Contacts of the strand formed by residues 876 - 879 (chain C) in PDB entry 4X52
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 876 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808C GLU* 5.4 0.7 - - - +
814C TYR* 3.8 18.4 - - + -
819C TYR* 3.7 31.9 - - + -
820C PHE 3.4 19.7 - - - +
821C ALA* 4.4 0.7 - - + +
826C TYR* 3.9 29.6 - - + +
868C VAL* 3.4 27.0 - - - +
869C ASP* 3.3 25.9 + - + +
874C PRO* 3.5 0.9 - - - +
875C SER* 1.3 79.5 - - - +
877C PHE* 1.3 66.0 + - - +
878C VAL* 4.4 1.6 - - + -
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Residues in contact with PHE 877 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783C LYS* 4.4 15.0 - - + -
785C LEU* 3.6 40.8 - - + -
818C ILE 3.2 4.3 - - - +
819C TYR* 3.4 2.4 - - - -
820C PHE* 2.8 38.3 + - + +
822C LYS* 4.6 16.2 - - + -
847C VAL* 3.7 24.9 - - + -
850C PHE* 4.0 19.1 - + - -
866C SER* 4.3 5.4 - - - +
867C CYS 3.4 3.8 - - - +
868C VAL* 3.4 25.1 - - + -
874C PRO* 3.5 29.2 - - + -
876C VAL* 1.3 77.2 - - - +
878C VAL* 1.3 63.0 + - - +
879C ILE* 4.1 7.1 + - + -
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Residues in contact with VAL 878 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814C TYR* 3.7 20.9 - - + +
815C GLY 3.8 8.7 - - - +
817C GLY* 3.7 24.9 - - - +
818C ILE 3.3 2.2 - - - -
819C TYR* 3.6 33.9 - - + -
866C SER* 3.4 9.0 - - - -
867C CYS* 2.7 43.2 + - + +
868C VAL* 4.9 1.6 - - - +
876C VAL* 5.2 1.6 - - + -
877C PHE* 1.3 75.9 - - - +
879C ILE* 1.3 63.1 + - - +
880C PHE* 3.5 26.4 - - + -
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Residues in contact with ILE 879 (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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804C SER* 5.4 0.2 - - - -
817C GLY* 3.3 2.2 - - - -
818C ILE* 2.8 43.7 + - + +
820C PHE* 3.9 18.8 - - + -
845C VAL* 3.5 33.4 - - + -
846C LEU 4.0 13.0 - - - +
847C VAL* 4.5 2.5 - - + -
865C ASP 4.4 1.1 - - - +
866C SER* 3.7 26.5 - - - -
877C PHE* 4.8 3.4 - - + +
878C VAL* 1.3 74.0 - - - +
880C PHE* 1.3 63.3 + - - +
881C GLN 3.1 28.2 + - - +
884C GLN* 3.8 13.7 - - + +
885C VAL* 3.6 15.5 - - + -
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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
------------------------------------------------------------
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