Contacts of the helix formed by residues 367 - 380 (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 367 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C CYS* 4.1 10.5 - - - -
28C ILE* 3.4 29.5 - - + +
36C ARG* 2.9 53.6 + - - +
37C THR* 4.9 4.5 - - + +
363C ILE* 4.8 2.9 - - + -
364C ASN* 3.1 37.7 + - + +
366C ASP* 1.3 84.9 - - + +
368C ALA* 1.4 57.3 + - - +
369C VAL 3.3 3.1 - - - -
370C ALA* 3.2 6.7 + - - +
371C TYR* 2.9 29.0 + - + +
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Residues in contact with ALA 368 (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 4.1 1.7 - - - +
179C ALA* 4.2 3.3 - - + -
182C ALA* 3.4 14.5 - - + +
183C TYR* 4.8 6.5 - - + -
336C LEU 5.1 0.4 - - - +
337C VAL* 3.6 26.7 - - + -
363C ILE* 3.8 25.6 - - + +
364C ASN 3.0 13.0 + - - +
365C PRO* 3.8 4.4 + - + +
366C ASP 3.8 1.2 - - - -
367C GLU* 1.4 75.3 - - - +
369C VAL* 1.4 56.3 + - - +
371C TYR* 3.4 3.5 - - - +
372C GLY* 3.0 22.9 + - - -
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Residues in contact with VAL 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASP* 3.7 22.7 - - + +
145C THR* 3.5 31.6 - - + +
175C GLU* 3.8 34.5 - - + +
178C ALA* 3.5 12.1 - - + +
179C ALA* 4.5 9.9 - - + +
199C ASP* 4.8 4.7 - - - +
337C VAL* 4.6 16.6 - - + -
365C PRO 5.1 0.8 + - - -
366C ASP 5.3 0.8 + - - -
367C GLU 3.3 0.8 - - - -
368C ALA* 1.4 73.9 - - - +
370C ALA* 1.3 60.5 + - - +
372C GLY 3.4 0.9 + - - -
373C ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY 4.1 7.4 - - - +
10C ASP* 3.8 11.6 - - + +
17C CYS* 3.6 51.4 - - + +
18C VAL 4.4 0.7 - - - +
19C GLY* 4.4 0.8 - - - +
28C ILE* 4.3 7.4 - - + -
367C GLU 3.2 5.8 + - - +
369C VAL* 1.3 74.3 - - - +
371C TYR* 1.3 59.0 + - - +
373C ALA* 3.3 7.2 + - - +
374C ALA* 2.9 31.1 + - - +
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Residues in contact with TYR 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LYS* 5.4 2.8 - - - +
26C VAL* 3.7 54.2 + - + +
28C ILE* 4.3 10.2 - - + +
182C ALA* 3.7 31.6 - - + -
363C ILE* 4.0 25.1 - - + -
367C GLU* 2.9 15.1 + - + +
368C ALA* 3.4 14.8 - - - +
369C VAL 3.3 0.2 - - - -
370C ALA* 1.3 74.4 - - - +
372C GLY* 1.3 60.1 + - - +
374C ALA* 3.2 4.7 + - - +
375C VAL* 3.1 34.5 + - + +
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Residues in contact with GLY 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ILE* 4.9 0.4 - - - -
178C ALA* 3.1 29.8 - - - -
181C ILE* 3.6 8.4 - - - +
182C ALA* 3.8 13.5 - - - -
368C ALA 3.0 10.3 + - - -
369C VAL 3.4 0.9 + - - -
370C ALA 3.4 0.2 - - - -
371C TYR* 1.3 72.2 - - - +
373C ALA* 1.4 59.2 + - - +
375C VAL* 3.4 4.8 + - - +
376C GLN* 3.0 28.2 + - - +
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Residues in contact with ALA 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY* 3.6 18.8 - - - -
9C ILE 4.1 2.7 - - - +
143C VAL* 3.7 17.4 - - + +
145C THR* 3.8 21.8 - - + -
173C ILE* 4.2 5.6 - - - -
178C ALA* 4.1 1.2 - - - +
369C VAL 3.0 18.1 + - - +
370C ALA* 3.3 6.5 + - - +
372C GLY* 1.4 75.6 - - - +
374C ALA* 1.4 50.3 + - - +
376C GLN* 3.3 3.2 + - - +
