Contacts of the strand formed by residues 1964 - 1969 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1982E ALA* 4.8 5.2 - - + +
1985E ALA* 4.7 6.7 - - + -
1986E ARG* 3.9 41.3 - - + +
1962F GLY 4.2 1.3 - - - +
1963F LYS* 1.3 78.6 - - - +
1965F MET* 1.3 65.9 + - - +
1984F MET* 3.6 3.7 - - - +
1990F ALA* 3.3 22.9 - - + +
1991F VAL 4.8 0.4 - - - -
1992F LEU* 3.7 37.7 - - + -
2017F TYR 4.0 3.1 - - - +
2018F ALA* 3.4 4.3 - - + +
2019F ASP* 2.7 37.0 + - - +
2020F VAL 3.4 4.3 + - - -
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Residues in contact with MET1965 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1964F VAL* 1.3 73.1 - - - +
1966F ALA* 1.3 64.4 + - - +
1967F SER* 4.0 20.4 - - - -
1977F SER 5.2 0.2 - - - +
1980F PHE* 3.4 45.1 - - + +
1981F ALA* 3.9 4.3 - - + +
1984F MET* 3.4 21.7 - - + +
1990F ALA 2.8 11.7 + - - +
1991F VAL* 3.9 17.0 - - + -
1992F LEU* 2.7 34.0 + - - +
2018F ALA* 4.0 2.7 - - - -
2020F VAL* 3.8 12.8 - - + +
2022F VAL* 4.0 23.3 - - + -
2218F LEU* 4.2 14.6 - - - -
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Residues in contact with ALA1966 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965F MET* 1.3 72.6 - - - +
1967F SER* 1.3 61.6 + - - +
1968F MET* 3.4 4.2 + - + +
1992F LEU* 3.9 8.3 - - + -
2014F MET* 4.0 32.3 - - + +
2018F ALA* 3.6 14.6 - - + +
2020F VAL 2.9 18.7 + - - +
2021F VAL* 3.5 8.3 - - + -
2022F VAL 2.8 30.4 + - - +
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Residues in contact with SER1967 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965F MET* 3.7 24.7 + - - +
1966F ALA* 1.3 69.1 - - - +
1968F MET* 1.3 58.9 + - - +
1969F PHE* 3.3 24.5 - - - -
1977F SER* 3.4 12.2 + - - -
1980F PHE* 6.1 0.4 - - - +
1981F ALA* 6.2 0.4 - - - -
1991F VAL* 4.3 8.3 - - - -
1992F LEU 3.0 13.8 + - - -
1993F SER* 4.8 2.6 - - - -
1994F PHE* 2.9 31.9 + - - +
2022F VAL* 3.7 8.5 - - - -
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Residues in contact with MET1968 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966F ALA* 4.0 11.2 - - + +
1967F SER* 1.3 73.4 + - - +
1969F PHE* 1.3 64.2 + - - +
1970F TYR* 4.0 9.9 - - + +
1994F PHE* 3.5 34.1 - - + -
2010F SER* 3.8 27.6 - - - -
2011F VAL* 4.1 16.2 - - + +
2014F MET* 3.8 32.1 - - + -
2021F VAL* 3.8 21.8 - - + -
2022F VAL 2.7 13.6 + - - +
2023F LEU* 3.3 12.0 - - + +
2024F ARG 3.0 25.5 + - - +
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Residues in contact with PHE1969 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967F SER* 3.3 27.8 - - - -
1968F MET* 1.3 75.5 - - - +
1970F TYR* 1.3 61.4 + - - +
1971F GLU 3.3 17.2 - - - +
1973F SER* 3.4 36.3 - - - +
1976F THR* 4.1 5.6 - - + -
1977F SER* 3.7 29.4 - - - -
1980F PHE* 5.6 0.9 - + + -
1994F PHE* 3.0 12.3 + - - +
1995F SER* 3.6 23.4 - - - -
1996F GLU* 3.7 3.1 + - - +
2022F VAL* 4.0 19.1 - - + -
2024F ARG* 3.6 25.4 - - + -
2045F ALA* 4.0 16.6 - - + -
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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