Contacts of the strand formed by residues 969 - 974 (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 THR 969 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896C CYS* 6.1 0.4 - - - -
897C ILE* 3.6 36.9 - - + +
943C GLU* 3.7 2.8 - - - +
944C ILE* 2.9 60.2 + - + +
966C THR 4.9 3.3 + - - -
967C SER 4.1 5.8 + - - -
968C ARG* 1.3 73.4 + - - +
970C PHE* 1.3 68.9 + - - +
971C ARG 4.8 0.7 - - - +
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Residues in contact with PHE 970 (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* 4.2 20.0 - + + -
895C LYS 5.1 1.5 + - - +
896C CYS* 3.1 10.4 - - + +
897C ILE* 2.9 25.8 + - - +
941C LEU* 3.9 24.0 - - + -
942C LEU 3.4 11.2 - - - -
943C GLU* 3.9 21.1 - - + -
953C HIS* 3.9 15.7 - + - -
962C LEU* 3.9 38.6 - - + -
963C SER 3.9 8.7 - - - -
964C PRO* 3.6 44.0 - - + -
968C ARG* 4.7 7.6 - - + -
969C THR* 1.3 74.2 - - - +
971C ARG* 1.3 59.9 + - - +
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Residues in contact with ARG 971 (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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897C ILE* 3.4 28.7 - - + +
899C LEU* 3.9 24.0 - - + +
905C GLU* 4.6 7.5 + - - -
940C ARG 3.7 0.2 - - - +
941C LEU* 3.3 6.4 - - - +
942C LEU* 2.8 40.6 + - + +
944C ILE* 3.5 37.4 - - + +
949C ILE* 4.0 14.8 - - - +
969C THR* 3.8 1.5 + - + -
970C PHE* 1.3 73.9 - - - +
972C ILE* 1.3 69.7 + - - +
973C GLU* 2.6 34.3 + - - +
1005C ILE* 3.4 14.6 - - - +
1006C PRO* 2.8 31.9 + - - +
1007C PHE* 4.0 6.7 - - - +
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Residues in contact with ILE 972 (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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896C CYS* 4.0 26.2 - - - -
897C ILE 2.8 10.5 + - - +
898C TRP* 3.2 9.1 - - + -
899C LEU* 3.0 26.3 + - - +
910C LEU* 4.1 4.7 - - + -
921C LEU* 4.1 14.1 - - + +
922C LEU* 3.7 28.5 - - + -
925C CYS* 3.6 44.9 - - + -
939C LEU* 4.4 9.0 - - + -
940C ARG 3.3 3.1 - - - +
941C LEU* 3.8 13.2 - - + -
971C ARG* 1.3 78.6 - - - +
973C GLU* 1.3 64.9 + - - +
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Residues in contact with GLU 973 (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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898C TRP* 4.1 4.9 - - - -
899C LEU* 3.4 24.2 - - + +
939C LEU* 3.4 6.2 - - - -
940C ARG* 2.9 67.8 + - + +
942C LEU* 3.3 24.9 - - + +
971C ARG* 2.6 41.8 + - - +
972C ILE* 1.3 77.7 - - - +
974C GLU* 1.3 68.0 + - - +
975C ILE 3.5 0.7 + - - -
1008C LEU* 4.8 3.1 + - - +
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Residues in contact with GLU 974 (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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898C TRP* 4.2 7.7 - - + -
899C LEU 4.6 2.2 + - - +
901C SER* 5.0 2.3 + - - -
931C LEU* 3.3 29.1 - - + +
932C GLY* 3.1 21.8 + - - +
935C ALA* 3.2 22.2 + - + +
936C SER* 3.7 11.2 - - - +
937C GLY* 3.1 22.8 + - - +
938C LYS 3.5 7.6 - - - +
939C LEU* 3.6 15.7 - - + +
973C GLU* 1.3 78.4 - - - +
975C ILE* 1.3 69.4 + - - +
976C PRO* 3.4 8.5 - - - +
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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