Contacts of the helix formed by residues 178 - 189 (chain B) in PDB entry 1QQW
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 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B SER 4.7 0.4 + - - +
169B LYS 4.4 5.7 + - - -
171B ASN* 2.6 27.6 + - + +
176B LEU 3.4 3.7 + - - +
177B LYS* 1.3 75.9 - - - +
179B PRO* 1.3 72.0 - - - +
180B ASP* 2.9 21.8 + - - +
181B MET* 2.8 43.3 + - + +
182B VAL* 3.1 16.3 + - - +
5C ARG* 5.2 1.4 + - - -
8C ALA 5.4 1.2 - - - +
9C SER* 4.0 18.3 - - - +
11C GLN* 5.0 1.2 - - - +
12C MET* 3.9 9.5 + - - +
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Residues in contact with PRO 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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177B LYS* 3.6 11.4 - - + +
178B ASP* 1.3 87.3 - - - +
180B ASP* 1.3 60.9 + - - +
182B VAL* 4.2 10.1 - - + -
183B TRP* 3.0 34.2 + - + +
466B HIS* 4.4 20.2 - - + +
469B ASP* 3.8 42.2 - - + +
470B ALA* 4.2 3.0 - - - +
5C ARG* 5.7 2.0 - - - +
9C SER* 5.8 4.0 - - - +
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Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PHE* 3.8 9.4 - - - -
178B ASP* 2.9 17.5 + - - +
179B PRO* 1.3 79.7 - - - +
181B MET* 1.3 54.6 + - - +
184B ASP* 3.0 30.8 + - - +
470B ALA* 3.7 1.3 - - - -
471B GLN* 2.7 40.4 + - - +
474B ILE* 3.7 13.2 - - - +
5C ARG* 2.8 38.9 + - - +
9C SER 4.7 2.8 - - - +
12C MET* 3.5 16.1 - - + +
13C GLN* 5.1 2.8 + - - +
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Residues in contact with MET 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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402A PRO* 6.5 0.2 - - - -
403A ASN* 3.3 31.2 - - - +
404A TYR* 4.0 13.3 - - + -
166B HIS 3.6 7.4 - - - +
167B SER* 3.4 34.1 - - - +
169B LYS 5.2 1.1 - - - +
170B ARG 4.8 3.4 - - - +
171B ASN* 3.4 34.3 - - - -
172B PRO* 4.4 1.1 - - - -
178B ASP* 2.8 31.1 + - + +
180B ASP* 1.3 71.0 - - - +
182B VAL* 1.3 64.7 + - - +
184B ASP* 3.2 0.9 + - - +
185B PHE* 3.2 26.0 + - - +
12C MET* 3.4 25.8 - - + +
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B SER* 3.6 21.4 + - - +
168B GLN* 3.7 25.7 + - - +
169B LYS 5.6 0.4 - - - +
177B LYS* 6.3 2.2 - - + -
178B ASP 3.1 17.0 + - - +
179B PRO* 3.7 11.4 - - + +
181B MET* 1.3 78.6 - - - +
183B TRP* 1.3 62.3 + - + +
185B PHE* 4.3 2.1 - - - +
186B TRP* 3.4 51.5 + - + +
466B HIS* 3.8 22.0 - - + +
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Residues in contact with TRP 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PRO* 3.0 24.6 + - + +
182B VAL* 1.3 79.8 - - + +
184B ASP* 1.3 58.8 + - - +
185B PHE 3.2 2.2 - - - -
186B TRP* 3.9 24.7 - + + -
187B SER* 2.6 39.4 + - - -
196B VAL* 4.6 4.0 - - + -
200B PHE* 3.7 33.2 - + - -
463B ILE* 3.7 23.6 - - + -
466B HIS* 3.4 21.6 + + - -
467B LEU* 3.5 50.1 - - + +
470B ALA* 4.5 5.2 - - + -
474B ILE* 3.7 19.7 - - + -
478B ALA* 4.3 10.1 - - + -
482B PHE* 4.2 23.6 - + - -
