Contacts of the strand formed by residues 566 - 571 (chain C) in PDB entry 3VI4
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 ALA 566 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458C LEU* 5.4 0.2 - - - -
504C GLU 4.1 0.5 - - - +
505C LEU* 3.5 5.2 - - - +
506C GLN* 2.9 54.9 + - + +
564C HIS* 6.2 1.1 - - + -
565C ILE* 1.3 80.6 - - - +
567C LEU* 1.3 60.4 + - - +
568C ASN* 4.3 1.1 - - - +
593C ARG* 4.8 14.8 - - - +
594C ILE 4.2 0.4 - - - -
595C GLU* 4.2 17.7 - - + +
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Residues in contact with LEU 567 (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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456C ALA* 4.2 22.4 - - + -
457C SER 4.5 1.1 - - - +
458C LEU* 3.8 30.9 - - + +
486C PHE* 3.5 37.0 - - + -
488C LEU* 5.1 4.9 - - + -
503C VAL* 4.4 12.1 - - + -
504C GLU 3.7 9.4 - - - +
505C LEU* 4.2 9.6 - - + -
566C ALA* 1.3 76.1 - - - +
568C ASN* 1.3 73.1 + - - +
569C PHE* 4.7 1.8 - - + +
592C SER 6.4 0.2 - - - -
593C ARG* 3.2 7.8 - - - +
594C ILE* 3.1 41.4 + - + +
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Residues in contact with ASN 568 (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 VAL* 3.9 6.8 - - - +
504C GLU* 3.2 35.4 + - - +
506C GLN* 4.4 2.8 - - - +
566C ALA 5.3 1.1 - - - +
567C LEU* 1.3 81.6 - - - +
569C PHE* 1.3 64.6 + - - +
592C SER* 3.2 10.8 - - - +
593C ARG* 3.0 30.2 - - - +
2016C NAG 1.4 70.6 + - - +
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Residues in contact with PHE 569 (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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454C ALA* 3.6 16.6 - - + -
455C SER* 3.5 28.3 - - - -
456C ALA* 3.4 33.7 - - + -
488C LEU* 3.6 33.4 - - + -
489C ASN 5.1 0.2 - - - -
501C PHE* 3.6 32.3 - + - -
502C THR 4.3 1.1 - - - -
503C VAL* 5.2 4.3 - - + -
567C LEU* 4.7 1.7 - - + +
568C ASN* 1.3 75.4 + - - +
570C SER* 1.3 60.7 + - - +
586C LEU* 4.4 9.4 - - + -
591C LYS 4.0 6.7 - - - -
592C SER* 2.7 49.0 + - - +
2016C NAG 3.0 13.2 - - - +
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Residues in contact with SER 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C PHE* 3.5 5.5 - - - -
502C THR* 2.6 54.7 + - - +
569C PHE* 1.3 72.9 - - - +
571C LEU* 1.3 64.3 + - - +
573C PRO* 4.9 4.3 - - - +
586C LEU* 4.8 5.2 - - - -
2016C NAG 2.8 26.2 - - - -
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Residues in contact with LEU 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C ARG* 5.2 0.7 - - - +
452C VAL* 4.3 17.0 - - + -
499C ILE* 3.9 21.3 - - + -
500C GLY 4.0 6.7 - - - +
501C PHE* 4.2 10.8 - - + -
570C SER* 1.3 74.4 + - - +
572C ASP* 1.3 75.6 + - - +
573C PRO* 3.0 13.7 - - + +
583C ARG* 4.7 4.9 - - + -
584C PRO* 3.0 57.9 - - + +
585C ALA* 4.4 2.9 - - - +
586C LEU* 3.6 27.9 - - + +
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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