Contacts of the helix formed by residues 225 - 235 (chain A) in PDB entry 1XZQ
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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221A ASN 3.8 2.9 + - - -
222A VAL* 2.6 29.3 + - - +
223A GLY 3.3 0.4 - - - +
224A LYS* 1.3 84.9 - - - +
226A THR* 1.3 63.8 + - - +
227A LEU* 3.8 2.3 + - - +
228A LEU* 3.6 18.2 + - - +
229A ASN* 3.3 21.0 + - - +
298A VAL* 5.7 1.7 - - - +
326A ASN* 3.8 21.4 + - - +
328A VAL* 5.9 3.1 - - - -
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Residues in contact with THR 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 72.9 - - - +
227A LEU* 1.3 72.2 + - - +
228A LEU 3.1 0.3 + - - -
229A ASN* 3.1 5.0 + - - -
230A ARG* 2.9 47.4 + - + +
326A ASN* 5.2 0.2 + - - -
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Residues in contact with LEU 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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225A SER* 3.4 3.7 - - - +
226A THR* 1.3 81.4 - - - +
228A LEU* 1.3 65.2 + - + +
230A ARG* 3.5 5.3 + - - +
231A LEU* 3.2 17.7 + - - +
298A VAL* 5.4 3.6 - - + -
324A VAL* 4.5 10.1 - - + -
326A ASN* 3.7 43.6 + - + +
352A ILE* 3.9 23.8 - - + -
359A GLY* 3.4 40.8 - - - +
360A LEU* 3.6 9.7 - - - +
363A LEU* 4.2 17.8 - - + +
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Residues in contact with LEU 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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216A ILE* 4.2 24.5 - - + -
222A VAL* 3.7 27.8 - - + +
223A GLY* 3.8 7.2 - - - +
225A SER* 3.6 11.4 + - - +
226A THR 3.2 1.0 - - - -
227A LEU* 1.3 79.8 - - + +
229A ASN* 1.3 60.2 + - - +
231A LEU* 3.0 28.8 + - + +
232A LEU* 2.8 28.6 - - + +
267A ALA* 4.8 2.0 - - + -
269A VAL* 3.6 26.0 - - + -
296A LEU* 5.0 4.5 - - + -
298A VAL* 3.9 28.0 - - + -
363A LEU* 5.3 5.4 - - + -
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Residues in contact with ASN 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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223A GLY 3.4 21.2 + - - -
224A LYS* 4.0 8.3 + - - +
225A SER 3.3 20.8 + - - +
226A THR* 3.1 5.5 + - - +
228A LEU* 1.3 78.1 - - - +
230A ARG* 1.3 61.5 + - + +
232A LEU* 4.5 3.5 - - - -
233A ASN* 2.8 42.2 + - - +
269A VAL* 4.5 9.8 - - - +
270A ARG 4.5 2.2 - - - +
271A SER* 3.7 32.7 + - - +
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Residues in contact with ARG 230 (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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226A THR* 2.9 38.0 + - + +
227A LEU* 3.7 5.3 - - - +
229A ASN* 1.3 76.6 - - + +
231A LEU* 1.3 67.3 + - - +
233A ASN* 4.7 0.9 - - - -
234A GLU* 2.5 77.4 + - - +
359A GLY* 4.8 2.2 - - - -
360A LEU* 3.2 36.8 - - + +
361A GLU* 3.1 30.3 + - - -
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Residues in contact with LEU 231 (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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214A MET* 5.8 1.1 - - - -
216A ILE* 5.3 5.6 - - + -
227A LEU 3.2 11.0 + - - +
228A LEU* 3.0 21.0 + - + +
230A ARG* 1.3 77.7 - - - +
232A LEU* 1.3 72.4 + - + +
235A ASP* 2.9 47.1 + - - +
254A ILE* 4.2 22.0 - - + -
256A ILE* 4.3 7.0 - - + -
263A ILE* 5.8 1.1 - - + -
296A LEU* 4.4 19.3 - - + -
360A LEU* 3.6 22.9 - - + +
363A LEU* 4.1 20.6 - - + -
364A GLU* 4.9 2.2 - - + -
367A ILE* 4.7 6.1 - - + -
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Residues in contact with LEU 232 (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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216A ILE* 5.9 3.8 - - + -
228A LEU* 2.8 31.8 + - + +
229A ASN* 4.6 3.6 - - - +
231A LEU* 1.3 84.9 - - + +
233A ASN* 1.3 61.3 + - - +
236A ARG* 3.0 31.0 + - - +
252A GLU* 3.3 42.9 - - + +
254A ILE* 4.1 12.6 - - + +
263A ILE* 5.2 8.7 - - + -
269A VAL* 3.3 40.4 - - + +
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Residues in contact with ASN 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 ASN* 2.8 37.0 + - - +
230A ARG* 4.2 1.3 - - - +
231A LEU 3.2 0.8 - - - -
232A LEU* 1.3 78.8 - - - +
234A GLU* 1.3 71.0 + - + +
235A ASP 3.3 0.5 + - - -
236A ARG* 3.3 18.4 + - - +
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Residues in contact with GLU 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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230A ARG* 2.5 69.1 + - - +
233A ASN* 1.3 76.0 - - + +
235A ASP* 1.3 62.0 + - - +
236A ARG 3.8 1.9 + - - +
360A LEU* 3.1 15.4 - - + +
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Residues in contact with ASP 235 (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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231A LEU* 2.9 31.0 + - + +
234A GLU* 1.3 80.7 - - - +
236A ARG* 1.3 69.6 + - - +
254A ILE* 3.2 13.7 - - + -
255A VAL* 3.0 35.9 + - - +
256A ILE* 3.1 23.0 - - - +
360A LEU* 4.4 6.6 - - - +
364A GLU* 2.9 28.5 - - - +
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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