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Residues in contact with ASP 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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404A TYR* 2.4 32.9 + - - +
407A ASN* 4.1 1.1 - - - -
408A SER* 2.6 42.1 + - - -
409A PHE* 3.4 9.8 - - + -
180B ASP 3.0 23.5 + - - +
181B MET 3.2 1.1 + - - +
183B TRP* 1.3 76.6 - - - +
185B PHE* 1.3 59.4 + - - +
187B SER* 3.2 7.7 + - - -
188B LEU* 2.8 27.4 - - - +
474B ILE* 4.1 12.5 - - + +
477B LYS* 3.7 5.9 + - - -
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Residues in contact with PHE 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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404A TYR* 4.2 22.6 - + + -
405A TYR 3.6 23.8 - - - -
406A PRO* 4.2 7.2 - - + -
154B PHE* 5.7 0.2 - - + -
155B ILE* 4.1 19.5 - - + -
160B LEU* 4.0 9.6 - - + -
163B SER* 4.5 2.0 - - - -
164B PHE* 3.5 55.0 - + + -
167B SER* 4.2 11.7 - - - +
181B MET 3.2 12.3 + - - +
182B VAL 4.3 1.3 - - - +
183B TRP 3.2 0.4 - - - -
184B ASP* 1.3 78.4 - - - +
186B TRP* 1.3 76.6 + + - +
188B LEU* 2.9 15.0 + - - +
189B ARG* 3.0 42.6 + - + +
192B SER* 5.6 1.6 - - - -
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Residues in contact with TRP 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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154B PHE* 3.3 41.5 - + - -
164B PHE* 3.4 10.5 - + - -
168B GLN* 3.4 26.0 - - - -
182B VAL* 3.4 35.5 + - + +
183B TRP* 3.3 32.4 + + + +
185B PHE* 1.3 93.6 - + - +
187B SER* 1.3 60.5 + - - +
189B ARG 3.3 21.1 + - - +
190B PRO* 4.0 2.8 - - - +
192B SER* 3.5 24.3 + - - +
196B VAL* 3.8 10.8 - - + -
199B LEU* 4.1 11.2 - - + -
200B PHE* 3.7 35.2 - + - -
466B HIS* 4.9 1.1 - + - -
481B ASN* 4.7 0.9 + - - -
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TRP* 2.6 24.5 + - - -
184B ASP* 3.2 4.5 + - - -
186B TRP* 1.3 72.5 - - - +
188B LEU* 1.3 60.4 + - - +
190B PRO* 4.4 1.2 - - - +
474B ILE* 4.3 4.3 - - - +
477B LYS* 3.0 50.9 + - - +
478B ALA* 3.9 20.0 - - - +
481B ASN* 2.9 26.6 + - - +
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Residues in contact with LEU 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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406A PRO* 3.8 25.7 - - + +
407A ASN* 3.6 31.9 - - - +
408A SER* 4.3 3.6 - - - +
184B ASP* 2.8 35.4 - - - +
185B PHE 2.9 6.5 + - - +
187B SER* 1.3 77.5 - - - +
189B ARG* 1.3 66.9 + - - +
190B PRO* 3.1 14.3 - - - +
477B LYS* 3.7 30.1 - - + +
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Residues in contact with ARG 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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406A PRO* 3.8 26.4 - - - +
155B ILE* 4.9 0.7 - - + -
160B LEU* 3.5 29.2 - - - +
185B PHE* 3.0 43.3 + - + +
186B TRP 3.3 4.0 + - - -
188B LEU* 1.3 87.3 + - - +
190B PRO* 1.3 51.9 - - - +
191B GLU* 2.7 54.5 + - + +
192B SER* 2.5 32.5 + - - +
433B ASN* 5.6 1.4 - - - +
435B ALA* 4.2 23.9 - - - +
39C LEU* 4.5 22.0 + - - +
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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