Contacts of the strand formed by residues 500 - 505 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499D GLY* 1.3 72.4 - - - -
501D SER* 1.3 67.2 + - - +
502D ILE* 5.5 1.6 - - + -
655D THR* 5.2 14.6 - - + +
658D PHE* 3.6 39.5 - - + -
659D PHE* 4.3 13.2 - - + -
703D LEU* 5.4 6.3 - - + -
704D LEU 4.0 11.2 - - - +
705D GLU* 5.2 1.6 - - - +
725D GLY 4.1 0.9 - - - +
726D ASN* 3.4 9.4 - - - +
727D LEU* 3.4 54.3 + - + +
728D ASP* 3.5 19.5 + - - +
730D LYS* 4.6 10.8 - - + +
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Residues in contact with SER 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499D GLY 3.5 0.2 + - - -
500D ILE* 1.3 77.9 - - - +
502D ILE* 1.3 64.3 + - - +
503D MET 4.2 0.2 - - - -
703D LEU* 3.7 3.1 - - - -
704D LEU* 2.7 52.4 + - - +
705D GLU 3.0 15.9 + - - -
706D SER* 3.5 20.4 - - - -
709D ASN* 3.3 23.0 - - - +
722D LYS* 4.3 10.3 - - - +
725D GLY 5.5 1.3 - - - -
726D ASN* 4.8 0.9 - - - -
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Residues in contact with ILE 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D ILE* 5.5 0.4 - - + -
501D SER* 1.3 77.3 - - - +
503D MET* 1.3 66.0 + - - +
504D ILE* 4.7 4.9 - - + -
633D ILE* 6.0 3.1 - - + -
635D SER* 5.0 4.9 - - - -
636D ALA* 4.4 23.8 - - + +
639D LEU* 4.6 16.2 - - + -
670D MET* 6.1 0.9 - - + -
701D ALA* 5.1 4.5 - - + -
702D TYR 3.7 4.5 - - - +
703D LEU* 3.6 25.1 - - + -
709D ASN* 3.8 2.0 - - - +
722D LYS* 3.5 4.7 - - - +
723D VAL* 2.9 59.9 + - + +
724D GLY* 5.8 2.2 - - - -
725D GLY 5.3 4.0 + - - +
727D LEU* 4.2 24.0 - - + -
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Residues in contact with MET 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D SER 4.2 0.2 - - - -
502D ILE* 1.3 72.5 - - - +
504D ILE* 1.3 77.7 + - - +
690D VAL* 5.0 11.4 - - + -
693D VAL* 5.2 10.0 - - + +
701D ALA* 3.7 0.7 - - - +
702D TYR* 2.9 49.3 + - + +
704D LEU* 3.6 36.6 - - + -
709D ASN* 3.1 29.2 - - - +
712D ILE* 4.1 22.4 - - + -
720D THR* 4.0 23.8 - - + -
721D MET 3.1 11.0 - - - +
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Residues in contact with ILE 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502D ILE* 4.7 2.7 - - + -
503D MET* 1.3 81.6 - - - +
505D LYS* 1.3 73.4 + - - +
507D PRO* 5.5 0.4 - - + -
631D SER* 5.7 0.7 - - - -
632D PRO* 3.9 31.9 - - + -
633D ILE* 5.1 16.8 - - + +
645D ILE* 6.1 2.0 - - + -
693D VAL* 4.3 9.9 - - - -
700D TYR 5.4 0.7 - - - -
701D ALA* 4.0 21.5 - - + +
720D THR* 3.5 4.3 - - - -
721D MET* 2.9 42.6 + - + +
723D VAL* 3.6 40.2 - - + -
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Residues in contact with LYS 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D ILE* 1.3 88.8 - - - +
506D LYS* 1.4 80.4 + - - +
507D PRO* 3.5 7.1 - - - +
632D PRO* 5.3 2.1 - - - +
693D VAL* 4.1 24.2 - - + +
694D ARG* 5.4 10.1 + - + +
697D LYS* 5.4 1.8 - - - -
698D GLY* 4.3 27.9 - - - +
700D TYR 5.5 1.2 + - - -
719D ASP* 3.3 43.9 + - + +
720D THR* 6.1 0.2 - - - -
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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