Contacts of the strand formed by residues 1048 - 1054 (chain C) in PDB entry 6RIP
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 LYS1048 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838C CYS 4.6 0.3 - - - +
839C VAL 4.2 0.5 - - - -
840C SER* 3.6 25.5 + - - +
850C ILE* 4.0 28.9 - - + +
933C VAL* 4.8 10.0 - - + +
934C PHE 3.2 15.0 - - - +
935C THR* 3.4 17.3 - - + +
939C VAL* 5.7 5.2 - - - -
940C GLU 4.8 8.7 - - - -
941C LYS* 4.6 2.0 - - - +
942C ASP* 3.0 46.1 + - - +
945C ALA* 4.4 5.9 - - - +
1042C LEU* 4.8 1.1 - - - -
1046C VAL* 4.9 0.2 - - - -
1047C LEU* 1.3 84.7 - - + +
1049C ILE* 1.3 64.5 + - - +
1050C VAL* 4.2 9.0 + - + -
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Residues in contact with ILE1049 (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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837C ALA* 6.1 1.1 - - + -
838C CYS 3.8 10.3 - - - +
839C VAL* 3.8 26.2 - - + -
932C GLN 3.9 0.3 - - - +
933C VAL* 3.3 4.9 - - - +
934C PHE* 2.9 46.5 + - + +
1042C LEU* 3.9 28.2 - - + +
1043C ALA 5.9 1.1 - - - +
1046C VAL* 4.4 13.2 - - + -
1048C LYS* 1.3 76.3 - - - +
1050C VAL* 1.3 71.8 + - - +
1051C LYS* 4.2 21.8 - - + -
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Residues in contact with VAL1050 (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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837C ALA 3.9 0.2 - - - -
838C CYS* 2.9 39.5 + - + +
850C ILE* 5.3 5.4 - - + -
870C ILE* 4.4 22.7 - - + -
884C VAL* 3.6 34.8 - - + -
931C VAL* 4.6 2.0 - - + -
932C GLN 3.5 5.2 - - - +
933C VAL* 3.6 25.6 - - + -
1048C LYS* 4.2 11.1 + - + -
1049C ILE* 1.3 75.5 - - - +
1051C LYS* 1.3 72.7 + - - +
1052C VAL* 4.4 5.3 + - + -
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Residues in contact with LYS1051 (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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87C ILE 6.0 0.6 + - - -
88C ARG 5.5 2.6 + - - -
835C GLU* 3.3 28.9 + - + +
836C LEU 4.4 13.0 - - - +
837C ALA* 4.8 9.4 - - + +
931C VAL* 3.3 8.1 - - - +
932C GLN* 2.9 46.4 + - + +
934C PHE* 4.8 19.7 - - + -
1049C ILE* 4.2 17.7 - - + -
1050C VAL* 1.3 77.5 - - - +
1052C VAL* 1.3 67.0 + - - +
1053C TYR* 5.0 8.4 + - + +
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Residues in contact with VAL1052 (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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835C GLU* 3.8 4.5 - - - +
836C LEU* 3.3 33.1 + - + +
837C ALA* 5.2 0.6 - - - +
870C ILE* 5.1 0.9 - - + -
871C VAL* 4.7 6.5 - - + -
883C LEU* 4.0 38.1 - - + -
884C VAL* 4.6 6.7 - - + -
918C LEU* 5.6 4.3 - - + -
928C VAL* 3.9 20.4 - - + -
930C ASP 3.7 3.8 - - - +
931C VAL* 4.5 9.9 - - + -
1050C VAL* 4.4 13.7 - - + +
1051C LYS* 1.3 77.6 - - - +
1053C TYR* 1.3 78.4 + - - +
1054C LEU* 4.0 6.5 - - + -
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Residues in contact with TYR1053 (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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757C THR* 5.9 3.4 - - - -
758C ARG* 4.4 11.9 - - + +
833C ILE* 4.7 11.4 - - + -
834C GLN 3.6 5.2 - - - +
835C GLU* 3.3 51.5 + - + -
928C VAL* 3.5 18.2 - - - +
929C ILE* 3.5 20.3 + - + -
930C ASP* 3.0 43.6 + - + +
931C VAL* 5.6 0.2 - - - -
932C GLN* 4.7 15.3 - - + +
1051C LYS* 5.0 8.2 + - + +
1052C VAL* 1.3 77.0 - - - +
1054C LEU* 1.3 71.4 + - - +
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Residues in contact with LEU1054 (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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833C ILE* 3.2 30.2 - - - +
834C GLN* 3.1 18.7 + - + +
836C LEU* 3.7 28.5 - - + -
877C VAL* 4.1 12.8 - - + -
883C LEU* 4.3 7.4 - - + -
920C VAL* 4.5 12.3 - - + -
924C VAL* 4.6 5.8 - - + +
925C SER 3.6 10.3 - - - +
926C GLY* 3.6 27.6 - - - -
927C THR 4.3 7.9 - - - +
928C VAL* 4.5 8.1 - - + -
929C ILE* 5.2 1.6 - - - -
1052C VAL* 4.0 14.4 - - + -
1053C TYR* 1.3 82.4 - - - +
1055C ALA* 1.3 61.5 + - - +
1056C VAL* 4.1 2.9 - - + +
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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