Contacts of the helix formed by residues 225 - 230 (chain A) in PDB entry 4H36
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 VAL 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LYS* 4.0 0.4 - - - -
223A TYR* 2.7 18.2 - - + +
224A VAL* 1.3 90.3 - - - +
226A THR* 1.3 62.0 + - - +
227A ARG* 3.4 28.2 + - + +
228A TYR* 3.5 40.4 - - + +
229A TYR* 3.8 8.0 - - - -
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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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188A ARG 5.0 0.2 - - - +
189A ASP* 3.6 45.5 - - + +
190A LEU 5.2 1.1 - - - +
191A LYS* 2.9 30.7 + - + +
212A ARG* 4.3 11.4 - - - +
223A TYR* 4.2 2.4 + - - -
225A VAL* 1.3 71.3 - - - +
227A ARG* 1.3 64.0 + - - +
228A TYR 3.3 1.6 - - - -
229A TYR* 3.2 15.8 + - + -
230A ARG* 3.3 38.7 + - + +
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Residues in contact with ARG 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 VAL* 3.3 20.4 - - + +
226A THR* 1.3 79.0 - - - +
228A TYR* 1.3 84.9 + - - +
229A TYR 3.2 0.9 + - - -
230A ARG* 3.5 14.2 + - - +
235A ILE* 5.1 0.2 - - - +
265A GLY 2.5 36.3 + - - -
266A ARG* 3.6 16.1 + - - +
267A ASP* 3.8 20.5 - - - +
268A TYR* 3.7 43.8 + - + +
271A GLN* 3.3 26.9 + - - +
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Residues in contact with TYR 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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224A VAL* 4.4 5.4 - - + -
225A VAL* 3.5 30.6 - - + +
226A THR 3.3 0.6 - - - -
227A ARG* 1.3 101.6 + - - +
229A TYR* 1.3 78.0 + + + +
230A ARG 3.9 1.7 + - - +
247A TRP* 4.9 0.5 + - - -
251A CYS* 4.1 11.6 - - - +
261A ILE* 3.6 41.3 - - + -
263A PHE* 3.3 24.9 + - - +
264A PRO* 3.6 16.3 - - + +
265A GLY 3.5 11.3 + - - -
271A GLN* 3.3 20.1 + - - +
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Residues in contact with TYR 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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188A ARG 5.5 0.9 - - - -
190A LEU 3.5 20.2 - - - +
191A LYS* 3.8 13.0 - - + -
192A PRO* 3.5 27.2 - - + +
224A VAL* 3.5 29.7 - - + +
225A VAL 3.8 6.3 - - - -
226A THR* 3.2 7.2 + - + +
228A TYR* 1.3 94.4 - + + +
230A ARG* 1.3 63.6 + - - +
247A TRP* 3.4 10.8 - - - -
248A SER* 3.3 22.6 + - - -
251A CYS* 3.6 35.7 - - + -
252A ILE* 4.4 5.6 - - + -
255A GLU* 2.5 35.8 + - - -
261A ILE* 4.0 11.5 - - + +
262A LEU 6.1 0.2 - - - -
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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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188A ARG* 3.1 37.1 - - - +
189A ASP* 2.3 33.7 + - - -
212A ARG* 5.0 8.7 - - - +
226A THR* 3.3 39.6 + - + +
227A ARG 3.5 8.0 + - - +
228A TYR 3.5 3.1 - - - +
229A TYR* 1.3 79.3 - - - +
231A ALA* 1.3 64.0 + - - +
232A PRO* 3.9 0.5 - - - +
234A VAL* 3.7 22.0 - - + -
235A ILE* 3.7 22.2 - - + +
247A TRP* 3.3 10.5 + - - -
268A TYR* 3.0 28.5 + - - -
271A GLN* 5.4 2.9 + - - +
275A VAL* 6.1 0.9 - - - +
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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