Contacts of the helix formed by residues 168 - 181 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A TYR* 3.3 2.8 + - - -
166A LEU 3.2 7.1 + - - +
167A VAL* 1.3 78.0 - - - +
169A VAL* 1.3 58.4 + - - +
170A PRO* 3.2 7.4 - - + +
171A ALA* 3.0 15.9 + - - +
172A PHE 2.9 24.4 + - - -
207A HIS* 2.9 34.1 + - - -
211A VAL* 4.4 14.4 - - - +
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A VAL* 4.4 19.1 - - + -
41A HIS* 4.1 25.5 - - + +
42A LEU* 4.6 12.1 - - + -
122A TYR* 3.6 18.8 + - + +
168A ASP* 1.3 71.2 - - - +
170A PRO* 1.3 79.0 - - + +
172A PHE* 3.0 6.6 + - - +
173A ALA* 2.9 20.5 + - + +
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Residues in contact with PRO 170 (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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34A LEU* 4.1 21.3 - - + +
38A VAL* 3.8 23.1 - - + -
168A ASP* 3.2 11.9 - - + +
169A VAL* 1.3 91.0 - - + +
171A ALA* 1.3 56.3 + - - +
173A ALA* 2.9 19.8 + - - +
174A CYS* 3.1 15.4 + - - -
207A HIS* 3.3 31.4 - - + +
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Residues in contact with ALA 171 (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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167A VAL* 3.9 14.4 - - + -
168A ASP* 3.0 23.0 + - - +
170A PRO* 1.3 74.1 - - - +
172A PHE* 1.3 57.8 + - - +
174A CYS* 3.1 4.4 + - - +
175A LEU* 2.8 30.0 + - - +
204A LEU* 4.0 23.7 - - + +
207A HIS* 3.7 12.9 - - + -
208A VAL* 5.0 3.1 - - + -
224A LEU* 4.4 10.0 - - + +
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Residues in contact with PHE 172 (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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41A HIS* 3.5 34.3 - + - -
118A LEU* 3.7 48.5 - - + -
119A ARG* 4.2 11.4 - - + -
122A TYR* 3.5 56.1 - + + -
162A LEU* 4.6 5.6 - - + -
167A VAL* 3.7 9.3 - - + +
168A ASP 2.9 18.1 + - - +
169A VAL* 3.0 4.5 + - - +
171A ALA* 1.3 76.5 - - - +
173A ALA* 1.3 51.2 + - - +
175A LEU* 4.0 9.4 - - + -
176A SER* 2.7 49.3 + - - -
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Residues in contact with ALA 173 (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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37A LEU* 3.7 38.0 - - + +
38A VAL* 4.2 7.6 - - + +
41A HIS* 3.9 18.6 - - + -
89A TRP* 5.1 3.9 + - - +
169A VAL 2.9 12.3 + - - +
170A PRO* 2.9 9.6 + - + +
172A PHE* 1.3 77.3 - - - +
174A CYS* 1.3 60.8 + - - +
176A SER* 3.6 6.2 + - - -
177A ALA* 3.5 20.1 + - - +
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Residues in contact with CYS 174 (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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34A LEU* 3.2 34.8 - - - -
37A LEU* 3.9 15.3 - - - -
170A PRO 3.1 7.4 + - - -
171A ALA 3.1 6.8 + - - +
173A ALA* 1.3 75.4 - - - +
175A LEU* 1.3 65.9 + - - +
176A SER 3.3 0.2 - - - -
177A ALA* 3.1 4.0 + - - +
178A LEU* 2.8 28.6 + - - +
200A ILE* 3.9 12.5 - - + +
203A CYS* 4.4 1.1 - - - -
204A LEU* 3.8 42.8 - - + -
207A HIS* 5.9 0.4 - - - -
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Residues in contact with LEU 175 (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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118A LEU* 3.9 22.7 - - + -
162A LEU* 6.1 2.5 - - + -
167A VAL* 5.8 0.2 - - + -
171A ALA 2.8 20.9 + - - +
172A PHE* 3.6 13.5 - - + +
