Contacts of the strand formed by residues 759 - 764 (chain A) in PDB entry 5VLR
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 LEU 759 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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692A LEU* 3.7 17.0 - - + +
695A LEU* 3.8 20.9 - - + -
696A ASN* 3.6 46.9 - - + +
699A VAL* 4.1 18.6 - - + -
715A MET* 4.3 5.8 - - - -
750A THR 3.8 2.2 - - - +
751A PHE* 4.0 17.7 - - + +
757A LYS 4.0 6.5 - - - +
758A PRO* 1.4 70.0 - - - +
760A TRP* 1.3 59.2 + - - +
761A ILE* 3.7 14.9 + - + +
776A ILE 3.5 2.1 - - - +
777A ILE* 3.3 8.7 - - - -
778A PHE* 2.9 43.5 + - + +
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Residues in contact with TRP 760 (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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748A GLN 3.7 12.5 + - - -
749A CYS* 3.2 6.2 - - - -
750A THR* 2.8 62.0 + - - +
751A PHE* 4.2 3.8 - - - +
752A MET* 4.2 13.2 - - + -
758A PRO 3.7 1.7 + - - +
759A LEU* 1.3 70.9 - - - +
761A ILE* 1.3 60.6 + - - +
762A MET* 3.5 24.3 - - + +
776A ILE 4.0 2.5 - - - -
777A ILE* 3.9 23.8 - - + +
827A VAL* 3.7 24.7 - - + -
828A VAL 5.4 0.2 - - - -
829A LEU* 5.7 2.0 - - + -
4001A 9EM 3.4 91.1 - + + +
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Residues in contact with ILE 761 (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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692A LEU* 3.8 30.1 - - + -
695A LEU* 4.7 3.4 - - + -
715A MET* 4.9 2.5 - - + -
719A MET* 4.6 10.3 - - + -
728A LEU* 5.7 2.9 - - + -
744A VAL* 3.9 17.3 - - + -
749A CYS* 3.8 11.0 - - + -
750A THR 4.6 2.0 - - - +
759A LEU* 3.7 30.1 - - + +
760A TRP* 1.3 83.0 - - - +
762A MET* 1.4 61.9 + - - +
763A TYR* 3.7 30.2 - - + +
775A GLY* 3.2 2.4 - - - -
776A ILE* 2.8 52.0 + - + +
778A PHE* 5.1 2.0 - - + -
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Residues in contact with MET 762 (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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744A VAL* 3.4 11.4 - - - +
745A CYS* 2.8 28.9 + - + +
748A GLN* 3.7 41.1 - - + +
749A CYS* 3.4 7.1 - - - -
760A TRP* 3.5 36.6 - - + +
761A ILE* 1.4 70.1 - - - +
763A TYR* 1.4 59.0 + - - +
773A SER* 3.3 26.2 - - - +
774A VAL 3.5 20.2 - - - +
775A GLY* 3.6 14.1 - - - +
827A VAL* 4.5 6.1 - - - -
829A LEU* 3.7 18.8 - - + -
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Residues in contact with TYR 763 (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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688A ALA* 5.7 0.9 - - - +
692A LEU* 5.7 2.4 - - - +
728A LEU* 3.1 35.6 + - - +
731A LEU* 4.1 7.0 - - + +
741A LEU* 3.6 54.7 - - + +
742A ALA 3.9 8.5 - - - +
743A GLU 3.3 5.6 - - - +
744A VAL* 3.7 21.4 - - + +
745A CYS* 3.9 5.9 - - - -
748A GLN* 5.5 0.5 - - - +
761A ILE* 3.7 36.0 - - + +
762A MET* 1.4 74.9 - - - +
764A SER* 1.3 60.9 + - - +
773A SER* 3.5 9.5 + - - -
774A VAL* 2.8 52.3 + - + +
775A GLY* 4.7 0.9 - - - -
776A ILE* 4.2 9.5 - - + +
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Residues in contact with SER 764 (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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742A ALA* 3.5 23.9 + - - +
743A GLU* 3.0 27.0 + - - +
745A CYS* 3.4 17.6 - - - -
763A TYR* 1.3 74.7 - - - +
765A ASN* 1.4 66.5 + - - +
766A GLU* 3.9 0.5 + - - +
773A SER* 5.1 2.0 - - - +
774A VAL* 5.7 2.0 - - - -
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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