Contacts of the strand formed by residues 2141 - 2144 (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 VAL2141 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2063E ILE* 3.8 28.5 - - + -
2067E LEU* 3.6 18.8 - - + -
2073E MET* 5.2 1.8 - - + -
2074E THR 3.2 4.4 + - - -
2075E ILE* 3.2 28.1 - - + +
2076E THR 2.7 28.1 + - - -
2139E THR* 3.2 3.7 - - - +
2140E ASP* 1.3 86.6 - - + +
2142E LEU* 1.3 66.3 + - - +
2143E TYR* 4.3 3.1 - - + +
2180E VAL* 3.5 8.5 - - + +
2182E MET* 3.5 28.7 - - + -
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Residues in contact with LEU2142 (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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2076E THR* 3.6 25.1 - - + +
2078E VAL* 3.9 19.1 - - + -
2132E ILE* 4.5 9.6 - - + -
2135E ALA* 5.8 0.9 - - + -
2136E LEU* 4.0 23.8 - - + -
2139E THR* 3.4 6.7 - - + +
2141E VAL* 1.3 73.4 - - - +
2143E TYR* 1.3 57.8 - - - +
2144E MET* 3.6 17.6 + - + +
2167E LEU* 3.2 35.2 - - + -
2179E MET* 3.9 19.3 - - + +
2180E VAL 2.9 9.2 + - - +
2181E VAL* 3.6 4.9 - - + +
2182E MET 2.9 28.6 + - - +
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Residues in contact with TYR2143 (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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2059E ASP* 3.2 28.5 + - - -
2075E ILE* 4.2 16.4 - - + -
2076E THR 2.7 14.8 + - - +
2077E MET* 3.2 7.4 - - + -
2078E VAL* 2.9 25.8 + - - +
2086E THR* 3.4 11.2 + - - -
2087E VAL* 3.6 32.5 - - + -
2090E LEU* 4.2 17.0 - - + -
2141E VAL* 3.5 2.8 + - + -
2142E LEU* 1.3 71.6 - - - +
2144E MET* 1.3 62.5 + - - +
2145E THR* 4.2 1.6 - - + -
2182E MET* 3.7 24.2 - - + -
2184E PRO* 3.1 39.1 - - + +
2206E GLN* 3.7 21.1 - - - -
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Residues in contact with MET2144 (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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2078E VAL* 3.8 33.4 - - + +
2132E ILE* 4.5 8.7 - - + -
2142E LEU* 3.9 31.2 - - + +
2143E TYR* 1.3 72.5 - - - +
2145E THR* 1.3 67.6 + - - +
2165E PHE* 4.6 4.7 - - + +
2167E LEU* 4.2 13.9 - - + +
2181E VAL* 4.7 3.1 - - + -
2182E MET 2.9 15.5 + - - +
2183E HIS* 3.4 9.6 + - + -
2184E PRO* 3.4 24.4 - - - +
2190E GLU* 3.5 34.3 - - + +
2191E ILE* 3.9 24.7 - - + -
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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