Contacts of the helix formed by residues 235 - 249 (chain A) in PDB entry 4Z30
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A VAL* 4.1 4.3 - - - -
233A GLN 3.4 5.3 + - - -
234A ALA* 1.3 75.0 - - - +
236A LYS* 1.3 63.2 + - - +
237A THR* 3.5 9.0 + - - -
238A SER* 2.6 48.0 + - - -
239A ILE* 3.1 14.0 + - - +
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Residues in contact with LYS 236 (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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220A VAL* 3.6 26.4 - - + +
221A LEU* 6.5 0.4 - - + -
224A VAL* 4.2 7.4 - - + +
235A SER* 1.3 71.6 - - - +
237A THR* 1.3 57.7 + - - +
240A GLY* 2.8 27.2 + - - -
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Residues in contact with THR 237 (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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190A GLN* 5.3 0.4 - - - +
235A SER* 3.1 9.4 + - - -
236A LYS* 1.3 74.8 - - - +
238A SER* 1.3 64.8 + - - +
240A GLY* 3.4 2.4 + - - -
241A HIS* 3.1 50.4 + - + +
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Residues in contact with SER 238 (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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190A GLN* 3.4 23.0 - - - +
192A LEU* 3.9 20.8 - - - +
196A MET* 5.3 0.9 - - - +
233A GLN 4.6 1.8 + - - -
234A ALA* 4.1 4.9 - - - -
235A SER* 2.6 43.9 + - - -
237A THR* 1.3 70.8 - - - +
239A ILE* 1.3 67.2 + - - +
241A HIS* 3.1 14.0 + - - +
242A VAL* 3.1 16.3 + - - +
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Residues in contact with ILE 239 (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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192A LEU* 4.0 20.2 - - + -
200A ALA* 4.7 6.7 - - + -
204A VAL* 6.1 0.9 - - + -
220A VAL* 4.0 21.3 - - + +
223A VAL* 3.9 30.3 - - + -
224A VAL* 3.4 26.2 - - + -
227A LEU* 3.8 26.5 - - + -
234A ALA* 4.5 8.1 - - + -
235A SER 3.1 11.9 + - - +
238A SER* 1.3 72.4 + - - +
240A GLY* 1.3 67.4 + - - +
242A VAL* 3.0 17.2 + - + +
243A VAL* 3.0 17.6 + - + +
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Residues in contact with GLY 240 (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 ARG* 4.9 6.2 + - - -
220A VAL* 4.1 15.8 - - - +
236A LYS 2.8 19.3 + - - -
237A THR* 3.6 2.9 - - - -
238A SER 3.3 0.4 - - - -
239A ILE* 1.3 75.1 - - - +
241A HIS* 1.3 58.7 + - - +
243A VAL* 3.0 8.6 + - - +
244A GLN* 2.8 27.6 + - - +
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Residues in contact with HIS 241 (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 GLY* 3.1 31.1 - - - +
189A CYS* 3.5 11.2 - - - -
190A GLN* 2.5 42.9 + - + +
237A THR* 3.1 34.5 + - + +
238A SER 3.1 6.6 + - - +
240A GLY* 1.3 76.8 - - - +
242A VAL* 1.3 56.6 + - - +
244A GLN* 3.7 3.3 - - + +
245A LEU* 2.8 24.6 + - - +
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Residues in contact with VAL 242 (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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190A GLN 4.3 5.8 - - - +
192A LEU* 3.5 20.2 - - + -
197A GLN* 3.2 33.0 - - - +
200A ALA* 4.7 11.9 - - + -
201A LEU* 4.2 24.0 - - + +
204A VAL* 5.7 3.4 - - + -
238A SER 3.1 14.5 + - - +
239A ILE* 3.0 14.7 + - + +
241A HIS* 1.3 75.8 - - - +
243A VAL* 1.3 63.9 + - + +
245A LEU* 3.1 23.1 - - + +
246A LEU* 3.1 13.0 + - + +