174A CYS* 1.3 75.0 - - - +
176A SER* 1.3 61.6 + - - +
178A LEU* 3.2 9.0 + - + +
179A VAL* 3.1 19.2 + - - +
204A LEU* 4.7 8.5 - - + +
224A LEU* 3.5 32.8 - - + +
225A LEU* 4.4 19.5 - - + -
227A LYS* 5.1 7.9 - - + -
228A LEU* 3.3 35.8 - - + +
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Residues in contact with SER 176 (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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41A HIS* 4.9 2.6 + - - -
89A TRP* 3.7 18.5 + - - -
115A LEU* 3.6 18.6 - - - +
118A LEU* 4.1 21.3 - - - +
119A ARG* 5.2 6.6 + - - -
172A PHE* 2.7 32.9 + - - -
173A ALA* 3.6 8.7 + - - -
175A LEU* 1.3 72.6 - - - +
177A ALA* 1.3 65.6 + - - +
179A VAL* 3.2 10.5 + - - +
180A LEU 3.3 8.0 + - - -
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Residues in contact with ALA 177 (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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37A LEU* 4.2 13.2 - - + -
89A TRP* 4.1 11.6 - - + -
93A ILE* 4.7 10.1 - - + -
173A ALA 3.5 13.3 + - - +
174A CYS 3.1 8.9 + - - +
176A SER* 1.3 79.4 + - - +
178A LEU* 1.3 52.4 + - - +
180A LEU* 3.0 5.1 + - - +
181A ILE* 2.7 38.4 + - + +
200A ILE* 4.0 25.8 - - + -
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Residues in contact with LEU 178 (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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174A CYS 2.8 18.9 + - - +
175A LEU* 3.5 14.4 - - + +
177A ALA* 1.3 72.9 - - - +
179A VAL* 1.3 65.5 + - - +
180A LEU 3.0 2.1 + - - -
181A ILE* 3.3 18.2 + - - +
182A THR* 3.6 9.9 + - - -
197A GLN* 3.8 40.1 + - + +
200A ILE* 4.0 10.1 - - + -
201A ALA* 4.0 17.9 - - + +
204A LEU* 4.0 26.5 - - + -
225A LEU* 5.0 3.1 - - + -
228A LEU* 5.0 10.8 - - + -
61C LEU* 4.1 20.6 - - + -
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Residues in contact with VAL 179 (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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111A ALA* 3.7 9.5 - - + +
114A GLU* 4.1 31.2 - - + +
115A LEU* 4.0 24.5 - - + +
118A LEU* 4.5 7.0 - - + -
175A LEU 3.1 9.5 + - - +
176A SER* 3.2 10.2 + - - +
178A LEU* 1.3 77.2 - - - +
180A LEU* 1.3 60.1 + - - +
182A THR* 3.8 11.7 - - - +
184A ARG* 3.9 2.9 + - - -
228A LEU* 3.6 34.3 - - + +
231A LEU* 4.2 14.1 - - + -
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Residues in contact with LEU 180 (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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89A TRP* 4.0 19.5 - - + -
90A ALA* 3.8 20.4 - - + -
93A ILE* 4.2 9.2 - - + -
96A PHE* 3.6 26.2 - - + -
107A LEU* 3.4 49.4 - - + +
108A LEU* 3.9 16.8 - - + +
111A ALA* 3.9 9.7 - - + +
115A LEU* 4.3 5.8 - - + +
176A SER 3.3 9.2 + - - +
177A ALA 3.0 7.5 + - - +
179A VAL* 1.3 80.2 - - - +
181A ILE* 1.3 68.2 + - + +
182A THR* 3.1 10.4 + - - +
184A ARG* 5.2 0.2 + - - -
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ILE* 3.8 29.2 - - + -
96A PHE* 3.9 28.9 - - + -
99A LEU* 5.3 0.9 - - + -
107A LEU* 4.8 5.2 - - + -
177A ALA 2.7 17.6 + - - +
178A LEU* 3.3 10.9 - - - +
180A LEU* 1.3 77.4 - - + +
182A THR* 1.3 60.3 + - - +
193A VAL* 3.8 19.7 - - + +
196A LEU* 3.9 19.7 - - + -
197A GLN* 3.2 49.0 - - - +
200A ILE* 3.8 15.9 - - + -
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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