Contacts of the helix formed by residues 168 - 181 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D TYR* 3.6 0.7 - - - -
166D LEU 3.3 8.2 + - - +
167D VAL* 1.3 78.0 - - - +
169D VAL* 1.3 68.4 + - + +
170D PRO* 3.3 8.2 - - + +
171D ALA* 3.4 20.1 - - - +
172D PHE* 3.0 19.2 + - - +
207D HIS* 2.9 30.8 + - - -
211D VAL* 4.0 18.6 - - - +
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Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D VAL* 4.4 13.2 - - + -
41D HIS* 3.8 25.9 - - + +
42D LEU* 4.3 22.2 - - + -
122D TYR* 3.6 14.6 + - + +
168D ASP* 1.3 72.2 - - + +
170D PRO* 1.3 67.6 - - + +
172D PHE* 3.1 6.2 + - - +
173D ALA* 2.8 27.0 + - - +
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Residues in contact with PRO 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.2 12.1 - - + -
38D VAL* 3.4 30.3 - - + -
168D ASP* 3.3 18.4 - - + +
169D VAL* 1.3 92.9 - - + +
171D ALA* 1.3 55.2 - - - +
173D ALA* 2.7 30.7 + - - +
174D CYS* 3.2 10.1 + - - -
207D HIS* 3.3 29.4 - - + +
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Residues in contact with ALA 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D VAL* 4.2 11.2 - - + -
168D ASP* 3.4 26.0 - - - +
170D PRO* 1.3 78.3 - - - +
172D PHE* 1.3 61.1 + - - +
174D CYS* 3.3 5.2 + - - +
175D LEU* 3.0 21.9 + - - +
204D LEU* 4.0 20.8 - - + +
207D HIS* 3.3 17.9 + - + -
208D VAL* 5.0 3.1 - - + -
224D LEU* 4.3 11.5 - - + +
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Residues in contact with PHE 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D HIS* 4.3 24.0 - + - -
118D LEU* 3.7 43.1 - - + -
119D ARG* 4.3 11.2 - - + -
122D TYR* 3.4 60.6 - + + -
162D LEU* 5.0 3.1 - - + -
167D VAL* 4.1 13.6 - - + +
168D ASP 3.0 13.9 + - - +
169D VAL* 3.5 7.9 - - - +
171D ALA* 1.3 72.3 - - - +
173D ALA* 1.3 61.1 + - - +
175D LEU* 3.0 12.7 + - + -
176D SER* 2.5 52.1 + - - -
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Residues in contact with ALA 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.8 16.9 - - + +
38D VAL* 3.6 34.5 - - + +
41D HIS* 4.6 13.5 - - + -
89D TRP* 4.7 4.7 + - - -
169D VAL 2.8 11.8 + - - +
170D PRO* 2.7 21.9 + - + +
172D PHE* 1.3 73.3 - - - +
174D CYS* 1.3 58.4 + - - +
176D SER* 3.3 10.7 + - - -
177D ALA* 3.4 13.5 + - - +
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Residues in contact with CYS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 5.0 8.3 - - - -
37D LEU* 3.9 16.2 - - - -
170D PRO 3.5 16.2 - - - -
171D ALA* 3.9 4.9 - - - +
172D PHE 3.2 0.6 - - - -
173D ALA* 1.3 73.3 - - - +
175D LEU* 1.3 68.8 + - - +
177D ALA* 3.0 2.8 + - - +
178D LEU* 2.8 27.8 + - + +
200D ILE* 3.8 15.7 - - + +
203D CYS* 4.0 12.3 - - - -
204D LEU* 3.9 40.8 - - + -
207D HIS* 5.7 0.2 - - - -
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LEU* 4.1 27.4 - - + -
162D LEU* 5.0 5.8 - - + -
171D ALA 3.0 12.8 + - - +
172D PHE* 3.0 20.5 + - + +
174D CYS* 1.3 73.9 - - - +
176D SER* 1.3 57.8 + - - +
178D LEU* 2.9 27.8 + - + +
179D VAL* 2.9 17.9 + - + +
