Contacts of the strand formed by residues 2162 - 2166 (chain A) in PDB entry 1T77
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 ALA2162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2154A GLU* 3.9 6.1 - - + +
2155A ILE 3.2 6.7 - - - +
2156A PHE* 3.7 33.7 - - + -
2157A MET* 5.8 0.2 - - - -
2160A ARG 3.7 3.0 + - - +
2161A VAL* 1.3 82.4 - - - +
2163A VAL* 1.3 60.7 + - - +
2238A ASN* 3.2 27.2 + - - +
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Residues in contact with VAL2163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2086A LEU* 3.7 26.7 - - + -
2104A LEU* 6.1 0.4 - - + -
2127A GLU 5.1 2.7 - - - +
2133A TRP* 3.7 45.3 - - + +
2153A LEU 4.1 0.3 - - - +
2154A GLU* 3.4 1.4 - - - +
2155A ILE* 2.8 46.7 + - + +
2157A MET* 5.8 1.3 - - + -
2161A VAL* 5.5 1.3 - - + -
2162A ALA* 1.3 75.4 - - - +
2164A MET* 1.3 62.9 + - - +
2165A PHE* 3.8 23.5 - - + -
2238A ASN* 3.9 4.7 - - - +
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Residues in contact with MET2164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2086A LEU* 3.7 4.3 - - - +
2087A VAL* 2.7 65.9 + - + +
2144A ARG* 4.6 11.9 - - + -
2145A ARG 3.5 25.4 - - - +
2146A TYR* 4.3 7.6 - - + -
2152A ALA* 4.0 11.7 - - + -
2153A LEU 3.4 13.9 - - - +
2154A GLU* 4.3 5.6 - - + -
2163A VAL* 1.3 77.7 - - - +
2165A PHE* 1.3 71.0 - - - +
2236A SER* 4.3 17.7 - - - -
2238A ASN* 4.0 10.2 - - + +
2239A ASP* 4.2 22.0 - - + +
2242A GLN* 4.3 1.6 - - - +
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Residues in contact with PHE2165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2084A ALA* 4.9 1.1 - - + -
2085A GLN 3.1 15.3 - - - +
2086A LEU* 4.0 12.3 - - + -
2087A VAL* 4.5 1.3 - - - +
2097A LEU* 3.5 23.6 - - + -
2104A LEU* 4.2 12.1 - - + -
2106A PHE* 3.4 36.1 - + + -
2133A TRP* 3.7 31.0 - + - -
2152A ALA* 3.0 5.5 - - - +
2153A LEU* 2.9 36.2 + - + +
2155A ILE* 4.7 10.3 - - + -
2163A VAL* 3.8 26.2 - - + -
2164A MET* 1.3 82.7 - - - +
2166A ASN* 1.3 60.7 + - - +
2167A PHE* 3.8 23.2 - + + -
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Residues in contact with ASN2166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2084A ALA* 3.4 5.9 - - - +
2085A GLN* 2.8 62.0 + - + +
2087A VAL* 4.2 8.5 - - + +
2146A TYR* 3.2 43.4 - - + +
2149A GLN* 6.1 0.4 - - - +
2151A THR* 2.7 35.1 + - - +
2152A ALA* 3.9 0.7 - - + -
2165A PHE* 1.3 75.2 - - - +
2167A PHE* 1.3 69.7 + - - +
2464A ARG* 6.1 0.6 - - - +
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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