Contacts of the helix formed by residues 187 - 196 (chain B) in PDB entry 2W7U
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 THR 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B GLY* 3.4 33.0 - - - +
141B THR* 3.7 11.4 - - + +
185B TYR* 3.0 13.5 + - + -
186B PHE* 1.3 73.8 - - - +
188B PRO* 1.3 70.1 - - + +
189B GLN* 3.8 11.9 + - - +
190B LEU* 2.8 39.1 + - - +
191B LYS* 2.9 14.3 + - - +
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Residues in contact with PRO 188 (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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105B ASP 6.1 0.4 - - - +
185B TYR* 6.1 0.7 - - + -
186B PHE 4.6 0.9 - - - +
187B THR* 1.3 90.1 - - + +
189B GLN* 1.3 58.0 + - + +
191B LYS* 3.9 18.7 - - + +
192B GLU* 3.1 33.9 + - - +
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Residues in contact with GLN 189 (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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73B TYR* 5.3 8.5 + - - +
187B THR* 3.1 11.1 - - - +
188B PRO* 1.3 80.3 - - + +
190B LEU* 1.3 61.1 + - + +
192B GLU* 3.6 10.2 + - - +
193B PHE* 3.2 23.6 + - - +
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Residues in contact with LEU 190 (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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73B TYR* 3.6 41.7 - - + +
77B GLU* 4.7 4.5 - - + -
79B LEU* 3.9 17.5 - - + -
141B THR* 3.8 18.4 - - + -
184B VAL* 3.7 22.7 - - + -
185B TYR 3.3 24.9 - - - +
186B PHE* 4.2 11.4 - - + -
187B THR* 2.8 17.4 + - - +
189B GLN* 1.3 75.0 - - + +
191B LYS* 1.3 61.2 + - - +
192B GLU 3.2 0.2 - - - -
193B PHE* 3.4 4.6 + - + +
194B ILE* 3.1 35.3 + - - +
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Residues in contact with LYS 191 (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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103B PHE* 3.9 35.6 - - + +
104B ALA 2.8 26.7 + - - -
105B ASP* 3.5 22.8 + - - +
106B GLY* 6.0 0.4 - - - -
165B LEU 5.9 0.4 - - - -
186B PHE* 3.4 27.6 - - + -
187B THR 2.9 17.1 + - - +
188B PRO* 3.9 15.3 - - + +
190B LEU* 1.3 78.2 - - - +
192B GLU* 1.3 55.7 + - - +
194B ILE* 3.5 7.6 + - - +
195B GLN* 3.0 47.5 + - - +
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Residues in contact with GLU 192 (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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188B PRO* 3.1 22.5 + - - +
189B GLN* 3.7 9.7 - - - +
190B LEU 3.2 0.2 - - - -
191B LYS* 1.3 74.9 - - - +
193B PHE* 1.3 63.7 + - - +
195B GLN* 4.0 7.4 - - - +
196B ASN* 3.0 43.5 + - - +
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Residues in contact with PHE 193 (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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71B VAL* 4.1 13.9 - - + -
72B GLU 3.9 7.2 - - - -
73B TYR* 3.5 54.7 - + + -
74B PRO* 3.8 19.7 - - + -
79B LEU* 4.8 9.2 - - + -
81B ILE* 3.6 21.8 - - + -
189B GLN 3.2 12.5 + - - +
190B LEU* 3.6 9.2 - - + +
191B LYS 3.3 0.2 - - - -
192B GLU* 1.3 80.2 - - - +
194B ILE* 1.3 68.4 + - + +
196B ASN* 3.6 3.6 + - - +
197B ASN* 2.8 48.7 + - - -
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Residues in contact with ILE 194 (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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29B VAL* 3.8 24.9 - - + -
33B THR* 5.1 0.2 - - - +
35B VAL* 4.1 16.4 - - + -
79B LEU* 4.6 9.2 - - + -
81B ILE* 3.8 17.3 - - + +
103B PHE* 3.7 31.9 - - + -
186B PHE* 3.8 35.2 - - + -
190B LEU 3.1 23.5 + - - +
191B LYS 3.8 3.6 - - - +
193B PHE* 1.3 83.3 - - + +
195B GLN* 1.3 62.4 + - - +
197B ASN* 3.1 14.2 + - - +
198B ILE* 3.2 13.7 + - + +
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Residues in contact with GLN 195 (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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103B PHE* 3.5 33.5 - - + +
191B LYS* 3.0 30.4 + - - +
192B GLU* 4.2 7.8 - - - +
194B ILE* 1.3 76.2 - - - +
196B ASN* 1.3 64.2 + - - +
197B ASN 3.2 1.4 + - - -
198B ILE* 3.5 32.9 + - + +
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Residues in contact with ASN 196 (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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192B GLU* 3.0 32.0 + - - +
193B PHE* 4.0 5.7 - - - +
194B ILE 3.3 0.2 - - - -
195B GLN* 1.3 79.3 + - - +
197B ASN* 1.3 64.9 + - - +
198B ILE 3.5 3.8 + - - +
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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