204D LEU* 4.8 4.2 - - + +
224D LEU* 3.7 37.9 - - + +
225D LEU* 4.4 14.8 - - + -
227D LYS* 5.9 2.5 - - + -
228D LEU* 4.0 34.5 - - + -
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Residues in contact with SER 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D HIS* 5.4 1.6 - - - +
89D TRP* 3.2 30.9 + - - -
115D LEU* 3.6 7.9 - - - +
118D LEU* 4.0 17.2 - - - +
119D ARG* 5.4 4.9 - - - -
172D PHE* 2.5 47.8 + - - -
173D ALA* 3.3 7.6 + - - -
175D LEU* 1.3 72.5 - - - +
177D ALA* 1.3 62.6 + - - +
179D VAL* 3.5 4.9 + - - +
180D LEU 3.2 13.7 + - - -
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Residues in contact with ALA 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 4.1 15.3 - - + -
89D TRP* 3.8 10.2 - - + -
93D ILE* 4.2 9.4 - - + -
173D ALA 3.4 12.3 + - - +
174D CYS 3.0 9.0 + - - +
176D SER* 1.3 75.2 - - - +
178D LEU* 1.3 56.3 + - - +
180D LEU 3.0 1.2 + - - -
181D ILE* 2.6 43.7 + - + +
200D ILE* 3.9 26.2 - - + -
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 4.5 12.8 - - + -
174D CYS* 2.8 22.3 + - + +
175D LEU* 3.3 12.1 - - + +
177D ALA* 1.3 74.7 - - - +
179D VAL* 1.3 65.8 + - + +
181D ILE* 2.9 23.5 + - - +
182D THR* 3.6 8.0 + - - -
197D GLN* 3.7 34.4 - - + +
200D ILE* 3.5 22.0 - - + -
201D ALA* 4.1 8.1 - - + +
204D LEU* 4.1 25.8 - - + -
225D LEU* 4.7 8.7 - - + -
228D LEU* 5.5 5.6 - - + -
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Residues in contact with VAL 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA* 3.9 3.2 - - - +
114D GLU* 3.7 40.0 - - + +
115D LEU* 3.9 18.4 - - + +
118D LEU* 3.7 18.6 - - + -
175D LEU* 2.9 17.2 + - + +
176D SER 3.6 8.1 - - - +
177D ALA 3.3 0.2 - - - -
178D LEU* 1.3 77.0 - - - +
180D LEU* 1.3 61.8 + - - +
182D THR* 4.1 2.8 - - - +
184D ARG* 3.7 18.7 + - - -
228D LEU* 3.5 32.5 - - + +
231D LEU* 4.5 1.6 - - + -
232D ARG* 5.8 0.2 + - - -
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Residues in contact with LEU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D TRP* 4.1 11.9 - - + -
90D ALA* 3.9 19.7 - - + -
93D ILE* 4.7 2.0 - - + -
96D PHE* 3.8 22.7 - - + -
107D LEU* 3.2 51.6 - - + +
108D LEU* 3.9 17.9 - - + -
111D ALA* 3.6 14.5 - - + +
115D LEU* 3.9 14.1 - - + +
176D SER 3.2 11.7 + - - +
177D ALA 3.0 6.7 + - - +
179D VAL* 1.3 79.4 - - - +
181D ILE* 1.3 78.6 + - + +
182D THR* 3.3 10.2 + - - +
184D ARG* 4.7 0.7 + - - -
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Residues in contact with ILE 181 (chain D).
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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93D ILE* 4.4 13.7 - - + -
96D PHE* 4.8 6.1 - - + -
99D LEU* 6.2 0.7 - - + -
107D LEU* 4.2 15.9 - - + -
177D ALA* 2.6 37.2 + - + +
178D LEU* 2.9 15.0 - - - +
180D LEU* 1.3 92.3 - - + +
182D THR* 1.3 59.6 + - - +
193D VAL* 3.6 29.6 - - + +
196D LEU* 4.3 17.9 - - + -
197D GLN* 3.4 30.8 - - + +
200D ILE* 4.2 14.8 - - + -
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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