377C ALA* 2.9 34.1 + - - +
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Residues in contact with ALA 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ALA 4.9 1.0 - - - +
7C VAL* 5.2 0.2 - - - +
8C GLY* 3.5 10.3 - - - +
19C GLY 3.6 28.7 - - - +
20C VAL* 3.8 7.4 - - - +
21C PHE* 3.8 7.5 + - - +
26C VAL* 3.9 14.4 - - + -
370C ALA 2.9 17.7 + - - +
371C TYR 3.2 6.0 + - - +
373C ALA* 1.4 71.3 - - - +
375C VAL* 1.3 61.1 + - - +
377C ALA* 3.4 3.3 + - - +
378C ALA* 3.0 28.1 + - - +
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Residues in contact with VAL 375 (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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21C PHE* 4.4 18.6 - - + -
26C VAL* 3.6 17.5 - - + -
181C ILE* 3.8 23.6 - - + +
182C ALA* 5.1 0.2 - - - -
371C TYR* 3.1 29.2 + - + +
372C GLY* 3.6 8.5 - - - +
374C ALA* 1.3 74.2 - - - +
376C GLN* 1.3 57.0 + - - +
378C ALA* 3.2 4.9 + - - +
379C ILE* 2.9 47.3 + - + +
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Residues in contact with GLN 376 (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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143C VAL* 4.2 6.1 - - + -
171C ARG* 3.3 31.2 + - - +
173C ILE* 4.2 24.2 - - + -
181C ILE* 3.5 21.0 - - + +
372C GLY 3.0 14.5 + - - +
373C ALA 3.3 9.4 + - - +
375C VAL* 1.3 76.5 - - - +
377C ALA* 1.4 55.6 + - - +
379C ILE* 3.2 23.8 + - - +
380C LEU* 2.9 71.0 + - + +
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Residues in contact with ALA 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ALA* 3.6 17.9 - - + +
7C VAL 3.3 31.9 - - - +
143C VAL* 3.6 16.3 - - + +
170C LEU* 3.9 4.5 - - + +
373C ALA 2.9 14.8 + - - +
374C ALA 3.6 6.3 - - - +
375C VAL 3.3 0.2 - - - -
376C GLN* 1.4 74.1 - - - +
378C ALA* 1.4 56.2 + - - +
380C LEU 3.4 2.6 + - - -
381C SER* 2.8 31.9 + - - -
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Residues in contact with ALA 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ALA* 5.0 3.5 + - - +
21C PHE* 3.6 43.5 - - + +
374C ALA 3.0 5.8 + - - +
375C VAL* 3.2 8.3 + - - +
377C ALA* 1.4 71.5 - - - +
379C ILE* 1.3 65.0 + - + +
381C SER* 3.3 23.2 + - - +
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Residues in contact with ILE 379 (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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181C ILE* 5.1 3.6 - - + -
186C ASP* 5.5 5.8 - - - +
375C VAL* 2.9 39.9 + - + +
376C GLN* 3.5 29.2 - - - +
378C ALA* 1.3 77.7 - - + +
380C LEU* 1.4 63.8 + - + +
381C SER* 3.5 4.9 + - - +
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Residues in contact with LEU 380 (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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143C VAL* 4.1 8.7 - - + -
170C LEU* 4.2 26.6 - - + +
171C ARG* 3.7 42.2 - - + +
376C GLN* 2.9 47.1 + - + +
377C ALA 3.4 4.9 + - - +
378C ALA 3.3 0.2 - - - -
379C ILE* 1.4 78.6 - - + +
381C SER* 1.3 61.8 + - - +
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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