Contacts of the helix formed by residues 175 - 183 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E ASP* 4.6 8.6 - - - +
11E LEU 4.3 1.2 - - - +
71E LYS* 2.7 29.6 + - - -
145E THR* 3.9 20.8 + - - +
146E VAL* 2.8 19.1 + - - +
147E PRO* 3.2 30.2 - - + +
173E ILE 4.5 0.2 - - - -
174E ASN* 1.3 70.1 - - - +
176E PRO* 1.4 63.1 - - + +
178E ALA* 3.1 10.9 + - - +
179E ALA* 3.0 27.3 + - - +
197E ILE* 5.6 0.2 - - - -
199E ASP* 4.5 16.6 - - - +
206E ASP* 5.0 6.2 - - - +
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Residues in contact with PRO 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E PRO* 5.1 0.2 - - + -
148E ALA* 3.8 24.0 - - + +
174E ASN* 3.6 8.5 - - + -
175E GLU* 1.4 92.1 - - + +
177E THR* 1.4 55.5 + - - +
179E ALA* 3.4 0.7 + - + -
180E ALA* 3.0 25.1 + - - +
197E ILE* 3.4 43.8 - - + +
208E SER* 3.6 28.7 - - - +
210E LEU* 3.8 13.6 - - + +
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Residues in contact with THR 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ILE* 4.9 10.1 - - + -
174E ASN* 3.2 30.2 + - - +
176E PRO* 1.4 77.3 - - - +
178E ALA* 1.4 56.4 + - - +
180E ALA* 3.3 6.2 + - - +
181E ILE* 2.9 46.8 + - + +
210E LEU* 4.0 14.0 - - - +
217E PHE* 3.7 41.8 - - + +
219E VAL* 5.1 0.3 - - - +
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Residues in contact with ALA 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E THR* 3.8 17.7 - - + -
173E ILE* 3.7 23.1 - - + +
174E ASN 2.9 12.7 + - - +
175E GLU* 3.1 10.5 + - - +
177E THR* 1.4 74.9 - - - +
179E ALA* 1.4 55.8 + - - +
181E ILE* 3.3 7.1 + - - +
182E ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E GLU 3.0 12.0 + - - +
176E PRO 3.4 7.8 + - - +
178E ALA* 1.4 75.5 - - - +
180E ALA* 1.3 61.4 + - - +
182E ALA* 3.4 14.1 + - - +
183E TYR* 3.4 26.9 - - + -
197E ILE* 4.2 22.2 - - + -
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Residues in contact with ALA 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E PRO 3.0 17.2 + - - +
177E THR* 3.5 6.3 - - - +
179E ALA* 1.3 71.9 - - - +
181E ILE* 1.4 65.1 + - - +
183E TYR 3.5 1.9 + - - -
184E GLY 3.3 3.5 + - - -
185E LEU* 3.2 49.7 + - + +
186E ASP* 5.2 0.4 - - - -
195E VAL* 4.7 2.5 - - + -
197E ILE* 4.2 8.0 - - + +
210E LEU* 4.7 2.7 - - + -
212E ILE* 4.4 7.6 - - + -
217E PHE* 4.1 20.4 - - + -
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Residues in contact with ILE 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ILE* 4.4 17.3 - - + -
177E THR* 2.9 39.0 + - + +
178E ALA* 3.3 6.0 + - - +
180E ALA* 1.4 72.0 - - - +
182E ALA* 1.4 65.2 + - - +
184E GLY* 3.1 14.1 + - - +
186E ASP* 3.9 17.5 - - - +
217E PHE* 3.9 20.9 - - + -
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Residues in contact with ALA 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E ALA 3.0 13.7 + - - +
179E ALA* 3.5 14.6 - - - +
180E ALA 3.4 0.6 - - - -
181E ILE* 1.4 76.8 - - - +
183E TYR* 1.4 65.1 + - + +
184E GLY 3.7 0.2 + - - -
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Residues in contact with TYR 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E ALA* 3.4 22.4 - - + +
180E ALA 3.5 2.5 + - - +
181E ILE 3.3 0.2 - - - -
182E ALA* 1.4 82.3 - - + +
184E GLY* 1.3 62.4 + - - +
185E LEU* 3.3 29.5 + - + +
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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