Contacts of the helix formed by residues 234 - 246 (chain A) in PDB entry 1E0C
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 HIS 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLN* 4.1 0.2 - - - +
90A GLU* 2.6 40.0 + - - -
93A GLY* 3.3 13.5 - - - +
94A TRP* 3.3 60.1 + + + -
97A ARG* 4.5 1.3 - - - +
195A TRP* 4.3 10.9 - + - -
230A CSS 3.4 4.5 - - - -
232A THR* 3.2 15.0 - - - +
233A HIS* 1.3 76.9 - - - +
235A ARG* 1.3 70.3 + - + +
236A SER 3.2 0.7 - - - -
237A GLY* 2.8 17.8 + - - -
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Residues in contact with ARG 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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168A ALA* 4.3 3.8 - - - +
169A ARG* 3.6 13.1 - - - +
170A SER* 3.6 14.8 - - - +
173A GLU* 2.8 43.2 + - - -
178A LYS* 5.9 0.4 - - - +
180A LEU* 5.1 2.6 - - - +
194A GLU* 5.1 1.8 + - - -
195A TRP* 3.2 72.8 - - + +
230A CSS 3.3 20.1 - - + -
231A GLN* 3.5 24.9 - - - +
234A HIS* 1.3 87.9 - - + +
236A SER* 1.3 57.8 + - - +
238A LEU* 3.1 19.6 + - - +
239A THR 3.8 0.7 + - - -
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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
----------------------------------------------------------
168A ALA* 4.0 2.7 - - - +
228A THR* 3.7 2.5 - - - +
229A HIS* 3.3 37.6 - - - -
230A CSS 3.3 6.0 - - - +
233A HIS* 2.8 38.3 + - - -
235A ARG* 1.3 74.7 - - - +
237A GLY* 1.3 63.8 + - - +
238A LEU 3.2 0.4 - - - -
239A THR* 3.1 16.4 - - - -
240A TYR* 2.9 26.0 + - - +
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Residues in contact with GLY 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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93A GLY 3.6 0.2 - - - -
96A GLY* 3.1 21.1 - - - -
97A ARG* 3.4 26.0 - - - -
233A HIS* 3.8 8.9 - - - -
234A HIS 2.8 14.5 + - - -
236A SER* 1.3 80.2 + - - +
238A LEU* 1.3 62.0 + - - +
240A TYR* 3.6 1.7 - - - +
241A LEU 3.0 17.2 + - - -
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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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91A GLY 3.5 25.6 - - - +
92A GLY* 3.5 24.1 + - - +
93A GLY* 3.9 4.2 - - - -
112A TYR* 5.0 1.6 - - - +
195A TRP* 3.4 29.8 - - + +
198A ALA* 4.4 1.6 - - + -
199A MET* 3.8 18.8 - - + -
207A ILE* 4.5 12.1 - - + -
235A ARG 3.1 12.7 + - - +
237A GLY* 1.3 78.1 - - - +
239A THR* 1.3 58.2 + - - +
241A LEU* 3.1 15.3 + - + +
242A ILE* 2.8 50.9 + - + +
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Residues in contact with THR 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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166A TRP* 3.2 54.3 - - + +
168A ALA* 3.6 20.3 - - + +
195A TRP* 4.1 19.1 - - + +
198A ALA* 5.4 0.4 - - + -
228A THR* 2.7 25.2 + - - -
236A SER* 3.1 15.5 + - - -
238A LEU* 1.3 78.1 - - + +
240A TYR* 1.3 63.7 + - - +
242A ILE* 3.3 2.4 + - + -
243A ALA* 3.0 21.3 + - - +
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Residues in contact with TYR 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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96A GLY 4.3 5.4 - - - -
99A ILE* 4.5 3.8 - - + -
100A TRP* 3.6 33.9 - + + -
103A ASP* 2.5 34.3 + - - +
