Contacts of the strand formed by residues 857 - 863 (chain C) in PDB entry 4OQB
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 ARG 857 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848C TYR* 3.4 24.7 - - - +
851C PHE 3.7 11.0 - - - +
852C LYS* 3.3 39.0 + - - +
853C GLN 5.2 0.2 - - - -
854C LEU 3.3 27.3 + - - +
855C HIS* 4.1 4.4 - - - +
856C ASN* 1.3 74.0 - - - +
858C ARG* 1.3 60.4 + - - +
923C GLU* 3.2 20.5 + - + +
924C VAL 4.1 4.5 - - - -
925C ALA* 4.5 5.4 - - - +
965C ASP 5.0 1.2 + - - -
966C GLY* 2.8 31.9 + - - +
967C VAL* 4.1 4.0 - - + -
968C ASP* 3.1 33.0 + - - +
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Residues in contact with ARG 858 (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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856C ASN* 3.5 24.4 + - - +
857C ARG* 1.3 78.5 - - - +
859C LEU* 1.3 61.6 + - - +
860C LEU* 3.5 13.1 + - + +
922C GLY 3.4 1.9 - - - +
924C VAL* 3.1 35.2 + - - +
926C LEU* 3.6 24.7 - - + +
929C MET* 5.2 3.6 - - - -
949C LYS* 4.2 11.9 - - - +
961C ASN* 5.1 8.9 + - - -
967C VAL* 3.7 4.9 - - - +
968C ASP* 3.5 25.2 + - + +
970C PRO* 4.1 22.8 - - - +
989C TYR* 3.0 37.2 + - - -
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Residues in contact with LEU 859 (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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814C ILE* 6.2 0.4 - - + -
817C TYR* 3.0 27.0 + - + -
858C ARG* 1.3 70.0 - - - +
860C LEU* 1.3 58.3 + - - +
921C LEU* 3.5 37.0 - - + -
922C GLY 3.7 7.0 - - - +
923C GLU* 3.8 25.1 - - + +
964C LEU* 5.0 6.7 - - + -
967C VAL* 3.5 14.2 - - + +
968C ASP 3.2 6.7 + - - -
969C VAL* 3.8 24.7 - - + -
970C PRO* 3.8 8.7 - - - +
1000C LYS* 4.0 23.1 - - + -
1001C TYR* 4.6 11.9 - - + -
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Residues in contact with LEU 860 (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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817C TYR* 3.9 2.9 - - - +
858C ARG* 3.8 19.3 - - + +
859C LEU* 1.3 80.5 - - - +
861C TRP* 1.3 62.0 + - - +
897C PHE* 3.9 17.8 - - + -
898C ALA 3.7 2.9 - - - +
899C ASP* 3.5 22.7 - - + -
921C LEU* 3.5 6.7 - - - -
922C GLY 3.1 29.7 + - - +
924C VAL* 3.5 25.4 - - + -
926C LEU* 4.1 2.7 - - + -
970C PRO* 4.4 8.5 - - + -
989C TYR* 3.3 54.1 - - + -
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Residues in contact with TRP 861 (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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814C ILE* 4.5 1.3 - - + -
817C TYR* 3.2 47.5 - + + -
818C VAL* 3.4 29.8 - - + -
821C THR* 3.7 1.2 + - - -
860C LEU* 1.3 71.7 - - - +
862C HIS* 1.3 63.6 + - - +
897C PHE* 3.4 7.4 - - - -
898C ALA 2.8 32.7 + - - +
899C ASP 3.5 12.1 - - - -
900C MET 3.4 5.6 - - - +
901C VAL* 3.3 48.8 - - + +
904C SER* 3.2 22.1 + - - +
919C ILE* 3.6 27.1 - - + -
920C LEU 3.4 14.4 - - - -
921C LEU* 3.2 31.0 - - + -
1003C LEU* 3.5 14.1 - - + -
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Residues in contact with HIS 862 (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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861C TRP* 1.3 76.0 - - - +
863C GLY* 1.3 71.7 + - - +
864C SER* 4.6 8.2 - - - -
869C PHE* 4.8 0.3 - - - -
872C ILE* 5.5 0.2 - - - +
877C LEU* 3.4 40.8 - - + +
895C ILE* 4.5 8.3 - - + -
896C TYR* 2.7 29.0 + - + -
897C PHE* 3.6 17.0 - + + +
904C SER* 3.9 2.5 - - - -
919C ILE* 3.9 1.7 - - - +
920C LEU* 2.8 56.5 + - + +
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Residues in contact with GLY 863 (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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862C HIS* 1.3 85.9 + - - +
864C SER* 1.3 64.4 + - - -
904C SER* 3.4 27.8 + - - +
907C TYR* 3.3 21.6 - - - +
908C CYS* 4.5 1.6 - - - -
918C LEU 4.5 0.7 - - - -
919C ILE* 3.6 15.7 - - - -
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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