Contacts of the helix formed by residues 175 - 183 (chain C) in PDB entry 5AQP
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 GLU 175 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ASP* 4.6 4.6 - - - +
11C LEU 4.3 0.9 - - - +
71C LYS* 2.7 29.8 + - - -
145C THR* 3.9 19.0 + - - +
146C VAL* 2.8 19.0 + - - +
147C PRO* 3.2 30.3 - - + +
174C ASN* 1.3 69.5 - - - +
176C PRO* 1.4 65.7 - - + +
178C ALA* 3.1 5.9 + - - +
179C ALA* 3.0 23.9 + - - +
197C ILE* 5.6 0.2 - - - -
199C ASP* 4.5 13.5 - - - +
206C ASP* 4.9 6.8 - - - +
337C VAL* 6.5 0.2 - - - -
369C VAL* 3.8 31.4 - - + +
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Residues in contact with PRO 176 (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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147C PRO* 5.1 0.4 - - + -
148C ALA* 3.8 22.7 - - + +
174C ASN* 3.6 7.6 - - + -
175C GLU* 1.4 91.8 - - + +
177C THR* 1.4 55.5 + - - +
179C ALA* 3.4 0.7 + - + -
180C ALA* 3.0 25.5 + - - +
197C ILE* 3.4 44.2 - - + +
208C SER* 3.6 30.1 - - - +
210C LEU* 3.8 13.5 - - + -
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Residues in contact with THR 177 (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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171C ARG* 5.7 3.6 - - - +
173C ILE* 4.9 11.0 - - + -
174C ASN* 3.2 29.9 + - - +
176C PRO* 1.4 76.1 - - - +
178C ALA* 1.4 56.8 - - - +
180C ALA* 3.3 4.8 + - - +
181C ILE* 3.0 48.3 + - + +
210C LEU* 3.8 21.3 - - - +
217C PHE* 3.8 32.6 - - + +
219C VAL* 5.1 0.3 - - - +
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Residues in contact with ALA 178 (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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145C THR* 3.8 11.0 - - + -
173C ILE* 3.8 22.2 - - + +
174C ASN 3.0 12.1 + - - +
175C GLU 3.3 9.0 - - - +
177C THR* 1.4 75.7 - - - +
179C ALA* 1.4 55.7 + - - +
181C ILE* 3.3 3.2 + - - -
182C ALA 3.1 22.3 + - - -
368C ALA 4.5 1.6 - - - -
369C VAL* 3.5 24.0 - - + +
372C GLY* 3.1 16.2 - - - -
373C ALA 4.1 1.8 - - - +
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Residues in contact with ALA 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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175C GLU 3.0 12.2 + - - +
176C PRO 3.4 7.8 + - - +
178C ALA* 1.4 75.1 - - - +
180C ALA* 1.4 61.7 + - - +
182C ALA* 3.4 10.0 + - - +
183C TYR* 3.4 23.2 - - - -
197C ILE* 4.2 10.3 - - + -
335C VAL* 4.1 10.8 - - + -
337C VAL* 3.7 30.1 - - + -
368C ALA* 4.2 11.4 + - - -
369C VAL* 4.5 5.5 - - + +
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Residues in contact with ALA 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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176C PRO 3.0 14.5 + - - +
177C THR* 3.3 9.6 + - - +
179C ALA* 1.4 72.4 - - - +
181C ILE* 1.3 63.3 + - - +
183C TYR 3.5 2.1 + - - -
184C GLY 3.3 2.9 + - - -
185C LEU* 3.1 51.5 + - + +
186C ASP* 4.7 1.1 - - - -
195C VAL* 4.6 0.9 - - + -
197C ILE* 4.2 9.3 - - + +
210C LEU* 4.5 4.3 - - + -
212C ILE* 4.4 6.3 - - + -
217C PHE* 3.8 20.4 - - + -
335C VAL* 4.9 0.2 - - - -
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Residues in contact with ILE 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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171C ARG* 5.3 2.9 - - - +
173C ILE* 4.7 4.0 - - + -
177C THR* 3.0 39.2 + - + +
178C ALA* 3.3 8.3 + - - +
180C ALA* 1.3 74.1 - - - +
182C ALA* 1.4 59.2 + - - +
184C GLY* 3.0 19.8 + - - -
186C ASP* 3.9 18.9 - - - +
217C PHE* 3.8 20.4 - - + -
372C GLY 3.6 18.8 - - - +
375C VAL* 3.8 26.4 - - + +
376C GLN* 3.5 31.4 - - + +
379C ILE* 5.1 2.2 - - + -
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Residues in contact with ALA 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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178C ALA 3.1 8.8 + - - +
179C ALA 3.4 11.4 - - - +
180C ALA 3.4 0.2 - - - -
181C ILE* 1.4 76.1 - - - +
183C TYR* 1.4 58.4 + - + +
184C GLY 3.6 0.3 + - - -
363C ILE* 3.4 24.1 - - + +
368C ALA* 3.4 26.5 - - - +
371C TYR* 3.7 33.0 - - + -
372C GLY* 3.8 4.4 - - - +
375C VAL* 5.1 1.5 - - - +
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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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179C ALA 3.4 18.2 - - - +
180C ALA 3.5 3.1 + - - +
181C ILE 3.3 0.4 - - - -
182C ALA* 1.4 73.1 - - + +
184C GLY* 1.3 62.1 + - - +
185C LEU* 3.2 28.8 + - + +
188C LYS* 5.2 3.6 - - - -
335C VAL* 3.6 26.9 - - + -
336C LEU 4.6 3.4 + - - -
360C ASN* 3.5 37.4 + - + +
361C LYS* 3.2 15.9 - - - -
362C SER* 3.7 19.7 - - - -
363C ILE* 2.9 48.4 + - + +
368C ALA* 4.8 9.0 - - + -
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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