Contacts of the strand formed by residues 939 - 945 (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 LEU 939 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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898C TRP* 3.8 19.5 - - + -
922C LEU* 3.4 46.5 - - + +
925C CYS* 4.4 4.0 - - + -
926C LYS* 3.6 34.7 - - + +
931C LEU* 4.1 10.1 - - + -
937C GLY 4.3 1.5 + - - +
938C LYS* 1.3 77.3 - - - +
940C ARG* 1.3 63.5 + - - +
955C GLU* 5.3 3.3 - - - +
972C ILE* 4.4 13.9 - - + -
973C GLU 3.4 4.9 - - - +
974C GLU* 3.6 33.2 - - + +
975C ILE* 4.1 6.7 - - - +
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Residues in contact with ARG 940 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922C LEU* 3.8 9.6 - - - -
939C LEU* 1.3 77.4 - - - +
941C LEU* 1.3 59.9 + - - +
942C LEU* 3.7 14.4 + - + +
952C VAL* 4.9 15.0 - - + +
953C HIS 5.9 0.4 - - - +
971C ARG 3.7 0.5 - - - +
972C ILE* 3.3 6.6 - - - +
973C GLU* 2.9 66.9 + - + +
975C ILE* 3.8 29.7 - - + +
976C PRO* 4.2 14.0 - - - +
979C GLN* 3.1 30.6 + - - +
989C LEU* 4.1 11.5 - - - +
1008C LEU* 3.4 34.4 + - - +
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Residues in contact with LEU 941 (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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894C PHE* 5.4 0.2 - - + -
918C VAL* 3.7 38.4 - - + -
921C LEU* 4.1 20.4 - - + -
922C LEU* 4.0 11.1 - - + +
940C ARG* 1.3 75.0 - - - +
942C LEU* 1.3 64.9 + - - +
952C VAL* 3.6 3.9 - - - +
953C HIS* 3.0 43.3 + - + +
962C LEU* 4.2 12.6 - - + -
970C PHE* 3.9 31.2 - - + -
971C ARG 3.3 15.7 - - - +
972C ILE* 3.8 16.4 - - + -
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Residues in contact with LEU 942 (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* 3.7 24.7 - - + +
941C LEU* 1.3 77.2 - - - +
943C GLU* 1.3 58.8 + - - +
944C ILE* 4.2 9.0 - - + -
949C ILE* 3.6 31.6 - - + -
951C GLY 3.4 1.1 - - - +
952C VAL* 3.5 28.5 - - + -
953C HIS* 4.8 0.7 - - - -
970C PHE* 3.4 8.3 - - - -
971C ARG* 2.8 44.5 + - + +
973C GLU* 3.3 38.1 - - + +
1008C LEU* 3.7 12.3 - - + -
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Residues in contact with GLU 943 (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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941C LEU 4.3 0.2 + - - -
942C LEU* 1.3 73.9 - - - +
944C ILE* 1.3 59.6 + - - +
945C VAL* 5.0 1.3 - - + -
949C ILE* 3.5 2.3 - - - -
950C ILE* 2.7 50.7 + - + +
951C GLY* 2.8 16.9 + - - +
953C HIS* 2.6 44.9 + - + +
962C LEU* 5.2 0.2 - - - +
968C ARG* 3.1 38.9 + - + +
969C THR 3.7 4.0 - - - +
970C PHE* 3.9 23.0 - - + -
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Residues in contact with ILE 944 (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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905C GLU* 5.4 3.4 - - - +
942C LEU* 4.5 3.8 - - + -
943C GLU* 1.3 80.4 - - - +
945C VAL* 1.3 63.8 + - - +
947C TYR* 3.9 8.1 - - - +
948C LYS 3.2 31.0 - - - +
949C ILE* 4.1 11.9 - - + -
967C SER 3.4 2.4 - - - +
969C THR* 2.9 53.0 + - + +
971C ARG* 3.5 52.3 - - + +
1006C PRO* 3.8 13.0 - - + -
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Residues in contact with VAL 945 (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* 4.8 1.1 - - + +
944C ILE* 1.3 80.1 - - - +
946C SER* 1.3 83.2 - - - +
947C TYR 3.2 1.6 - - - -
948C LYS* 2.8 29.0 + - - +
950C ILE* 3.7 34.9 - - + +
967C SER* 3.7 29.8 - - - +
968C ARG* 4.0 26.5 - - + +
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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