Contacts of the helix formed by residues 225 - 234 (chain A) in PDB entry 3QOW
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 SER 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A ASP* 3.0 28.4 + - - -
223A PHE 3.4 0.2 - - - -
224A LEU* 1.3 82.4 - - - +
226A GLU* 1.3 64.5 + - - +
227A GLU* 3.7 8.9 + - - +
228A TRP* 3.2 31.9 + - - +
229A ARG* 3.4 12.6 + - - +
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Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A SER* 1.3 69.4 - - - +
227A GLU* 1.3 66.9 + - - +
229A ARG* 3.2 51.2 + - - +
230A GLU* 4.1 2.1 + - - +
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLU* 4.2 1.7 - - - +
225A SER* 3.4 7.3 + - - +
226A GLU* 1.3 79.0 - - - +
228A TRP* 1.3 77.3 + - - +
229A ARG 3.3 0.7 + - - -
230A GLU* 3.6 11.6 + - - +
231A ARG* 2.7 49.1 + - + +
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Residues in contact with TRP 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 3.8 31.0 - - + -
162A LEU* 4.4 5.4 - - + -
183A TYR* 4.5 8.5 - - + -
185A VAL* 3.5 40.6 - - + +
219A GLU* 3.9 7.4 + - - -
220A ARG 5.8 0.2 + - - -
221A GLY* 5.2 1.8 - - - -
222A ASP 3.4 13.6 - - - +
223A PHE* 3.4 27.1 - - - +
225A SER* 3.2 25.1 + - - +
226A GLU 3.2 1.0 - - - -
227A GLU* 1.3 94.4 + - - +
229A ARG* 1.3 58.4 + - - +
230A GLU 3.4 0.2 - - - -
231A ARG* 3.3 58.9 - - + +
232A ILE* 2.9 47.6 + - + +
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU 4.9 0.6 + - - -
225A SER 3.4 12.1 + - - +
226A GLU* 3.2 41.6 + - - +
228A TRP* 1.3 77.3 - - - +
230A GLU* 1.3 58.2 + - - +
232A ILE* 3.6 3.1 + - - +
233A ALA* 3.1 24.8 + - - +
255A GLU* 2.9 28.1 + - - +
256A ARG* 3.2 44.0 - - + +
259A ASN* 5.5 5.2 + - - +
419A SO4 2.5 38.8 + - - -
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A GLU 4.1 2.2 + - - +
227A GLU 3.6 8.1 + - - +
228A TRP 3.4 0.4 - - - -
229A ARG* 1.3 76.2 - - - +
231A ARG* 1.3 66.7 + - + +
233A ALA* 3.3 13.6 + - - +
234A ASN* 3.0 51.0 + - - +
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Residues in contact with ARG 231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A VAL* 6.3 0.2 - - + -
183A TYR* 3.2 30.5 - - - -
219A GLU* 2.8 40.2 + - - -
227A GLU* 2.7 53.2 + - + +
228A TRP* 3.2 46.7 + - + +
230A GLU* 1.3 76.8 - - + +
232A ILE* 1.3 57.5 + - - +
234A ASN* 3.2 14.2 + - - +
235A THR* 2.8 25.0 + - - +
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Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A LEU* 4.2 27.1 - - + -
223A PHE 3.6 22.4 - - - +
228A TRP* 2.9 33.8 + - + +
229A ARG 3.8 3.8 - - - +
231A ARG* 1.3 75.3 - - - +
233A ALA* 1.3 62.1 + - - +
235A THR* 3.2 20.8 + - - -
238A ILE* 4.2 9.9 - - + -
253A LEU* 4.6 5.2 - - + -
256A ARG* 3.8 36.6 - - + +
257A PHE* 3.9 24.0 - - + -
260A MET* 3.5 13.0 - - + +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ARG 3.1 14.8 + - - +
230A GLU* 3.5 24.5 - - - +
232A ILE* 1.3 77.1 - - - +
234A ASN* 1.3 62.4 + - - +
235A THR 3.7 1.7 + - - +
256A ARG 4.7 0.6 + - - -
259A ASN* 3.6 36.9 - - + +
260A MET* 3.6 18.6 - - - +
261A LYS* 3.9 11.3 + - - +
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Residues in contact with ASN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 3.6 21.8 - - + +
230A GLU* 3.0 42.5 + - - +
231A ARG* 3.2 8.3 + - - +
233A ALA* 1.3 77.7 - - - +
235A THR* 1.3 61.2 + - - +
236A SER* 3.8 1.9 + - - -
261A LYS* 3.4 36.1 + - - +
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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