Contacts of the strand formed by residues 748 - 753 (chain A) in PDB entry 1VDV
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 CYS 748 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A CYS* 3.6 31.8 - - + -
594A ASP* 3.9 17.5 - - - -
745A GLU* 4.7 3.4 - - - +
746A THR 3.5 5.3 + - - +
747A HIS* 1.3 77.9 - - - +
749A THR* 1.3 72.5 + - - +
750A ILE* 5.2 2.5 - - - -
764A VAL* 3.6 2.1 - - - +
765A SER* 3.1 34.5 + - - -
808A VAL* 4.7 2.6 - - - +
824A ARG* 5.7 2.0 - - - -
825A CYS 3.3 9.9 - - - -
826A MET* 3.7 27.1 - - + -
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Residues in contact with THR 749 (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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593A CYS* 4.3 0.7 - - - -
748A CYS* 1.3 79.9 + - - +
750A ILE* 1.3 78.4 + - - +
762A LEU* 4.1 9.4 - - + -
763A PHE 3.4 4.5 - - - -
764A VAL* 3.3 15.3 - - + +
805A SER 4.7 0.5 + - - -
808A VAL* 4.1 9.9 - - - +
809A SER* 2.6 44.8 + - - -
812A VAL* 3.9 14.5 - - + +
824A ARG* 3.2 4.3 - - - +
825A CYS 3.0 31.8 + - - -
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Residues in contact with ILE 750 (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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593A CYS* 3.4 33.9 - - - +
596A ILE* 3.8 18.8 - - + -
602A GLU* 3.7 16.6 - - - +
748A CYS* 5.2 1.8 - - - -
749A THR* 1.3 77.4 - - - +
751A ALA* 1.3 62.6 + - - +
752A ILE* 3.8 22.9 - - + -
761A GLU 4.0 0.3 - - - +
762A LEU* 3.1 6.8 - - - +
763A PHE* 2.8 44.4 + - + +
823A VAL 3.4 5.8 - - - +
824A ARG* 3.2 40.6 - - + +
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Residues in contact with ALA 751 (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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750A ILE* 1.3 73.0 - - - +
752A ILE* 1.3 64.1 + - - +
753A PRO* 3.4 3.6 - - - +
760A MET* 4.1 2.9 - - - -
761A GLU 3.9 2.5 - - - -
762A LEU* 3.9 22.0 - - + -
812A VAL* 3.6 24.1 - - + +
813A ALA* 4.0 4.7 - - - -
816A ALA* 3.7 16.8 - - + +
822A PRO* 3.3 4.7 - - - +
823A VAL 2.8 31.3 + - - -
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Residues in contact with ILE 752 (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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599A TYR* 3.5 31.6 - - + +
602A GLU* 4.5 0.2 - - - +
750A ILE* 3.8 16.6 - - + -
751A ALA* 1.3 75.2 - - - +
753A PRO* 1.3 70.5 - - + +
754A LYS* 3.6 23.6 + - + -
760A MET* 3.4 4.9 - - - +
761A GLU* 2.8 44.5 + - + +
763A PHE* 4.0 20.6 - - + -
822A PRO* 3.4 27.8 - - + -
597B PRO* 6.1 5.6 - - + -
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Residues in contact with PRO 753 (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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751A ALA 3.4 5.8 - - - +
752A ILE* 1.3 90.0 - - + +
754A LYS* 1.3 63.5 + - - +
755A GLY* 3.5 3.4 - - - +
759A GLU 3.9 6.3 - - - +
760A MET* 4.2 10.5 - - + -
816A ALA* 3.5 29.2 - - + +
817A TYR* 4.9 2.0 - - - -
820A GLY* 3.6 20.7 - - - +
821A HIS 3.4 28.0 - - - +
822A PRO* 3.7 7.7 - - + +
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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