Contacts of the helix formed by residues 2142 - 2157 (chain B) in PDB entry 1WUF
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 ASN2142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2140B GLN* 3.4 15.2 - - - +
2141B GLN* 1.3 88.4 - - - +
2143B VAL* 1.3 61.7 + - - +
2144B GLU* 3.8 9.9 - - + +
2145B THR* 2.9 53.1 + - + +
2146B LEU 3.5 1.7 + - - -
2173B PHE* 3.6 4.9 - - - -
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Residues in contact with VAL2143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2141B GLN 5.3 1.1 - - - +
2142B ASN* 1.3 74.7 - - - +
2144B GLU* 1.3 64.4 + - - +
2146B LEU* 3.1 5.4 + - + +
2147B LEU* 3.0 24.3 + - + +
2172B GLN* 4.3 19.7 - - + +
2173B PHE* 4.3 26.7 - - + -
2176B ALA* 3.2 33.7 - - + -
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Residues in contact with GLU2144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2142B ASN* 4.1 9.8 - - + +
2143B VAL* 1.3 81.5 - - - +
2145B THR* 1.3 62.1 + - - +
2147B LEU* 3.4 7.7 + - - +
2148B GLN* 3.2 42.0 + - + +
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Residues in contact with THR2145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2140B GLN* 3.8 13.8 + - - +
2141B GLN 4.7 0.5 + - - -
2142B ASN* 2.9 49.0 + - + +
2144B GLU* 1.3 77.7 - - + +
2146B LEU* 1.3 67.7 + - - +
2148B GLN* 3.4 20.3 + - - +
2149B LEU* 3.1 27.7 + - - +
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Residues in contact with LEU2146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2137B ILE* 3.7 31.0 - - + -
2138B GLY 4.9 2.2 - - - +
2140B GLN* 3.8 17.3 - - + -
2142B ASN 3.5 9.6 + - - +
2143B VAL 3.1 9.7 + - - +
2145B THR* 1.3 81.3 + - - +
2147B LEU* 1.3 53.4 + - - +
2149B LEU* 3.1 4.7 + - - +
2150B VAL* 2.8 50.3 + - + +
2163B LEU* 4.4 12.1 - - + -
2173B PHE* 3.4 37.2 - - + +
2176B ALA* 5.3 2.5 - - + -
2177B VAL* 3.5 23.1 - - + -
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Residues in contact with LEU2147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2143B VAL* 3.0 11.6 + - + +
2144B GLU* 3.6 11.4 - - - +
2145B THR 3.3 0.2 - - - -
2146B LEU* 1.3 78.9 - - - +
2148B GLN* 1.3 56.4 + - - +
2150B VAL* 3.7 3.8 - - + +
2151B ASN* 3.1 40.8 + - - +
2176B ALA* 3.3 38.8 - - + +
2177B VAL* 3.9 13.0 - - + +
2180B SER* 3.6 20.4 - - - +
2181B PHE* 3.7 8.5 - - + -
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Residues in contact with GLN2148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2144B GLU* 3.2 34.6 + - + +
2145B THR* 3.6 22.6 - - - +
2146B LEU 3.1 0.6 - - - -
2147B LEU* 1.3 74.4 - - + +
2149B LEU* 1.3 67.4 + - + +
2151B ASN* 3.1 16.7 + - - +
2152B GLN* 3.1 25.2 + - - +
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Residues in contact with LEU2149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2137B ILE* 4.0 14.6 - - + -
2140B GLN* 3.5 39.7 - - + +
2145B THR* 3.1 17.3 + - - +
2146B LEU 3.1 6.5 + - - +
2148B GLN* 1.3 77.8 - - + +
2150B VAL* 1.3 62.9 + - - +
2151B ASN 3.2 0.7 + - - -
2152B GLN* 3.2 32.1 + - - +
2153B TYR* 2.8 41.2 + - + +
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Residues in contact with VAL2150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2137B ILE* 3.8 22.4 - - + -
