Contacts of the strand formed by residues 176 - 190 (chain B) in PDB entry 2QC1
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 TRP 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.2 11.2 - - + +
43B VAL* 3.6 38.8 - - + +
45B GLU* 3.9 25.8 - - + -
140B GLN* 5.0 6.1 - - + -
170B PHE* 6.2 0.2 - - - -
172B GLU* 5.5 1.4 - - - +
173B SER* 3.2 44.0 + - - +
175B GLU* 1.3 92.6 - - + +
177B VAL* 1.3 62.7 + - - +
178B ILE* 5.1 5.0 - - + +
207B MET* 3.3 34.5 - - + -
208B GLN* 3.3 7.9 - - - +
209B ARG* 4.0 41.7 - - + -
210B LEU* 4.1 5.7 - - - +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TRP* 1.3 74.6 - - - +
178B ILE* 1.3 78.0 + - - +
179B LYS* 3.5 9.3 + - + +
207B MET* 3.2 3.2 - - - -
208B GLN* 2.9 52.9 + - + +
210B LEU* 3.7 21.8 - - + -
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Residues in contact with ILE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 5.2 4.5 - - + -
40B LEU* 5.8 6.7 - - + -
167B LEU* 4.2 23.8 - - + -
170B PHE* 3.4 38.3 - - + -
173B SER* 6.3 0.7 - - - +
176B TRP* 5.1 5.6 - - + +
177B VAL* 1.3 88.5 - - - +
179B LYS* 1.3 61.2 + - - +
180B GLU 3.7 24.5 - - - +
181B ALA* 4.3 2.0 - - + -
205B PHE* 4.0 30.7 - - + -
206B VAL 3.4 4.9 - - - +
207B MET* 4.7 7.6 - - + -
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Residues in contact with LYS 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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139B GLU* 2.8 31.1 + - + +
177B VAL* 4.0 13.2 - - + +
178B ILE* 1.3 75.5 - - - +
180B GLU* 1.3 60.9 + - + +
206B VAL* 2.8 21.5 + - + +
208B GLN* 2.8 57.2 + - + +
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Residues in contact with GLU 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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178B ILE* 3.5 4.6 - - - +
179B LYS* 1.3 82.3 - - + +
181B ALA* 1.3 69.2 + - - +
182B ARG* 5.2 8.3 - - + +
204B HIS* 4.5 18.7 - - + -
205B PHE* 3.1 4.2 - - - +
206B VAL* 2.7 42.0 + - + +
1C NAG 5.1 9.8 - - - +
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Residues in contact with ALA 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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37B LEU* 5.4 0.2 - - + -
164B GLN* 3.5 22.4 + - + +
165B PRO* 3.5 26.0 - - + +
167B LEU* 4.9 9.0 - - + -
178B ILE* 4.3 8.5 - - + -
180B GLU* 1.3 83.9 - - - +
182B ARG* 1.3 70.9 + - - +
204B HIS* 3.1 12.1 - - - +
205B PHE* 3.9 10.3 - - + -
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Residues in contact with ARG 182 (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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163B ASP* 3.2 45.8 + - - +
164B GLN* 3.9 9.9 - - + +
165B PRO* 3.7 9.1 - - - +
180B GLU* 5.2 9.2 - - + +
181B ALA* 1.3 80.6 - - - +
183B GLY* 1.3 77.3 + - - +
184B TRP* 3.4 53.0 - - - +
203B TYR* 3.3 1.1 - - - -
204B HIS* 2.9 53.7 + - + +
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Residues in contact with GLY 183 (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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160B PRO* 5.5 5.6 - - - +
162B SER 5.1 1.6 - - - +
163B ASP* 2.9 16.9 + - - +
165B PRO* 4.3 0.2 - - - +
182B ARG* 1.3 96.5 + - - +
184B TRP* 1.3 61.4 + - - -
201B ILE* 4.6 4.3 - - - -
202B THR 3.4 7.4 - - - -
203B TYR* 3.5 25.1 - - - -
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Residues in contact with TRP 184 (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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182B ARG* 3.4 49.1 - - + +
183B GLY* 1.3 74.4 - - - -
185B LYS* 1.3 60.1 + - - +
186B HIS* 3.3 24.0 - - + +