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Residues in contact with VAL 243 (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 VAL* 4.9 11.7 - - + -
216A ARG* 4.3 20.0 - - + +
219A LEU* 4.4 15.5 - - + -
220A VAL* 4.3 16.4 - - + -
223A VAL* 6.1 0.4 - - + -
239A ILE* 3.0 18.7 + - + +
240A GLY* 3.0 9.1 + - - +
242A VAL* 1.3 75.1 - - + +
244A GLN* 1.3 66.5 + - - +
246A LEU* 2.9 10.5 + - - +
247A TYR* 2.9 19.8 + - - +
252A PHE* 3.7 19.5 - - + -
264A MET* 3.9 20.9 - - + -
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Residues in contact with GLN 244 (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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187A ARG 4.7 5.6 + - - +
188A GLY* 4.0 23.1 - - - +
189A CYS* 4.2 4.5 - - - -
216A ARG* 2.7 38.7 + - - +
240A GLY 2.8 17.2 + - - +
241A HIS* 3.3 9.2 + - + +
243A VAL* 1.3 72.7 - - - +
245A LEU* 1.3 56.6 + - - +
247A TYR* 3.1 25.5 + - - +
248A ARG* 2.8 35.7 + - + +
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Residues in contact with LEU 245 (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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184A VAL* 5.6 1.1 - - + -
189A CYS* 3.5 27.3 - - + -
190A GLN 3.7 19.3 - - - +
197A GLN* 4.3 1.3 - - - +
241A HIS 2.8 14.3 + - - +
242A VAL* 3.1 12.8 - - + +
244A GLN* 1.3 76.1 - - - +
246A LEU* 1.3 61.5 + - + +
248A ARG* 3.2 3.1 + - - +
249A ALA* 3.1 20.6 + - - +
280A HIS* 3.3 39.5 - - + +
283A GLN* 3.9 24.9 - - + -
284A ILE* 3.9 21.3 - - + -
287A ILE* 4.3 5.8 - - + -
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Residues in contact with LEU 246 (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* 3.7 31.0 - - + -
204A VAL* 4.4 26.9 - - + -
242A VAL* 3.1 13.0 + - + +
243A VAL* 2.9 10.5 + - - +
245A LEU* 1.3 74.5 - - + +
247A TYR* 1.3 64.9 + - - +
249A ALA* 3.3 5.2 + - + +
250A SER 3.1 4.9 + - - -
251A CYS* 3.1 35.7 + - + +
252A PHE* 3.6 19.5 - - + -
276A LEU* 3.9 25.1 - - + -
280A HIS* 4.1 24.9 - - + -
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Residues in contact with TYR 247 (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 ARG* 3.5 24.7 - - - +
243A VAL 2.9 11.3 + - - +
244A GLN* 3.1 35.4 + - - +
246A LEU* 1.3 75.3 - - - +
248A ARG* 1.3 62.1 + - - +
250A SER* 2.9 22.8 + - - +
251A CYS 4.8 0.7 - - - +
252A PHE* 3.7 22.1 - + + +
254A VAL* 4.1 25.6 - - + +
264A MET* 5.2 1.1 - - - -
1003A UNX 4.4 14.6 - - - -
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Residues in contact with ARG 248 (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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187A ARG* 3.8 29.3 + - - +
189A CYS* 4.2 19.5 - - - -
244A GLN* 2.8 21.0 + - - +
245A LEU 3.2 9.2 + - - +
247A TYR* 1.3 77.1 - - - +
249A ALA* 1.3 57.0 - - - +
250A SER* 3.4 8.1 + - - -
283A GLN* 2.6 48.0 + - + +
286A HIS* 4.0 3.6 + - - -
287A ILE* 3.6 11.7 - - - +
290A GLU* 2.9 42.8 + - - -
1003A UNX 4.6 4.3 - - - -
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Residues in contact with ALA 249 (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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245A LEU* 3.1 9.7 + - + +
246A LEU* 3.7 9.2 - - - +
247A TYR 3.2 0.4 - - - -
248A ARG* 1.3 75.9 - - - +
250A SER* 1.3 68.2 + - - +
251A CYS* 3.4 6.7 + - - -
270A PHE* 5.0 0.2 - - - -
279A GLU* 3.7 49.5 - - + +
280A HIS* 5.0 2.5 - - - +
283A GLN* 3.7 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