Contacts of the strand formed by residues 1964 - 1969 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1962D GLY 3.5 11.2 - - - +
1963D LYS* 1.3 82.9 - - - +
1965D MET* 1.3 63.7 + - - +
1984D MET* 3.7 4.3 - - - -
1990D ALA* 3.3 9.4 - - + +
1992D LEU* 3.4 42.6 - - + -
2017D TYR 4.0 13.7 - - - +
2018D ALA* 3.4 1.5 - - + +
2019D ASP* 2.7 41.2 + - - +
2020D VAL* 3.6 4.2 + - - +
1982F ALA* 4.7 3.4 - - + +
1985F ALA* 4.5 13.9 - - + -
1986F ARG* 3.9 25.1 - - + +
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Residues in contact with MET1965 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1964D VAL* 1.3 75.4 - - - +
1966D ALA* 1.3 64.5 + - - +
1967D SER* 3.6 30.9 + - - +
1977D SER 5.1 0.2 - - - +
1980D PHE* 3.5 48.7 - - + +
1981D ALA* 4.1 2.9 - - + +
1984D MET* 3.6 20.6 - - + +
1990D ALA 2.8 9.1 + - - +
1991D VAL* 3.4 19.7 - - + -
1992D LEU* 2.8 31.5 + - - +
2018D ALA* 4.0 2.5 - - - -
2020D VAL* 3.4 16.2 - - + +
2022D VAL* 4.0 15.0 - - + -
2218D LEU* 4.6 7.2 - - - -
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Residues in contact with ALA1966 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965D MET* 1.3 72.9 - - - +
1967D SER* 1.3 57.8 + - - +
1968D MET* 3.7 6.1 - - + +
1992D LEU* 3.9 7.4 - - + -
2014D MET* 4.0 33.7 - - + -
2018D ALA* 3.5 18.2 - - + +
2020D VAL 2.9 11.7 + - - +
2021D VAL* 4.2 9.6 - - + -
2022D VAL* 2.8 34.0 + - - +
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Residues in contact with SER1967 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965D MET* 3.6 26.7 + - - +
1966D ALA* 1.3 70.1 - - - +
1968D MET* 1.3 60.0 + - - +
1969D PHE* 3.1 26.2 + - - -
1977D SER* 4.9 6.6 + - - -
1981D ALA* 5.9 0.6 - - - +
1991D VAL* 3.9 9.0 - - - -
1992D LEU 2.9 16.2 + - - -
1993D SER* 4.5 4.0 - - - -
1994D PHE* 2.9 28.9 + - - +
2022D VAL* 3.9 3.4 - - - -
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Residues in contact with MET1968 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966D ALA* 4.3 12.8 - - + +
1967D SER* 1.3 73.1 - - - +
1969D PHE* 1.3 61.9 + - - +
1970D TYR* 4.1 4.3 - - + -
1994D PHE* 3.7 40.8 - - + -
2010D SER* 3.3 34.1 - - - +
2011D VAL* 4.2 14.6 - - + +
2014D MET* 3.5 23.8 - - + -
2021D VAL* 3.8 21.8 - - + -
2022D VAL 2.8 17.7 + - - +
2023D LEU* 3.3 15.6 - - + +
2024D ARG 3.0 22.3 + - - -
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Residues in contact with PHE1969 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965D MET* 5.8 0.2 - - + -
1967D SER* 3.1 30.1 - - - -
1968D MET* 1.3 76.2 - - - +
1970D TYR* 1.3 63.7 + - - +
1971D GLU 3.5 10.7 - - - +
1973D SER* 3.7 26.2 - - - +
1976D THR* 4.0 6.1 - - - -
1977D SER* 3.7 30.1 - - - -
1994D PHE* 3.6 16.6 + - - +
1995D SER* 4.3 10.9 - - - -
1996D GLU* 4.3 6.3 + - - +
2022D VAL* 3.8 26.5 - - + -
2024D ARG* 3.2 40.8 - - + -
2045D ALA* 4.2 7.0 - - + -
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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