147A PRO* 3.5 24.1 - - - +
228A THR* 3.7 10.4 - - + +
233A HIS* 4.3 4.0 - - - +
236A SER 2.9 18.7 + - - +
237A GLY 3.6 4.7 - - - +
239A THR* 1.3 77.6 + - - +
241A LEU* 1.3 64.9 + - - +
243A ALA* 3.4 2.9 + - - +
244A LYS* 2.9 47.8 + - + +
251A VAL* 3.8 23.1 + - + +
252A LYS 3.9 4.5 - - - -
253A GLY* 3.6 32.5 - - - -
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Residues in contact with LEU 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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9A LEU* 3.4 33.7 - - + -
10A VAL* 4.9 0.2 - - + -
92A GLY 4.4 4.9 - - - +
96A GLY* 3.8 22.9 - - - +
99A ILE* 3.8 17.3 - - + -
112A TYR* 3.4 43.7 - - + -
207A ILE* 5.2 4.0 - - + -
237A GLY 3.0 10.1 + - - +
238A LEU* 3.1 13.7 + - + +
240A TYR* 1.3 85.0 - - + +
242A ILE* 1.3 58.1 + - - +
244A LYS* 3.2 6.3 + - - +
245A ALA* 2.8 29.4 + - + +
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Residues in contact with ILE 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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166A TRP* 3.9 17.3 - - + -
198A ALA* 3.5 31.6 - - + -
207A ILE* 4.0 31.6 - - + -
211A ILE* 3.7 25.6 - - + -
215A LEU* 4.1 1.3 - - + -
238A LEU* 2.8 39.1 + - + +
239A THR* 3.3 5.6 + - - +
241A LEU* 1.3 72.8 - - - +
243A ALA* 1.3 64.9 + - - +
245A ALA* 3.1 6.5 + - - +
246A LEU* 2.8 37.0 + - + +
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Residues in contact with ALA 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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166A TRP* 4.5 10.1 - - + -
215A LEU* 5.5 0.2 - - - -
226A ILE* 4.7 8.5 - - + -
239A THR 3.0 16.8 + - - +
240A TYR 3.8 2.2 - - - +
242A ILE* 1.3 78.8 - - - +
244A LYS* 1.3 64.0 + - - +
246A LEU* 3.4 1.4 + - - -
247A GLY 3.4 2.8 + - - -
248A TYR* 3.0 49.0 + - + +
251A VAL* 3.7 25.6 - - + -
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Residues in contact with LYS 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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9A LEU* 4.0 18.4 - - + +
99A ILE* 5.5 2.2 - - + -
103A ASP* 3.6 16.4 + - - +
110A TYR* 4.5 8.9 + - - +
240A TYR* 2.9 56.2 + - + +
241A LEU* 3.5 6.7 - - - +
243A ALA* 1.3 76.5 - - - +
245A ALA* 1.3 59.9 + - - +
247A GLY* 3.0 19.4 + - - -
248A TYR 4.6 7.8 + - - +
249A PRO 5.6 3.2 + - - -
251A VAL* 3.6 33.3 + - + +
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Residues in contact with ALA 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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9A LEU* 3.8 20.1 - - + +
10A VAL* 3.5 31.2 - - + -
207A ILE* 5.3 1.6 - - + -
241A LEU 2.8 21.3 + - - +
242A ILE* 3.1 9.1 + - - +
244A LYS* 1.3 73.3 - - - +
246A LEU* 1.3 63.4 + - + +
247A GLY* 3.3 1.4 + - - -
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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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211A ILE* 4.0 24.2 - - + -
212A ALA* 4.2 20.6 - - + -
215A LEU* 3.7 30.5 - - + -
242A ILE* 2.8 27.7 + - + +
244A LYS 3.2 0.4 - - - -
245A ALA* 1.3 78.6 - - + +
247A GLY* 1.3 59.4 + - - +
248A TYR* 3.5 25.8 - - + -
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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