2146B LEU* 2.8 29.9 + - + +
2147B LEU* 3.7 7.4 - - - +
2149B LEU* 1.3 76.0 - - - +
2151B ASN* 1.3 61.2 + - - +
2153B TYR* 3.8 3.5 + - - +
2154B VAL* 3.1 23.1 + - + +
2161B VAL* 4.9 5.7 - - + +
2163B LEU* 4.6 2.9 - - + -
2177B VAL* 3.8 34.3 - - + -
2181B PHE* 3.4 33.9 - - + -
2184B LEU* 4.3 11.0 - - + -
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Residues in contact with ASN2151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2147B LEU* 3.1 36.6 + - - +
2148B GLN* 3.3 12.5 - - - +
2149B LEU 3.1 0.2 - - - -
2150B VAL* 1.3 75.2 - - - +
2152B GLN* 1.3 67.4 + - - +
2154B VAL* 3.4 1.2 + - - +
2155B ASP* 3.1 37.3 + - - +
2180B SER* 5.4 0.2 + - - -
2181B PHE* 3.7 18.7 - - - -
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Residues in contact with GLN2152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2148B GLN* 3.4 20.0 + - - +
2149B LEU* 3.5 36.3 - - - +
2151B ASN* 1.3 78.6 - - + +
2153B TYR* 1.3 67.6 + - + +
2155B ASP* 3.2 6.6 + - - +
2156B GLN* 2.9 41.1 + - - +
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Residues in contact with TYR2153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2135B VAL* 3.4 31.1 - - + +
2136B SER 5.0 2.9 + - - -
2137B ILE* 4.0 26.4 - - + +
2149B LEU* 2.8 45.6 + - + +
2150B VAL* 4.2 3.4 - - - +
2151B ASN 3.4 0.4 - - - -
2152B GLN* 1.3 77.3 - - + +
2154B VAL* 1.3 58.7 + - - +
2156B GLN* 2.7 35.1 + - - +
2157B GLY 3.0 9.7 + - - -
2158B TYR* 3.3 38.2 + + + -
2161B VAL* 5.2 3.8 - - + -
2322B ARG* 3.5 28.6 + - - -
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Residues in contact with VAL2154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2150B VAL* 3.1 20.0 + - + +
2151B ASN 3.8 4.0 - - - +
2153B TYR* 1.3 75.2 - - - +
2155B ASP* 1.3 68.8 + - - +
2157B GLY* 3.0 15.2 + - - -
2158B TYR 4.1 10.3 - - - +
2161B VAL* 5.0 3.8 - - + +
2181B PHE* 3.6 32.5 - - + -
2184B LEU* 4.2 27.6 - - + -
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Residues in contact with ASP2155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2151B ASN* 3.1 24.5 + - - +
2152B GLN* 3.5 9.9 - - - +
2154B VAL* 1.3 82.7 - - - +
2156B GLN* 1.3 62.2 + - + +
2157B GLY 3.4 0.5 + - - -
2181B PHE* 5.9 0.2 - - - -
2337B GLN* 4.1 10.0 + - - +
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Residues in contact with GLN2156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2152B GLN* 2.9 47.7 + - - +
2153B TYR* 2.7 27.8 + - - +
2155B ASP* 1.3 78.3 - - + +
2157B GLY* 1.3 55.3 + - - -
2158B TYR* 3.6 24.1 + - + -
2322B ARG* 4.8 5.4 + - - -
2335B LEU* 4.6 14.0 - - + +
2337B GLN* 3.5 25.9 + - - +
2338B GLY 4.0 1.7 + - - -
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Residues in contact with GLY2157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2153B TYR 3.0 2.0 + - - -
2154B VAL 3.0 10.3 + - - -
2155B ASP 3.2 1.2 - - - -
2156B GLN* 1.3 78.5 - - - +
2158B TYR* 1.3 66.8 + - - +
2159B GLU* 3.0 14.4 + - - +
2337B GLN* 3.8 14.7 - - - +
2338B GLY* 3.2 25.1 + - - -
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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