Contacts of the strand formed by residues 774 - 780 (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 VAL 774 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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739A THR* 4.3 19.5 - - + +
740A LEU 4.7 10.3 - - - +
741A LEU* 4.1 18.6 - - + -
762A MET* 3.5 6.4 - - - +
763A TYR* 2.8 55.2 + - + +
764A SER* 5.6 2.0 - - - -
765A ASN* 5.0 8.3 - - - +
773A SER* 1.3 84.0 + - - +
775A GLY* 1.3 55.1 + - - +
826A GLU* 6.1 0.9 - - - +
827A VAL 6.1 0.2 - - - -
829A LEU* 4.8 3.4 - - - -
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Residues in contact with GLY 775 (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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761A ILE 3.2 11.7 - - - -
762A MET* 3.6 17.9 - - - +
763A TYR* 4.7 0.9 - - - -
774A VAL* 1.3 75.0 - - - +
776A ILE* 1.3 69.5 + - - +
826A GLU* 4.2 5.0 - - - +
827A VAL* 3.2 34.2 + - - +
829A LEU* 5.4 0.6 - - - +
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Residues in contact with ILE 776 (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* 5.2 6.3 - - + -
733A SER* 4.7 4.3 - - - +
734A PRO* 5.7 0.2 - - + -
735A LEU* 4.4 17.5 - - + -
741A LEU* 3.9 32.1 - - + -
759A LEU 3.5 1.4 - - - +
760A TRP* 4.0 0.2 - - - -
761A ILE* 2.8 53.0 + - + +
763A TYR* 4.2 12.3 - - + +
775A GLY* 1.3 76.6 - - - +
777A ILE* 1.3 65.1 + - - +
778A PHE 5.3 0.2 - - - +
824A LEU* 4.5 24.5 - - + -
825A ILE 3.9 5.4 - - - +
826A GLU* 5.1 0.2 - - - +
827A VAL* 3.8 2.1 - - - +
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Residues in contact with ILE 777 (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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752A MET* 5.0 4.9 - - - -
758A PRO* 3.7 26.9 - - + +
759A LEU 3.3 8.3 - - - +
760A TRP* 3.9 22.4 - - + -
776A ILE* 1.3 73.2 - - - +
778A PHE* 1.3 62.5 + - - +
779A LYS 3.6 1.8 + - - +
824A LEU* 3.2 10.6 - - - -
825A ILE* 2.8 42.5 + - + +
826A GLU 4.2 0.2 - - - +
827A VAL* 3.6 19.7 - - + -
4001A 9EM 3.3 66.9 - - + +
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Residues in contact with PHE 778 (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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689A LEU* 3.8 25.8 - - + -
692A LEU* 3.7 39.3 - - + -
693A LYS* 3.7 33.2 - - + -
696A ASN* 4.0 11.8 - - + +
757A LYS 4.8 0.2 - - - +
758A PRO* 3.4 3.6 - - - +
759A LEU* 2.9 44.9 + - + +
761A ILE* 5.1 2.2 - - + -
776A ILE* 4.1 1.4 + - + -
777A ILE* 1.3 69.7 - - - +
779A LYS* 1.3 58.3 + - - +
780A ASN* 3.7 22.1 + - + -
822A THR* 3.3 32.8 - - + -
823A GLY 3.8 3.6 - - - -
824A LEU* 3.8 15.3 - - + -
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Residues in contact with LYS 779 (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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754A SER* 5.2 6.7 + - - +
756A MET* 4.5 8.7 - - + -
758A PRO* 3.9 21.5 - - + +
777A ILE* 3.6 1.4 + - + -
778A PHE* 1.3 73.4 - - - +
780A ASN* 1.3 65.0 + - - +
782A ASP* 3.4 33.4 + - + +
784A LEU* 4.4 19.2 - - + +
821A ARG 4.0 0.6 - - - +
822A THR* 3.4 3.6 - - - +
823A GLY 3.0 34.1 + - - +
825A ILE* 3.9 19.5 - - + -
911A ASP* 3.4 18.0 + - - -
4001A 9EM 3.0 41.5 - - - -
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Residues in contact with ASN 780 (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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693A LYS* 3.4 33.9 - - - +
696A ASN* 3.0 28.3 + - - +
697A ASP* 3.6 3.8 - - - +
700A LYS* 3.7 14.5 + - - -
756A MET* 3.3 26.1 + - - +
758A PRO* 5.6 0.2 - - - +
778A PHE* 3.7 16.2 + - + -
779A LYS* 1.3 74.8 - - - +
781A GLY* 1.3 62.4 + - - +
782A ASP 3.8 2.0 - - - -
820A ASP 4.0 4.8 + - - -
821A ARG* 3.3 6.8 + - - +
822A THR* 3.2 20.5 + - - +
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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