201B ILE* 4.3 3.3 - - - +
202B THR 2.9 34.5 + - - +
204B HIS* 4.4 18.1 + + - -
1C NAG 4.2 2.2 - - - -
2C NAG 3.7 58.9 + - - +
3C MAN 3.6 35.7 - - - -
4C MAN 5.8 0.2 - - - -
5C MAN 4.4 18.4 - - - -
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Residues in contact with LYS 185 (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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157B ALA* 4.9 2.8 - - - +
158B ILE 3.0 26.5 + - - +
159B ASN* 3.0 17.0 + - - -
160B PRO* 4.3 20.6 - - + +
184B TRP* 1.3 75.7 - - - +
186B HIS* 1.3 64.9 + - - +
187B TRP* 3.6 45.1 - - + +
199B LEU* 4.1 23.8 - - + +
200B ASP 3.3 12.1 - - - +
201B ILE* 4.2 12.7 - - + +
3C MAN 3.5 23.6 - - - -
7C MAN 3.6 1.7 - - - +
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Residues in contact with HIS 186 (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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145B LYS* 4.8 1.6 - - - -
184B TRP* 3.3 25.2 + - + -
185B LYS* 1.3 75.4 + - - +
187B TRP* 1.3 66.4 + - - +
188B VAL* 3.9 7.9 - - + -
198B TYR 3.9 0.2 - - - +
199B LEU* 3.4 10.0 - - - +
200B ASP* 2.9 64.5 + - - +
202B THR* 3.8 4.0 + - - -
2C NAG 2.7 64.0 + - + +
3C MAN 4.3 0.2 - - - -
7C MAN 3.7 16.2 - - - +
10C MAN 3.6 20.6 + - - +
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Residues in contact with TRP 187 (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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6A THR 4.4 11.5 - - - +
9A SER* 4.0 33.9 - - - -
185B LYS* 3.6 50.3 - - + +
186B HIS* 1.3 75.7 - - - +
188B VAL* 1.3 61.7 + - - +
189B PHE* 4.3 5.2 + - + -
197B PRO* 4.2 10.8 - - + -
198B TYR 3.8 3.1 - - - -
199B LEU* 3.3 24.5 - - + +
3C MAN 5.3 0.7 - - - -
7C MAN 3.3 48.1 + - - +
8C MAN 4.1 9.9 + - - +
9C MAN 3.4 34.9 - - - -
10C MAN 4.8 5.7 + - - +
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Residues in contact with VAL 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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39A VAL* 3.8 28.7 - - + -
40A VAL 5.4 0.9 - - - +
186B HIS* 4.1 7.6 - - + -
187B TRP* 1.3 78.8 - - - +
189B PHE* 1.3 67.3 + - - +
190B TYR* 3.9 20.9 - - + +
197B PRO* 3.5 1.1 - - - +
198B TYR* 2.7 48.3 + - + +
200B ASP* 3.3 27.4 - - + +
10C MAN 5.1 14.4 - - - +
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Residues in contact with PHE 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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6A THR* 3.8 28.3 - - + -
8A THR 3.6 18.4 - - - -
9A SER* 3.7 22.9 - - - -
10A PRO* 4.2 1.1 - - + -
11A ILE* 3.8 33.4 - - + -
39A VAL* 3.7 3.6 - - - -
40A VAL* 2.9 41.0 + - + +
68A HIS* 4.7 4.3 - - + +
187B TRP 4.4 7.4 - - - -
188B VAL* 1.3 79.2 - - - +
190B TYR* 1.3 64.0 + - - +
193B CYS 4.1 9.2 - - - -
194B PRO 4.2 2.2 - - - -
195B THR 4.0 14.8 - - - -
196B THR 4.1 5.4 - - - -
197B PRO* 3.6 38.8 - - + -
10C MAN 5.9 0.4 + - - -
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Residues in contact with TYR 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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30A ASP* 2.6 38.5 + - - -
32A PHE* 4.0 5.5 - + + -
36A ARG* 3.4 55.3 + - + +
37A GLY 3.4 20.2 - - - -
38A LYS 3.5 2.9 - - - -
39A VAL* 3.6 20.0 - - + +
40A VAL* 3.9 0.9 - - - -
68A HIS* 2.9 21.3 - - - -
93B TYR* 4.8 6.8 + - - -
188B VAL* 3.9 18.9 - - + +
189B PHE* 1.3 77.9 - - - +
191B SER* 1.3 63.1 + - - +
192B CYS* 4.0 7.2 - - - -
193B CYS 3.0 12.4 + - - +
196B THR 5.3 0.6 + - - -
198B TYR* 3.7 31.1 - + + -
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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