Contacts of the strand formed by residues 929 - 933 (chain A) in PDB entry 4B87
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 929 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874A VAL* 3.1 13.2 - - + +
876A CYS* 4.8 4.9 - - - -
887A PHE* 4.4 18.8 - - + +
890A ILE* 3.8 17.0 - - + -
891A ALA* 3.7 32.8 - - + -
894A LEU* 3.8 20.4 - - + -
896A SER* 4.1 3.4 + - - +
897A LYS 4.3 2.9 + - - +
898A VAL* 3.5 11.1 - - + -
899A GLY 2.9 24.6 + - - -
927A SER* 3.7 0.3 + - - -
928A LEU* 1.3 84.4 - - + +
930A HIS* 1.3 70.7 + - - +
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Residues in contact with HIS 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A LEU* 3.6 21.8 - - + +
874A VAL 2.8 7.3 + - - -
875A VAL* 3.3 13.1 - - + +
876A CYS* 2.9 26.2 + - - +
898A VAL* 4.7 0.2 - - - -
899A GLY* 3.4 3.4 - - - -
924A MET* 2.9 52.2 + - + +
927A SER* 3.3 26.6 + - - -
929A VAL* 1.3 79.9 - - - +
931A LEU* 1.3 62.5 + - - +
932A LEU* 4.0 2.0 - - + -
945A HIS* 2.8 36.3 + + + +
949A CYS* 4.7 5.2 - - + -
953A TYR* 3.9 13.2 - + - -
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Residues in contact with LEU 931 (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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876A CYS* 3.3 24.5 - - + +
877A GLY 4.3 0.9 - - - +
878A THR* 3.8 20.2 - - + -
887A PHE* 3.6 46.4 - - + -
898A VAL* 3.9 7.8 - - + +
899A GLY 2.9 17.5 + - - +
900A MET* 3.8 34.1 - - + +
901A SER 5.0 1.6 + - - -
904A LYS* 4.0 24.5 - - + -
908A LEU* 5.0 0.2 - - + -
924A MET* 4.7 1.7 - - - +
930A HIS* 1.3 73.4 - - - +
932A LEU* 1.3 65.4 + - - +
933A PRO* 4.8 0.5 - - - +
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Residues in contact with LEU 932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A VAL* 3.7 21.8 - - + -
876A CYS 2.8 10.9 + - - -
877A GLY* 3.1 2.9 - - - -
878A THR* 2.8 29.8 + - - +
924A MET* 4.6 8.7 - - + -
930A HIS* 4.7 2.5 - - + -
931A LEU* 1.3 79.0 - - - +
933A PRO* 1.4 74.8 - - + +
936A GLN* 3.8 23.6 - - + +
937A ILE* 4.1 9.2 - - + -
942A LEU* 4.1 11.0 - - + -
945A HIS* 3.7 52.5 - - + +
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Residues in contact with PRO 933 (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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878A THR* 3.4 9.8 - - + +
931A LEU 4.8 0.4 - - - +
932A LEU* 1.4 93.2 - - + +
934A MET* 1.3 66.3 + - - +
935A MET* 3.0 3.1 - - + +
936A GLN* 2.8 37.0 + - + +
937A ILE* 3.9 3.6 - - - +
2044A EDO 3.3 25.4 - - - +
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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