Contacts of the helix formed by residues 178 - 189 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ARG* 5.6 0.2 + - - -
9B SER* 4.2 19.3 + - - +
11B GLN* 5.2 1.4 - - - +
12B MET* 3.7 11.3 + - - +
169C LYS 4.3 6.3 + - - -
171C ASN* 3.3 22.7 + - + +
176C LEU 3.2 6.0 + - - +
177C LYS* 1.3 74.9 - - - +
179C PRO* 1.3 57.7 - - - +
180C ASP* 2.9 20.0 + - - +
181C MET* 2.8 53.8 + - + +
182C VAL* 3.2 16.7 + - - +
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Residues in contact with PRO 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG* 5.8 0.7 - - - +
9B SER* 5.7 6.1 - - - +
177C LYS* 3.5 12.3 - - + +
178C ASP* 1.3 86.7 - - - +
180C ASP* 1.3 61.2 + - - +
181C MET 3.4 0.2 - - - -
182C VAL* 3.9 11.0 - - + -
183C TRP* 3.2 35.4 + - + +
466C HIS* 4.4 18.2 - - + +
469C ASP* 3.6 40.8 - - + +
470C ALA* 3.9 3.0 - - - +
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Residues in contact with ASP 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG* 3.0 33.0 + - - -
9B SER 4.4 3.6 - - - +
12B MET* 3.6 17.6 - - + +
13B GLN* 5.3 1.4 + - - +
178C ASP* 2.9 16.0 + - - +
179C PRO* 1.3 79.2 - - - +
181C MET* 1.3 57.3 + - - +
184C ASP* 2.9 33.3 + - - +
470C ALA* 3.7 1.1 - - - -
471C GLN* 3.0 39.0 + - - +
474C ILE* 3.5 18.1 - - - +
409D PHE* 4.1 6.6 - - - -
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Residues in contact with MET 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B MET* 3.4 26.7 - - + +
166C HIS 3.4 21.5 - - - +
167C SER* 3.5 26.5 - - - +
169C LYS 4.8 1.3 - - - +
170C ARG 4.6 3.8 - - - +
171C ASN* 3.6 28.0 - - - -
172C PRO* 4.5 0.4 - - - -
178C ASP* 2.8 30.7 + - + +
180C ASP* 1.3 74.3 - - - +
182C VAL* 1.3 66.0 + - - +
184C ASP* 3.9 0.7 - - - +
185C PHE* 3.3 18.7 + - - +
403D ASN* 3.3 29.4 - - - +
404D TYR* 3.8 16.0 - - + -
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C PHE* 6.1 0.3 - - - -
167C SER* 3.4 25.9 + - - +
168C GLN* 3.6 22.6 - - - +
177C LYS* 6.3 2.7 - - + -
178C ASP 3.6 16.4 - - - +
179C PRO* 3.9 10.8 - - + +
181C MET* 1.3 78.7 - - - +
183C TRP* 1.3 60.2 + - + +
185C PHE* 4.1 2.4 - - - +
186C TRP* 3.3 56.0 + - + +
466C HIS* 4.1 19.1 - - + +
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Residues in contact with TRP 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C PRO* 3.2 29.5 + - + +
182C VAL* 1.3 76.8 - - + +
184C ASP* 1.3 59.7 + - - +
185C PHE 3.2 1.8 - - - -
186C TRP* 3.6 41.7 - + + -
187C SER* 2.7 38.7 + - - -
196C VAL* 4.6 7.6 - - + -
200C PHE* 3.9 20.6 - + - -
463C ILE* 4.1 19.7 - - + -
466C HIS* 3.5 21.2 + - - -
467C LEU* 3.5 48.4 - - + +
470C ALA* 4.2 4.3 - - + -
474C ILE* 3.6 20.9 - - + -
478C ALA* 4.6 7.9 - - + -
482C PHE* 4.4 19.1 - + - -
