Contacts of the helix formed by residues 168 - 181 (chain B) in PDB entry 2QW4
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 ASP 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B TYR* 3.5 2.5 - - - -
166B LEU 3.5 5.3 + - - +
167B VAL* 1.3 74.9 - - - +
169B VAL* 1.3 67.1 + - - +
170B PRO* 2.8 28.4 - - + +
171B ALA* 3.1 14.5 + - - +
172B PHE* 3.2 9.9 + - - +
207B HIS* 3.0 24.2 + - - -
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Residues in contact with VAL 169 (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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38B VAL* 3.9 25.8 - - + -
41B HIS* 3.7 29.4 - - + +
42B LEU* 4.4 14.8 - - + -
122B TYR* 3.5 15.5 + - + +
168B ASP* 1.3 74.3 - - - +
170B PRO* 1.3 69.6 - - + +
172B PHE* 3.5 4.8 + - - +
173B ALA* 2.9 20.7 + - + +
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Residues in contact with PRO 170 (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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34B LEU* 4.2 16.0 - - + +
38B VAL* 4.2 21.5 - - + -
168B ASP* 2.8 24.9 - - + +
169B VAL* 1.3 87.9 - - + +
171B ALA* 1.3 65.9 + - - +
173B ALA* 3.0 11.9 + - + +
174B CYS* 3.2 16.2 + - - -
207B HIS* 3.5 31.9 - - + +
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Residues in contact with ALA 171 (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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167B VAL* 4.1 12.6 - - + -
168B ASP* 3.1 18.8 + - - +
170B PRO* 1.3 75.0 - - - +
172B PHE* 1.3 56.3 + - - +
174B CYS* 2.8 30.8 + - - +
175B LEU* 2.9 11.8 + - - +
204B LEU* 4.1 22.2 - - + +
207B HIS* 3.8 13.5 - - + -
208B VAL* 5.0 4.0 - - + -
224B LEU* 4.3 10.3 - - + -
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Residues in contact with PHE 172 (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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41B HIS* 3.5 37.0 - + - -
118B LEU* 3.7 42.4 - - + -
119B ARG* 4.2 13.7 - - + -
122B TYR* 3.4 54.1 - + + -
162B LEU* 4.5 4.5 - - + -
167B VAL* 3.8 14.7 - - + +
168B ASP 3.2 8.8 + - - +
169B VAL 3.6 7.2 - - - +
171B ALA* 1.3 79.4 - - - +
173B ALA* 1.3 58.8 + - - +
175B LEU* 3.4 13.2 - - + +
176B SER* 2.9 41.8 + - - -
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Residues in contact with ALA 173 (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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37B LEU* 3.6 37.5 - - + +
38B VAL* 4.1 7.0 - - + +
41B HIS* 3.9 15.7 - - + -
89B TRP* 4.8 3.7 + - - +
169B VAL 2.9 16.8 + - - +
170B PRO* 3.0 10.0 + - + +
172B PHE* 1.3 75.8 - - - +
174B CYS* 1.3 61.4 + - - +
176B SER* 3.6 6.0 + - - -
177B ALA* 3.2 23.0 + - - +
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Residues in contact with CYS 174 (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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34B LEU* 3.6 24.9 - - - -
37B LEU* 4.4 7.6 - - - -
170B PRO 3.5 14.4 - - - -
171B ALA* 2.8 7.5 + - - +
173B ALA* 1.3 75.2 - - - +
175B LEU* 1.3 66.3 + - - +
177B ALA* 3.1 2.7 + - - +
178B LEU* 2.7 28.3 + - - +
200B ILE* 4.1 14.1 - - + -
203B CYS* 4.0 6.3 - - - -
204B LEU* 3.7 40.8 - - + -
207B HIS* 5.6 0.2 - - - -
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Residues in contact with LEU 175 (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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118B LEU* 4.9 15.9 - - + -
162B LEU* 5.5 6.5 - - + -
167B VAL* 5.6 1.6 - - + -
