Contacts of the strand formed by residues 204 - 213 (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 THR 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C THR* 4.3 12.2 + - - +
72C ARG* 3.5 16.2 - - - +
149C TYR* 5.2 8.5 - - - +
199C ASP* 3.8 1.9 + - - +
200C LEU* 4.0 0.5 - - - -
201C GLY 3.2 31.9 + - - +
202C GLY 3.2 7.4 + - - +
203C GLY* 1.3 78.3 - - - +
205C PHE* 1.3 59.3 + - - +
206C ASP* 3.3 22.3 + - - +
225C ASP 3.8 4.3 - - - -
226C THR* 3.4 24.5 - - - +
228C LEU 3.2 10.2 + - - +
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Residues in contact with PHE 205 (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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198C PHE* 3.6 34.8 - + - -
199C ASP 3.4 13.5 - - - -
200C LEU* 3.7 24.5 - - + -
204C THR* 1.3 72.5 - - - +
206C ASP* 1.3 65.9 + - - +
207C VAL* 3.4 22.9 - - + -
224C GLY* 3.2 4.9 - - - -
225C ASP* 2.8 50.4 + - + +
228C LEU* 4.1 20.9 - - + -
313C THR* 3.3 37.7 - - - -
316C PRO* 3.5 26.0 - - + -
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Residues in contact with ASP 206 (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* 5.6 3.1 - - - +
149C TYR* 3.1 36.0 + - + -
175C GLU* 4.9 6.8 - - - +
197C ILE* 3.6 1.7 - - - +
199C ASP* 2.8 60.1 + - + +
204C THR* 3.3 24.6 + - - -
205C PHE* 1.3 78.5 - - - +
207C VAL* 1.3 62.1 + - - +
208C SER* 4.2 7.8 + - - +
223C ALA 3.6 4.8 - - - +
224C GLY* 5.6 0.2 - - - -
226C THR* 5.7 3.6 - - - +
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Residues in contact with VAL 207 (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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196C LEU* 4.1 22.2 - - + -
197C ILE 3.3 6.5 - - - +
198C PHE* 4.2 6.7 - - + -
205C PHE* 3.4 37.9 - - + -
206C ASP* 1.3 70.5 - - - +
208C SER* 1.3 64.6 + - - +
221C SER 4.2 0.2 - - - +
222C THR* 3.3 4.2 - - - -
223C ALA 2.8 42.6 + - - +
316C PRO* 4.2 7.9 - - + +
317C VAL* 4.0 21.5 - - + -
320C ALA* 3.6 25.0 - - + +
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Residues in contact with SER 208 (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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148C ALA* 4.4 1.7 - - - +
176C PRO* 3.6 39.0 - - - +
195C VAL 3.7 0.3 - - - +
196C LEU* 3.4 4.2 - - - +
197C ILE* 2.8 36.6 + - - +
206C ASP* 4.2 7.6 - - - +
207C VAL* 1.3 77.1 + - - +
209C ILE* 1.3 65.6 + - - +
210C LEU* 5.0 2.9 - - - -
219C VAL* 5.3 0.4 - - - -
221C SER 3.4 8.5 - - - -
222C THR* 4.2 13.1 - - - +
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Residues in contact with ILE 209 (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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194C ASN* 5.2 0.2 - - + -
195C VAL 3.2 7.4 - - - +
196C LEU* 3.8 17.9 - - + -
208C SER* 1.3 79.9 - - - +
210C LEU* 1.3 71.3 + - - +
219C VAL* 3.8 3.1 - - - +
220C LYS* 2.9 29.1 + - + -
221C SER* 3.0 24.0 + - - +
320C ALA* 3.5 12.8 - - + +
321C LEU* 3.5 50.0 - - + +
324C ALA* 4.1 9.6 - - + -
326C LEU* 4.0 22.9 - - + -
331C ILE* 4.4 7.9 - - + -
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Residues in contact with LEU 210 (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* 3.8 45.5 - - + +
177C THR* 3.8 17.0 - - - +
180C ALA* 4.5 6.5 - - + -
193C ARG 3.5 0.3 - - - +
194C ASN* 3.4 3.8 - - - -
195C VAL* 2.7 48.9 + - + +
197C ILE* 4.3 8.3 - - + -
208C SER* 5.1 0.9 - - - -
209C ILE* 1.3 79.4 - - - +
211C THR* 1.3 68.1 + - - +
212C ILE* 4.2 1.3 - - + -
217C PHE* 4.3 13.7 - - + -
218C GLU 3.2 9.6 - - - +
219C VAL* 3.4 41.1 - - + +
220C LYS 4.5 0.2 - - - +
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Residues in contact with THR 211 (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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192C GLU* 4.1 19.7 - - - +
193C ARG 3.1 5.6 - - - -
194C ASN* 3.6 19.3 - - - +
209C ILE* 5.6 1.1 - - + -
210C LEU* 1.3 76.6 - - - +
212C ILE* 1.3 62.4 + - - +
213C GLU* 4.2 1.3 - - - -
216C ILE 3.3 4.2 - - - +
217C PHE* 3.5 1.4 - - - -
218C GLU* 2.9 48.6 + - - +
220C LYS* 3.1 33.2 - - + +
326C LEU* 5.6 1.6 - - + -
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Residues in contact with ILE 212 (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 ALA* 4.4 4.3 - - + -
185C LEU* 3.9 28.7 - - + +
186C ASP* 4.0 24.9 - - + +
191C ALA 4.4 1.6 - - - +
192C GLU* 3.4 2.8 - - - -
193C ARG* 2.8 42.6 + - + +
195C VAL* 3.7 29.4 - - + -
210C LEU* 5.1 1.6 - - + -
211C THR* 1.3 77.7 - - - +
213C GLU* 1.3 62.5 + - - +
214C ASP 5.3 0.2 - - - +
215C GLY* 4.3 5.4 - - - +
216C ILE 3.2 18.2 - - - +
217C PHE* 3.6 34.5 - - + -
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Residues in contact with GLU 213 (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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191C ALA 5.5 1.1 - - - -
192C GLU* 4.3 25.6 - - + +
211C THR* 4.2 0.6 - - - -
212C ILE* 1.3 74.7 - - - +
214C ASP* 1.3 67.3 + - - +
215C GLY 3.2 0.7 - - - -
216C ILE* 2.9 36.7 + - + +
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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