Contacts of the helix formed by residues 233 - 244 (chain A) in PDB entry 4D2W
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 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLU* 2.8 30.8 + - - -
231A TRP 3.5 4.8 + - - -
232A LEU* 1.3 73.2 - - - +
234A PRO* 1.3 73.5 - - - +
235A SER* 3.5 6.5 + - - -
236A SER* 3.1 21.4 + - - -
237A ILE* 3.1 20.1 + - - +
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Residues in contact with PRO 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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232A LEU 4.5 1.8 - - - +
233A SER* 1.3 84.6 - - - +
235A SER* 1.4 61.1 + - - +
237A ILE* 3.2 14.3 + - + +
238A LEU* 3.0 25.7 + - - +
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Residues in contact with SER 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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106A GLU* 4.7 0.4 - - - -
233A SER* 3.3 8.5 + - - -
234A PRO* 1.4 78.6 - - - +
236A SER* 1.3 56.8 + - - +
238A LEU* 3.4 7.8 + - - +
239A LEU* 3.1 25.5 + - - +
260A HIS* 5.0 2.6 - - - -
261A PRO* 5.6 1.0 - - - +
262A TRP* 3.4 23.5 + - - +
265A GLN* 2.8 33.6 + - - -
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Residues in contact with SER 236 (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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106A GLU* 3.7 4.7 + - - -
199A LEU* 4.9 1.0 - - - +
203A MET* 3.3 31.9 - - - -
232A LEU* 4.3 7.2 - - - -
233A SER* 3.1 27.4 + - - -
235A SER* 1.3 71.8 - - - +
237A ILE* 1.3 60.1 + - - +
239A LEU* 3.5 2.5 + - - +
240A LEU* 2.9 35.7 + - - +
262A TRP* 2.9 27.4 + - - +
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Residues in contact with ILE 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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226A TYR* 4.9 0.9 + - - -
228A VAL* 3.6 41.5 - - + -
232A LEU* 3.7 22.9 - - + +
233A SER 3.1 19.3 + - - +
234A PRO* 3.2 13.7 + - + +
236A SER* 1.3 75.2 - - - +
238A LEU* 1.3 59.3 + - - +
240A LEU* 3.4 9.3 + - - +
241A GLN* 3.0 34.6 + - + +
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Residues in contact with LEU 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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234A PRO 3.0 16.6 + - - +
235A SER* 3.7 7.9 - - - +
237A ILE* 1.3 74.3 - - - +
239A LEU* 1.3 65.4 + - - +
241A GLN* 3.1 43.0 - - - +
242A GLN* 3.1 31.3 + - + +
260A HIS* 5.2 6.5 - - + +
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Residues in contact with LEU 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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113A PHE* 4.7 4.0 - - + -
199A LEU* 3.7 22.0 - - + -
235A SER 3.1 15.2 + - - +
236A SER* 4.1 3.4 - - - +
238A LEU* 1.3 74.4 - - - +
240A LEU* 1.3 62.7 + - - +
242A GLN* 3.2 9.4 + - + +
243A MET* 3.1 32.6 + - + +
252A ILE* 4.5 4.3 - - + -
257A LEU* 3.8 20.6 - - + -
260A HIS* 3.8 35.4 - - + +
262A TRP* 3.6 41.5 - - + -
263A ILE* 4.6 7.4 - - + -
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Residues in contact with LEU 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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196A GLY* 3.5 26.0 - - - +
199A LEU* 3.8 16.2 - - + -
200A TYR* 3.7 32.5 - - + +
203A MET* 4.4 8.5 - - + -
226A TYR* 3.7 15.9 - - + +
228A VAL* 6.2 0.9 - - + -
232A LEU* 3.9 29.8 - - + -
236A SER 2.9 24.5 + - - +
237A ILE* 3.7 6.5 - - - +
239A LEU* 1.3 75.7 - - - +
241A GLN* 1.3 56.9 + - - +
243A MET* 3.4 2.1 + - - +
244A LEU* 2.9 44.1 + - + +
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Residues in contact with GLN 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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226A TYR* 3.7 12.7 + - - +
237A ILE* 3.0 25.6 + - - +
238A LEU* 3.1 43.7 - - - +
240A LEU* 1.3 76.4 - - - +
242A GLN* 1.3 63.0 + - - +
244A LEU* 3.7 6.4 + - - +
245A GLN* 2.8 34.1 + - - +
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Residues in contact with GLN 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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238A LEU* 3.1 31.7 + - + +
239A LEU* 3.2 6.7 + - + +
241A GLN* 1.3 81.1 - - + +
243A MET* 1.4 59.4 + - - +
245A GLN* 3.7 6.2 - - - +
250A LYS 4.5 0.8 - - - +
251A ARG* 3.5 8.5 - - - +
252A ILE* 2.9 55.0 + - + +
260A HIS* 2.8 30.2 + - - -
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Residues in contact with MET 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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113A PHE* 3.9 13.5 - - + -
192A VAL* 3.5 26.5 - - + +
193A TRP* 3.8 12.0 + - - -
195A MET* 3.6 20.2 - - + -
196A GLY* 3.7 19.5 - - - +
199A LEU* 4.0 26.0 - - - -
239A LEU* 3.1 27.2 + - + +
240A LEU* 4.1 2.7 - - - +
242A GLN* 1.4 74.3 - - - +
244A LEU* 1.3 59.2 + - - +
245A GLN 3.3 2.5 - - - -
251A ARG* 3.0 26.1 - - - +
252A ILE* 3.8 15.7 - - + -
257A LEU* 3.9 22.9 - - + -
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Residues in contact with LEU 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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193A TRP* 3.6 48.4 - - + +
196A GLY* 3.8 10.3 - - - +
197A ILE* 3.7 23.1 - - + +
200A TYR* 5.0 0.9 - - + -
208A PRO* 4.5 17.0 - - + -
209A PHE* 4.6 1.6 - - + -
224A GLY 4.9 4.7 - - - +
226A TYR* 3.7 42.8 + - + +
240A LEU* 2.9 32.5 + - + +
241A GLN* 3.8 7.3 - - - +
243A MET* 1.3 76.3 - - - +
245A GLN* 1.3 59.4 + - - +
246A VAL* 3.8 2.8 + - - +
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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