171B ALA 2.9 7.2 + - - +
172B PHE* 3.4 21.5 - - + +
174B CYS* 1.3 77.1 - - - +
176B SER* 1.3 64.4 + - - +
178B LEU* 3.0 8.1 + - + +
179B VAL* 3.0 24.0 + - - +
204B LEU* 4.5 4.9 - - + +
224B LEU* 3.9 38.4 - - + +
225B LEU* 3.6 30.3 - - + -
227B LYS* 5.1 5.2 - - + -
228B LEU* 3.8 27.6 - - + -
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Residues in contact with SER 176 (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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41B HIS* 5.0 1.9 + - - -
89B TRP* 3.7 25.2 + - - -
115B LEU* 3.7 6.8 - - - +
118B LEU* 3.9 24.1 - - - +
119B ARG* 5.5 7.0 - - - -
172B PHE* 2.9 29.5 + - - -
173B ALA* 3.6 6.8 + - - -
175B LEU* 1.3 77.3 - - - +
177B ALA* 1.3 64.5 + - - +
179B VAL* 2.9 16.2 + - - +
180B LEU 3.0 10.2 + - - -
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Residues in contact with ALA 177 (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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37B LEU* 3.8 23.8 - - + -
89B TRP* 3.6 11.5 - - + -
93B ILE* 4.0 11.7 - - + -
173B ALA 3.2 20.1 + - - +
174B CYS 3.1 5.2 + - - +
176B SER* 1.3 76.9 + - - +
178B LEU* 1.3 48.9 + - - +
180B LEU* 3.0 7.1 + - - +
181B ILE* 2.8 37.8 + - - +
200B ILE* 3.9 16.2 - - + -
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Residues in contact with LEU 178 (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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174B CYS 2.7 18.0 + - - +
175B LEU* 3.3 10.5 - - + +
177B ALA* 1.3 68.3 - - - +
179B VAL* 1.3 65.4 + - - +
181B ILE* 2.9 23.5 - - - +
182B THR* 3.9 6.4 - - - -
197B GLN* 3.6 34.1 - - + +
200B ILE* 3.6 23.3 - - + -
201B ALA* 3.8 14.6 - - + +
204B LEU* 3.8 28.5 - - + -
225B LEU* 4.4 15.0 - - + -
228B LEU* 5.2 8.3 - - + -
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Residues in contact with VAL 179 (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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111B ALA* 3.5 10.0 - - + +
114B GLU* 3.5 37.1 - - + +
115B LEU* 3.4 23.3 - - + +
118B LEU* 4.2 13.2 - - + -
175B LEU 3.0 15.0 + - - +
176B SER 2.9 13.5 + - - +
178B LEU* 1.3 72.2 - - - +
180B LEU* 1.3 58.2 + - - +
182B THR* 3.6 13.1 - - - +
184B ARG* 3.8 2.9 + - - -
228B LEU* 3.9 33.0 - - + -
231B LEU* 4.5 5.8 - - + -
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Residues in contact with LEU 180 (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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89B TRP* 3.7 21.8 - - + -
90B ALA* 3.5 31.9 - - + -
93B ILE* 4.3 7.2 - - + -
96B PHE* 3.8 20.0 - - + -
107B LEU* 3.5 46.6 - - + +
108B LEU* 3.2 25.8 - - + -
111B ALA* 4.0 9.8 - - + +
115B LEU* 4.2 5.3 - - + +
176B SER 3.0 7.8 + - - +
177B ALA 3.0 8.9 + - - +
179B VAL* 1.3 78.6 - - - +
181B ILE* 1.3 62.9 + - + +
182B THR* 3.3 8.5 + - - +
184B ARG* 5.0 0.2 + - - -
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Residues in contact with ILE 181 (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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93B ILE* 4.0 25.6 - - + -
96B PHE* 4.7 11.0 - - + -
99B LEU* 6.0 1.1 - - + -
107B LEU* 4.9 6.1 - - + -
177B ALA 2.8 22.9 + - - +
178B LEU* 2.9 14.4 - - - +
180B LEU* 1.3 80.8 - - + +
182B THR* 1.3 60.9 - - - +
193B VAL* 3.7 21.5 - - + +
196B LEU* 4.1 18.6 - - + -
197B GLN* 3.2 47.6 - - + +
200B ILE* 3.4 27.1 - - + -
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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