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Residues in contact with ASP 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C ASP 2.9 21.3 + - - +
181C MET 3.9 0.4 - - - +
183C TRP* 1.3 76.9 - - - +
185C PHE* 1.3 59.8 + - - +
187C SER* 3.3 5.8 + - - -
188C LEU* 2.9 33.3 + - - +
474C ILE* 3.9 15.1 - - + +
477C LYS* 4.6 1.0 + - - -
404D TYR* 2.6 28.8 + - - +
408D SER* 2.8 33.5 + - - -
409D PHE* 2.9 18.7 - - + -
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Residues in contact with PHE 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C PHE* 5.7 0.7 - - + -
155C ILE* 4.1 18.8 - - + -
160C LEU* 4.1 11.2 - - + -
163C SER* 4.4 2.2 - - - -
164C PHE* 3.7 51.8 - + + -
167C SER* 4.2 9.0 - - - +
181C MET 3.3 13.7 + - - +
182C VAL 4.1 2.9 - - - +
183C TRP 3.2 0.2 - - - -
184C ASP* 1.3 77.3 - - - +
186C TRP* 1.3 68.5 + + - +
188C LEU* 2.8 24.9 + - - -
189C ARG* 3.0 45.1 + - + +
192C SER* 5.5 1.8 - - - -
404D TYR* 4.1 17.2 - + + -
405D TYR 3.6 24.5 - - - -
406D PRO* 4.2 9.2 - - + -
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Residues in contact with TRP 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C PHE* 3.3 41.6 - + - -
164C PHE* 3.6 12.6 - + - -
168C GLN* 3.8 21.1 - - - -
182C VAL* 3.3 34.7 + - + +
183C TRP* 3.6 36.3 - + + +
185C PHE* 1.3 91.3 - + - +
187C SER* 1.3 61.4 + - - +
188C LEU 3.3 0.5 + - - -
189C ARG 3.3 20.3 + - - +
190C PRO* 4.0 1.7 - - - +
192C SER* 3.3 25.8 + - - +
193C LEU* 6.1 0.3 - - - +
196C VAL* 3.7 11.4 - - + -
199C LEU* 4.2 10.3 - - + -
200C PHE* 3.7 33.9 - + - -
466C HIS* 4.9 1.3 - + - -
481C ASN* 4.4 2.4 + - - -
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C TRP* 2.7 22.5 + - - -
184C ASP* 3.3 10.4 + - - -
186C TRP* 1.3 73.1 - - - +
188C LEU* 1.3 59.5 + - - +
189C ARG 3.5 0.2 - - - -
190C PRO* 4.5 1.6 - - - +
474C ILE* 4.3 7.1 + - - +
477C LYS* 3.5 46.0 + - - +
478C ALA* 4.1 16.6 - - - +
481C ASN* 2.9 25.7 + - - +
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ASP* 2.9 34.3 - - - +
185C PHE* 2.8 9.6 + - - +
187C SER* 1.3 79.8 - - - +
189C ARG* 1.3 66.4 + - - +
190C PRO* 3.3 11.1 - - - +
477C LYS* 4.0 27.6 - - + +
406D PRO* 3.8 24.2 - - + +
407D ASN* 3.7 31.0 - - - +
408D SER* 4.2 4.0 - - - +
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Residues in contact with ARG 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.1 27.9 + - - +
155C ILE* 4.8 1.3 - - + -
160C LEU* 3.8 27.9 - - - +
185C PHE* 3.0 44.9 + - + +
186C TRP 3.3 3.8 + - - +
188C LEU* 1.3 88.3 + - - +
190C PRO* 1.3 53.6 - - - +
191C GLU* 2.7 55.6 + - + +
192C SER* 2.8 24.3 + - - +
433C ASN* 5.7 0.2 - - - +
434C THR 5.6 0.2 - - - -
435C ALA* 3.8 26.3 - - - +
406D PRO* 3.7 22.7 - - - +
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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