Contacts of the strand formed by residues 500 - 505 (chain A) in PDB entry 5VOT
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 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A GLY* 1.3 73.8 - - - -
501A SER* 1.3 69.6 + - - +
655A THR* 5.4 9.6 - - + +
658A PHE* 3.6 41.5 - - + -
659A PHE* 4.6 13.7 - - + -
703A LEU* 4.7 13.5 - - + -
704A LEU* 4.3 7.6 - - - +
705A GLU* 4.5 6.7 - - + +
726A ASN* 3.4 8.7 - - - +
727A LEU* 3.2 58.7 + - + +
728A ASP* 3.8 15.5 + - - +
730A LYS* 5.1 7.4 - - + +
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Residues in contact with SER 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A ILE* 1.3 76.8 - - - +
502A ILE* 1.3 66.3 + - - +
703A LEU* 3.7 5.9 - - - +
704A LEU* 2.3 53.7 + - - +
705A GLU 2.8 13.9 + - - -
706A SER* 3.8 8.7 - - - -
709A ASN* 3.1 19.1 + - - +
722A LYS* 3.8 22.2 - - - -
723A VAL 5.3 0.7 - - - -
724A GLY 5.9 0.2 - - - -
725A GLY 4.8 3.8 - - - -
726A ASN* 5.2 1.1 - - - -
727A LEU* 4.7 0.9 - - - -
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Residues in contact with ILE 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A SER* 1.3 79.1 - - - +
503A MET* 1.3 67.2 + - - +
504A ILE* 4.3 5.4 - - + -
635A SER* 3.8 9.6 - - - +
636A ALA* 3.7 40.6 - - + +
639A LEU* 4.0 20.4 - - + -
701A ALA* 4.9 1.8 - - + -
702A TYR 3.9 4.7 - - - +
703A LEU* 3.6 19.1 - - + -
709A ASN* 3.4 6.9 + - - -
723A VAL* 3.0 57.5 + - + +
724A GLY* 5.3 4.7 - - - -
725A GLY 5.4 1.5 + - - +
727A LEU* 4.7 12.3 - - + -
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Residues in contact with MET 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A SER 4.2 0.2 + - - -
502A ILE* 1.3 72.3 - - - +
504A ILE* 1.3 79.5 + - - +
690A VAL* 5.2 18.2 - - + -
693A VAL* 4.8 6.6 - - + +
701A ALA* 3.6 1.7 - - - +
702A TYR* 2.9 54.2 + - + +
704A LEU* 3.7 32.8 - - + -
709A ASN* 3.2 33.2 - - - +
712A ILE* 4.6 16.4 - - + -
720A THR* 4.3 23.1 - - + +
721A MET 3.6 5.8 - - - +
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Residues in contact with ILE 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A ILE* 4.3 5.2 - - + -
503A MET* 1.3 80.3 - - - +
505A LYS* 1.3 73.1 + - - +
631A SER* 5.7 5.2 - - - -
632A PRO* 6.0 4.0 - - + -
633A ILE 4.2 17.5 - - - +
634A GLU* 5.1 1.1 - - + -
639A LEU* 5.8 3.8 - - + -
645A ILE* 6.0 3.8 - - + -
693A VAL* 4.1 12.3 - - - -
700A TYR 5.2 0.7 - - - +
701A ALA* 4.0 18.4 - - + +
720A THR* 3.5 9.4 - - - -
721A MET* 2.9 42.2 + - + +
723A VAL* 3.6 37.9 - - + -
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Residues in contact with LYS 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A ILE* 1.3 96.6 - - - +
506A LYS* 1.3 64.6 + - - +
507A PRO* 4.3 3.9 - - - +
693A VAL* 4.2 16.2 - - + +
694A ARG* 5.9 1.8 - - - -
698A GLY* 4.4 25.4 - - - +
719A ASP 4.3 7.2 - - - +
720A THR* 4.5 2.5 - - + +
721A MET* 4.6 0.4 - - - +
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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