Contacts of the strand formed by residues 948 - 953 (chain C) in PDB entry 4YOC
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 LYS 948 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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944C ILE* 3.2 5.5 - - - +
945C VAL 2.8 40.9 + - - +
946C SER* 3.4 20.2 - - - +
947C TYR* 1.3 82.2 - - - +
949C ILE* 1.3 65.6 + - - +
950C ILE* 3.2 8.2 + - + +
993C ALA* 4.3 11.9 - - + -
999C VAL 5.4 1.7 + - - +
1002C THR* 4.2 13.9 - - + -
1006C PRO* 4.3 1.6 - - - -
1076C TRP* 3.8 39.2 - - + +
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Residues in contact with ILE 949 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942C LEU* 3.6 35.0 - - + -
943C GLU 3.6 5.4 - - - +
944C ILE* 4.1 10.5 - - + +
948C LYS* 1.3 73.6 - - - +
950C ILE* 1.3 60.0 + - - +
951C GLY* 3.6 15.9 - - - +
952C VAL* 5.2 0.9 - - + -
971C ARG* 4.0 12.1 - - - +
991C THR* 3.6 28.6 + - - +
993C ALA* 5.5 0.4 - - - +
1006C PRO* 3.8 19.4 - - + +
1007C PHE* 3.9 36.3 - - - +
1008C LEU* 4.1 11.4 - - + -
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Residues in contact with ILE 950 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943C GLU* 2.7 41.3 + - + +
945C VAL* 3.7 27.6 - - + +
948C LYS* 3.7 19.5 - - + +
949C ILE* 1.3 74.2 - - - +
951C GLY* 1.3 55.7 + - - +
968C ARG* 3.4 29.4 - - - +
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Residues in contact with GLY 951 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942C LEU* 3.4 8.7 - - - +
943C GLU* 2.8 37.4 + - - +
949C ILE* 3.4 6.8 - - - +
950C ILE* 1.3 82.4 - - - +
952C VAL* 1.3 64.3 + - - -
953C HIS* 4.2 3.1 - - - -
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Residues in contact with VAL 952 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940C ARG* 4.9 18.4 - - + +
941C LEU 3.6 12.6 - - - +
942C LEU* 3.5 22.9 - - + -
949C ILE* 5.2 1.8 - - + -
951C GLY* 1.3 72.6 - - - -
953C HIS* 1.3 73.8 + - - +
954C GLN 3.8 1.7 + - - -
957C GLU* 4.4 2.6 - - - +
1008C LEU* 3.9 16.6 - - + -
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Residues in contact with HIS 953 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918C VAL* 4.2 13.4 - - + +
922C LEU* 5.8 0.7 - - - +
940C ARG* 5.9 0.3 - - - +
941C LEU* 3.0 41.3 + - + +
943C GLU* 2.6 46.4 + - + +
951C GLY* 4.5 2.8 - - - -
952C VAL* 1.3 83.4 - - - +
954C GLN* 1.3 63.3 + - - +
955C GLU* 3.6 1.7 + - - -
957C GLU* 2.8 27.2 + - - +
962C LEU* 3.4 27.6 - - + +
970C PHE* 3.9 9.6 - + - -
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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