Contacts of the helix formed by residues 222 - 231 (chain A) in PDB entry 4Y2H
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 LEU 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A TRP* 4.1 26.2 - - + -
219A MET* 3.0 39.7 + - + +
221A CYS* 1.3 84.7 - - - +
223A GLU* 1.3 63.9 + - - +
224A GLY 3.3 2.5 - - - -
225A PHE* 3.1 16.1 + - + +
226A ALA* 2.9 22.9 + - - +
93B THR* 4.1 18.6 - - + -
119B GLN* 3.6 37.9 - - + +
122B GLU* 5.0 6.7 - - + +
123B VAL* 4.0 19.1 - - + -
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Residues in contact with GLU 223 (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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205A LEU* 3.7 32.7 - - + +
206A GLY* 4.5 4.2 - - - -
208A TRP* 4.3 4.2 - - + +
209A SER* 4.4 12.2 + - - +
220A SER 3.3 17.0 + - - +
221A CYS 3.3 0.4 - - - -
222A LEU* 1.3 77.8 - - - +
224A GLY* 1.3 57.8 + - - +
226A ALA* 3.3 8.1 + - - +
227A THR* 2.8 39.3 + - - +
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Residues in contact with GLY 224 (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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221A CYS 4.2 5.7 + - - -
222A LEU 3.3 0.6 - - - -
223A GLU* 1.3 77.0 - - - +
225A PHE* 1.3 60.8 + - - +
227A THR* 3.3 9.2 + - - -
228A ARG* 3.1 39.3 + - - +
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Residues in contact with PHE 225 (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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208A TRP* 6.1 0.2 - + - -
221A CYS 5.0 1.0 + - - +
222A LEU* 3.1 23.3 + - + +
224A GLY* 1.3 72.2 - - - +
226A ALA* 1.3 67.2 + - - +
228A ARG* 3.4 26.1 + - + +
229A CYS* 3.1 42.4 + - - -
52B SER 3.4 24.7 - - - -
54B VAL* 3.7 29.6 - - + -
57B HIS* 6.4 0.2 - - + -
116B ILE* 3.6 26.5 - - + -
119B GLN* 3.6 39.5 - - + +
122B GLU* 6.0 0.7 - - - +
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Residues in contact with ALA 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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204A ARG 4.8 1.3 - - - +
205A LEU* 4.0 17.3 - - + -
208A TRP* 3.7 27.1 - - + +
222A LEU 2.9 13.6 + - - +
223A GLU* 3.5 9.0 - - - +
225A PHE* 1.3 78.2 - - - +
227A THR* 1.3 56.7 + - - +
229A CYS* 3.3 1.4 + - - +
230A LEU* 2.8 38.9 + - + +
54B VAL* 4.0 17.3 - - + -
58B GLU* 6.2 0.2 - - - +
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Residues in contact with THR 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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205A LEU* 3.9 18.6 - - + +
223A GLU* 2.8 25.2 + - - +
224A GLY* 3.4 11.0 - - - -
226A ALA* 1.3 76.3 - - - +
228A ARG* 1.3 57.7 + - + +
231A MET* 2.7 45.0 + - - +
232A GLY 3.3 0.5 + - - -
326A ASN 3.8 17.5 - - - +
327A GLU* 3.8 22.4 - - + -
328A PRO* 4.1 10.1 - - + +
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Residues in contact with ARG 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 GLY* 3.1 30.8 + - - +
225A PHE* 3.7 37.3 - - + +
226A ALA 3.4 0.2 - - - -
227A THR* 1.3 76.4 - - + +
229A CYS* 1.3 64.4 + - - +
232A GLY* 3.1 28.5 + - - +
233A HIS* 3.9 0.7 + - - +
326A ASN 5.1 1.6 - - - -
119B GLN* 3.9 11.3 - - - +
122B GLU* 5.6 2.0 + - - -
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Residues in contact with CYS 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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225A PHE* 3.1 40.9 + - - +
226A ALA 3.7 0.2 - - - +
227A THR 3.3 0.2 - - - -
228A ARG* 1.3 78.7 - - - +
230A LEU* 1.3 60.3 + - + +
233A HIS* 3.3 21.3 - - - +
52B SER 4.7 0.4 - - - -
53B ASP* 3.2 30.4 - - - +
54B VAL* 3.4 34.3 - - + -
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Residues in contact with LEU 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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201A LEU* 3.9 29.5 - - + +
204A ARG* 3.6 52.3 - - + +
205A LEU* 3.9 16.4 - - + -
226A ALA* 2.8 21.1 + - + +
229A CYS* 1.3 75.7 - - + +
231A MET* 1.3 62.7 + - - +
233A HIS* 2.9 20.6 + - - -
324A TYR* 3.8 11.8 - - - -
53B ASP* 5.1 1.1 - - - +
54B VAL* 3.7 20.6 - - + -
55B SER* 3.8 6.5 - - - +
58B GLU* 4.6 2.5 - - - +
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Residues in contact with MET 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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201A LEU* 3.8 22.0 - - + -
205A LEU* 3.8 21.3 - - + -
227A THR* 2.7 22.8 + - + +
230A LEU* 1.3 78.8 - - + +
232A GLY* 1.3 55.7 + - - +
233A HIS* 3.4 5.9 + - - +
286A HIS* 3.3 41.1 - - + +
324A TYR* 4.0 10.4 - - + +
325A LEU 3.0 22.3 - - - +
326A ASN 3.5 6.7 - - - +
327A GLU 3.6 19.7 - - - -
328A PRO* 3.7 20.0 - - - -
369A LYS* 3.0 23.7 + - - -
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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