Contacts of the strand formed by residues 500 - 505 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499C GLY* 1.3 75.3 - - - -
501C SER* 1.3 69.4 + - - +
655C THR* 5.4 10.8 - - + +
658C PHE* 3.5 40.8 - - + -
659C PHE* 4.6 12.8 - - + -
703C LEU* 4.7 13.2 - - + -
704C LEU 4.3 7.4 - - - +
705C GLU* 4.5 7.0 - - + +
726C ASN* 3.4 8.5 - - - +
727C LEU* 3.2 58.5 + - + +
728C ASP* 3.7 17.5 + - - +
730C LYS* 5.1 7.2 - - + +
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Residues in contact with SER 501 (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 ILE* 1.3 76.0 - - - +
502C ILE* 1.3 67.5 + - - +
703C LEU* 3.7 5.5 - - - +
704C LEU* 2.3 53.3 + - - +
705C GLU 2.8 14.0 + - - -
706C SER* 3.8 9.0 - - - -
709C ASN* 3.1 19.3 + - - +
722C LYS* 3.7 22.2 - - - -
723C VAL 5.3 0.4 - - - -
725C GLY 4.8 4.5 - - - -
726C ASN* 5.1 1.3 - - - -
727C LEU* 4.7 0.4 - - - -
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Residues in contact with ILE 502 (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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501C SER* 1.3 78.5 - - - +
503C MET* 1.3 64.1 + - - +
504C ILE* 4.3 8.7 - - + -
635C SER* 3.8 9.0 - - - +
636C ALA* 3.7 40.6 - - + +
639C LEU* 4.0 21.3 - - + -
701C ALA* 4.9 1.6 - - + -
702C TYR 3.9 5.4 - - - +
703C LEU* 3.6 19.1 - - + -
709C ASN* 3.4 6.6 + - - -
723C VAL* 3.0 57.1 + - + +
724C GLY* 5.3 4.3 - - - -
725C GLY 5.4 1.5 + - - +
727C LEU* 4.7 13.2 - - + -
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Residues in contact with MET 503 (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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501C SER 4.2 0.2 + - - -
502C ILE* 1.3 71.2 - - - +
504C ILE* 1.3 78.9 + - - +
690C VAL* 5.2 18.6 - - + -
693C VAL* 4.8 7.2 - - + +
701C ALA* 3.6 1.7 - - - +
702C TYR* 2.9 55.0 + - + +
704C LEU* 3.7 32.3 - - + -
709C ASN* 3.2 34.3 - - - +
712C ILE* 4.6 15.3 - - + -
720C THR* 4.3 24.2 - - + +
721C MET 3.6 5.6 - - - +
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Residues in contact with ILE 504 (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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502C ILE* 4.3 5.2 - - + -
503C MET* 1.3 80.7 - - - +
505C LYS* 1.3 74.6 + - - +
631C SER* 5.7 5.2 - - - -
632C PRO* 6.0 3.4 - - + -
633C ILE 4.1 18.2 - - - +
634C GLU* 5.0 1.1 - - + -
639C LEU* 5.7 4.7 - - + -
645C ILE* 6.0 3.4 - - + -
693C VAL* 4.1 12.3 - - - -
700C TYR 5.2 0.7 - - - +
701C ALA* 4.0 18.6 - - + +
720C THR* 3.5 8.3 - - - -
721C MET* 2.9 42.1 + - + +
723C VAL* 3.6 37.5 - - + -
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Residues in contact with LYS 505 (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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504C ILE* 1.3 97.8 - - - +
506C LYS* 1.3 64.5 + - - +
507C PRO* 4.8 0.7 - - - +
693C VAL* 4.2 17.1 - - + +
694C ARG* 5.9 2.7 - - - +
698C GLY* 4.5 24.6 - - - +
719C ASP 4.3 9.4 - - - +
720C THR* 4.5 2.5 - - + +
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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