - +
579C LEU* 1.3 82.2 - - - +
581C GLY* 1.3 67.7 + - - +
582C LYS* 2.7 18.6 + - - +
583C GLY* 2.9 24.7 + - - -
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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