Contacts of the strand formed by residues 1964 - 1969 (chain C) in PDB entry 5G1N
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 VAL1964 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1982B ALA* 4.9 5.2 - - + +
1985B ALA* 5.3 3.1 - - + -
1986B ARG* 3.2 47.3 - - + +
1962C GLY 3.9 4.0 - - - +
1963C LYS* 1.3 80.2 - - - +
1965C MET* 1.3 62.2 + - - +
1984C MET* 3.8 2.8 - - - +
1990C ALA* 3.2 12.6 - - + +
1992C LEU* 3.3 44.2 - - + -
2017C TYR 3.9 2.7 - - - +
2018C ALA* 3.6 9.3 - - + +
2019C ASP* 2.9 29.7 + - - +
2020C VAL* 3.5 6.4 + - - +
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Residues in contact with MET1965 (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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1964C VAL* 1.3 75.0 - - - +
1966C ALA* 1.3 57.9 + - - +
1967C SER* 3.2 40.4 + - - +
1980C PHE* 3.8 38.8 - - + +
1981C ALA* 4.5 1.8 - - + +
1984C MET* 3.8 26.9 - - + -
1990C ALA 2.8 10.3 + - - +
1991C VAL* 3.5 17.0 - - + +
1992C LEU* 2.7 33.4 + - - +
2018C ALA* 4.2 1.3 - - - -
2020C VAL* 3.6 20.9 - - + -
2022C VAL* 4.0 23.6 - - + -
2218C LEU* 4.5 3.6 - - + -
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Residues in contact with ALA1966 (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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1965C MET* 1.3 70.8 - - - +
1967C SER* 1.3 59.9 + - - +
1968C MET* 3.7 2.5 - - + -
1992C LEU* 3.6 7.9 - - + -
2014C MET* 3.9 34.5 - - + +
2018C ALA* 3.6 20.7 - - + +
2020C VAL 2.9 10.5 + - - +
2021C VAL* 4.3 9.6 - - + -
2022C VAL* 2.9 31.9 + - - +
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Residues in contact with SER1967 (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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1965C MET* 3.2 29.1 + - - +
1966C ALA* 1.3 70.5 - - - +
1968C MET* 1.3 60.5 + - - +
1969C PHE* 3.1 27.1 - - - -
1977C SER* 4.2 9.9 + - - -
1980C PHE* 5.4 0.3 - - - +
1981C ALA* 6.2 0.4 - - - -
1991C VAL* 4.5 7.6 - - - -
1992C LEU 2.9 12.6 + - - -
1993C SER* 4.5 7.0 - - - -
1994C PHE* 2.8 32.2 + - - +
2022C VAL* 4.0 2.9 - - - +
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Residues in contact with MET1968 (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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1966C ALA* 4.4 8.5 - - + +
1967C SER* 1.3 74.9 + - - +
1969C PHE* 1.3 62.5 - - - +
1970C TYR* 3.7 29.2 - - + +
1994C PHE* 3.8 26.2 - - + -
2010C SER* 4.1 12.1 - - - +
2011C VAL* 3.4 33.4 - - + -
2014C MET* 3.8 27.1 - - + -
2021C VAL* 3.9 12.8 - - - -
2022C VAL 2.8 17.5 + - - +
2023C LEU* 3.2 10.1 - - + +
2024C ARG 2.9 26.3 + - - +
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Residues in contact with PHE1969 (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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1967C SER* 3.1 27.4 - - - -
1968C MET* 1.3 75.0 - - - +
1970C TYR* 1.3 63.5 + - - +
1971C GLU 3.5 10.9 - - - +
1973C SER* 3.5 34.3 - - - +
1976C THR* 3.8 14.4 - - + -
1977C SER* 3.7 29.2 - - - +
1980C PHE* 4.9 0.9 - + - -
1994C PHE* 3.8 18.0 + - - +
1995C SER* 4.7 0.9 - - - -
1996C GLU* 4.1 12.8 + - - +
2022C VAL* 4.1 16.2 - - + -
2024C ARG* 3.3 36.3 - - + -
2045C ALA* 3.8 10.3 - - + -
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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