Contacts of the strand formed by residues 1964 - 1969 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1982D ALA* 4.7 4.5 - - + +
1985D ALA* 4.7 5.2 - - + -
1986D ARG* 3.6 35.4 - - + +
1962E GLY 3.6 11.7 - - - +
1963E LYS* 1.3 79.4 - - - +
1965E MET* 1.3 61.8 + - - +
1984E MET* 4.9 1.6 - - - -
1990E ALA* 3.6 19.5 - - + +
1992E LEU* 3.6 35.0 - - + +
2017E TYR 4.1 3.1 - - - +
2018E ALA* 3.8 11.7 - - + -
2019E ASP* 2.7 35.8 + - - +
2020E VAL* 3.4 7.7 + - - +
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Residues in contact with MET1965 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1964E VAL* 1.3 72.8 - - - +
1966E ALA* 1.3 65.7 + - - +
1967E SER* 3.8 15.5 + - - -
1977E SER 5.3 0.2 - - - +
1980E PHE* 3.8 36.3 - - + +
1981E ALA* 4.0 2.5 - - + +
1984E MET* 3.6 21.8 - - + -
1990E ALA 3.0 10.6 + - - +
1991E VAL* 3.2 40.0 - - + -
1992E LEU* 2.7 32.1 + - - +
2018E ALA* 4.0 2.9 - - - -
2020E VAL* 3.4 16.4 - - + +
2022E VAL* 4.0 21.1 - - + -
2218E LEU* 4.4 12.6 - - - -
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Residues in contact with ALA1966 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965E MET* 1.3 74.6 - - - +
1967E SER* 1.3 60.2 + - - +
1968E MET* 3.8 4.5 - - + -
1992E LEU* 3.6 7.6 - - + -
2014E MET* 3.9 36.3 - - + -
2018E ALA* 3.6 18.7 - - + +
2020E VAL 2.9 11.0 + - - +
2021E VAL* 3.6 7.7 - - + +
2022E VAL 3.0 28.9 + - - +
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Residues in contact with SER1967 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965E MET* 3.8 23.2 + - - -
1966E ALA* 1.3 70.9 - - - +
1968E MET* 1.3 59.2 + - - +
1969E PHE* 3.1 27.8 - - - -
1977E SER* 4.7 7.1 + - - -
1980E PHE* 6.2 0.4 - - - -
1981E ALA* 6.1 0.7 - - - -
1991E VAL* 4.3 7.6 - - - -
1992E LEU 2.8 14.5 + - - -
1993E SER* 4.5 7.0 + - - -
1994E PHE* 2.7 35.3 + - - +
2022E VAL* 3.9 5.2 - - - -
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Residues in contact with MET1968 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966E ALA 4.3 5.2 - - - +
1967E SER* 1.3 74.9 + - - +
1969E PHE* 1.3 62.5 + - - +
1970E TYR* 4.1 8.5 - - + +
1994E PHE* 3.3 48.0 - - + -
2010E SER* 3.9 17.0 - - - -
2011E VAL* 4.0 17.7 - - + +
2014E MET* 3.6 27.8 - - + -
2021E VAL* 3.8 24.2 - - + -
2022E VAL 2.8 17.0 + - - +
2023E LEU* 3.2 14.4 - - + +
2024E ARG 2.9 25.5 + - - -
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Residues in contact with PHE1969 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967E SER* 3.1 31.9 - - - -
1968E MET* 1.3 77.5 - - - +
1970E TYR* 1.3 63.8 - - - +
1971E GLU 3.4 9.5 - - - +
1973E SER* 3.5 29.8 - - - +
1976E THR* 4.1 13.2 - - + -
1977E SER* 3.5 30.1 - - - -
1980E PHE* 5.2 1.8 - + + -
1994E PHE* 3.0 13.9 + - - +
1995E SER* 3.8 6.0 + - - -
1996E GLU* 3.7 19.6 + - - +
2022E VAL* 4.5 12.3 - - + -
2024E ARG* 3.5 38.6 - - + -
2045E ALA* 4.3 8.3 - - + -
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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