Contacts of the helix formed by residues 180 - 188 (chain C) in PDB entry 5GQQ
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 TYR 180 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179C SER* 1.3 69.4 - - - +
181C GLU* 1.3 76.3 + - + +
183C TYR* 2.9 20.1 + - - +
184C LEU* 3.1 33.5 + - + +
124D TYR* 3.6 21.1 - + - -
125D ARG 5.1 5.2 - - - -
126D LEU* 3.5 25.2 - - + +
158D LEU* 4.0 5.7 - - - +
162D THR* 2.9 43.6 + - + +
165D PHE* 3.5 39.2 - + + -
166D ARG* 6.2 0.4 - - + -
174D GLY* 2.9 18.1 + - - +
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Residues in contact with GLU 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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179C SER* 3.4 5.6 + - - +
180C TYR* 1.3 85.4 - - + +
182C GLN* 1.3 58.5 + - - +
184C LEU* 3.6 6.2 + - - -
185C SER* 3.4 10.0 + - - -
125D ARG 4.2 2.4 - - - +
126D LEU* 3.2 26.7 - - + -
127D SER* 2.5 53.9 + - - -
130D PHE* 3.3 37.1 - - + +
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Residues in contact with GLN 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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168C TYR* 3.8 17.4 + - + +
177C GLN 3.6 8.1 - - - +
178C VAL* 3.5 19.2 - - + +
179C SER* 3.1 43.4 + - - +
180C TYR 3.2 0.8 - - - -
181C GLU* 1.3 76.0 - - - +
183C TYR* 1.3 63.8 + - - +
184C LEU 3.3 0.4 - - - -
185C SER* 3.1 11.3 + - - +
186C MET* 3.1 23.4 + - - +
175D TRP* 4.3 9.2 - - - -
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Residues in contact with TYR 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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178C VAL* 4.6 3.8 - - + -
179C SER 2.7 14.4 + - - +
180C TYR 2.9 9.6 + - - +
182C GLN* 1.3 79.0 - - - +
184C LEU* 1.3 72.0 + - + +
186C MET* 3.2 31.5 + - + +
187C VAL* 3.2 37.5 + - + +
161D LEU* 4.0 24.5 - - + +
164D ILE* 4.3 6.3 - - + +
165D PHE* 3.4 37.7 - + + -
176D ILE* 4.6 5.4 - - + -
183D TYR* 4.9 2.5 - + - -
186D MET* 3.6 35.8 - - + +
187D VAL* 3.2 28.0 - - + +
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Residues in contact with LEU 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 TYR* 3.1 65.7 + - + +
181C GLU* 3.7 4.3 - - - +
183C TYR* 1.3 81.2 - - + +
185C SER* 1.3 58.0 + - - +
186C MET 3.1 0.3 + - - -
187C VAL* 3.1 1.2 + - - -
188C PHE* 2.7 44.6 + - + +
130D PHE* 3.4 26.9 - - + -
158D LEU* 4.1 17.7 - - + -
161D LEU* 3.5 42.2 - - + -
162D THR 4.9 0.4 - - - +
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Residues in contact with SER 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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168C TYR* 3.5 11.0 + - - -
181C GLU 3.4 8.0 + - - -
182C GLN* 3.1 19.6 + - - +
184C LEU* 1.3 78.5 - - - +
186C MET* 1.3 60.8 + - - +
188C PHE* 2.8 24.8 - - - +
130D PHE* 4.3 3.8 - - - -
133D ILE* 4.4 32.5 - - - -
137D LYS* 5.0 3.5 + - - +
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Residues in contact with MET 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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164C ILE* 3.4 43.8 - - + +
165C PHE* 5.3 1.1 - - - -
168C TYR* 3.9 35.2 - - + -
176C ILE* 3.7 32.1 - - + -
178C VAL* 3.7 15.9 - - + -
182C GLN 3.1 16.1 + - - +
183C TYR* 3.3 34.5 - - + +
184C LEU 3.0 0.2 - - - -
185C SER* 1.3 84.4 + - - +
187C VAL* 1.3 59.9 + - + +
188C PHE 3.7 2.8 - - - +
183D TYR* 4.2 16.4 - - + +
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Residues in contact with VAL 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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161C LEU* 4.2 14.8 - - + -
164C ILE* 5.1 0.4 - - - -
183C TYR* 3.4 28.3 - - + +
184C LEU 3.1 1.3 + - - +
186C MET* 1.3 79.5 - - + +
188C PHE* 1.3 62.7 + - - +
189C SER 3.7 0.2 - - - -
190C ILE* 2.9 29.8 + - + +
191C VAL* 4.5 5.6 - - + +
157D VAL* 5.8 0.2 - - - +
161D LEU* 3.5 36.3 - - + +
183D TYR* 5.6 1.8 - - + -
187D VAL* 3.4 39.3 - - + -
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Residues in contact with PHE 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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164C ILE* 5.7 0.2 - - - +
184C LEU* 2.7 46.5 + - + +
185C SER* 2.8 24.9 - - - +
186C MET 3.7 4.7 - - - +
187C VAL* 1.3 72.5 - - - +
189C SER* 1.3 60.8 + - - +
190C ILE* 5.1 0.4 - - - -
130D PHE* 5.2 0.7 - + - -
133D ILE* 6.0 2.0 - - + -
134D LEU* 3.6 18.6 - - + -
137D LYS* 3.7 39.3 - - + -
138D PHE* 3.7 33.4 - + - -
154D GLY* 4.2 6.3 - - - -
157D VAL* 3.6 37.9 - - + -
158D LEU* 4.2 8.7 - - + -
161D LEU* 4.2 9.2 - - + -
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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