Contacts of the helix formed by residues 234 - 249 (chain A) in PDB entry 3HPD
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 TYR 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A LEU* 4.0 0.7 - - - -
232A ALA* 3.4 1.2 - - - +
233A LYS* 1.3 107.7 - - + +
235A PRO* 1.3 67.2 - - + +
236A GLY 3.3 2.8 + - - +
237A SER* 3.4 11.8 + - - +
238A PHE* 2.8 35.4 + - - +
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Residues in contact with PRO 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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186A LEU* 4.1 12.0 - - + -
189A ARG* 3.8 41.1 - - + +
190A VAL* 4.0 8.9 - - + +
233A LYS 4.6 0.2 - - - +
234A TYR* 1.3 89.1 - - + -
236A GLY* 1.3 57.8 + - - +
238A PHE* 3.8 5.7 - - + +
239A HIS* 3.0 29.6 + - - +
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Residues in contact with GLY 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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234A TYR* 3.3 2.0 + - - +
235A PRO* 1.3 78.6 - - - +
237A SER* 1.3 62.0 + - - +
239A HIS* 3.3 14.4 + - - +
240A VAL* 3.3 18.1 + - - +
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Residues in contact with SER 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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232A ALA* 3.5 17.7 - - - -
234A TYR* 3.4 13.6 + - - +
236A GLY* 1.3 72.5 - - - +
238A PHE* 1.3 65.5 + - - +
240A VAL* 3.3 10.1 + - - +
241A LYS* 3.1 28.2 + - - +
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Residues in contact with PHE 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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184A HIS* 4.8 2.9 - - + -
186A LEU* 3.5 50.3 - - + -
187A LEU* 3.8 32.1 - - + -
190A VAL* 3.6 20.4 - - + -
225A ALA* 3.3 26.7 - - + -
228A ALA* 3.7 6.7 - - + -
229A TYR* 3.7 23.1 - - + -
232A ALA* 3.5 17.2 - - - +
234A TYR 2.8 20.5 + - - +
235A PRO 3.8 1.3 - - - +
237A SER* 1.3 75.5 - - - +
239A HIS* 1.3 63.4 + - - +
241A LYS* 3.2 12.0 + - - +
242A LEU* 3.2 22.7 + - + +
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Residues in contact with HIS 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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29A THR* 3.5 13.5 + - - -
190A VAL* 3.8 29.6 - - + +
191A THR* 5.8 2.9 - - + -
196A MET* 3.6 10.0 - - + +
235A PRO 3.0 18.6 + - - +
236A GLY* 3.5 7.4 - - - +
237A SER 3.3 0.4 - - - -
238A PHE* 1.3 76.5 - - - +
240A VAL* 1.3 64.5 + - + +
242A LEU* 3.2 25.1 + - + +
243A TYR* 2.7 39.6 + + - -
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Residues in contact with VAL 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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236A GLY 3.3 14.1 + - - +
237A SER* 3.6 10.5 - - - +
238A PHE 3.3 0.6 - - - -
239A HIS* 1.3 79.1 - - + +
241A LYS* 1.3 67.3 + - + +
242A LEU 3.2 0.7 + - - -
243A TYR* 3.3 24.8 + - + +
244A ASP* 3.5 20.1 + - - +
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Residues in contact with LYS 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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228A ALA* 3.5 25.5 - - + +
231A GLU* 3.0 50.5 + - + +
232A ALA* 4.0 12.8 - - + -
237A SER* 3.1 15.7 + - - +
238A PHE 3.2 3.8 + - - +
240A VAL* 1.3 77.0 - - + +
242A LEU* 1.3 64.5 + - - +
244A ASP* 3.6 23.9 + - + +
245A TRP* 3.0 28.3 + - + +
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Residues in contact with LEU 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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187A LEU* 4.1 20.9 - - + -
190A VAL* 4.6 1.8 - - + -
193A THR* 4.6 5.4 - - + -
196A MET* 4.4 10.8 - - - -
221A PHE* 4.3 22.0 - - + -
224A ALA* 4.2 3.7 - - + +
225A ALA* 3.7 33.0 - - + +
228A ALA* 3.9 10.1 - - + -
238A PHE* 3.2 24.3 + - + +
239A HIS* 3.3 28.0 - - + +
240A VAL 3.2 1.0 - - - -
241A LYS* 1.3 77.6 - - - +
243A TYR* 1.3 58.9 + - + +
245A TRP* 3.4 2.1 + - - +
246A LEU* 3.0 35.6 + - + +
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Residues in contact with TYR 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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29A THR* 2.9 38.1 + - - -
32A ASN* 3.8 30.3 - - + -
33A ALA* 3.7 13.7 - - + -
36A ALA* 3.3 19.2 - - + +
196A MET* 3.2 13.4 - - + +
239A HIS* 2.7 53.2 + + - -
240A VAL* 3.3 13.0 + - + +
241A LYS 3.3 0.4 - - - -
242A LEU* 1.3 74.8 - - + +
244A ASP* 1.3 69.4 + - - +
246A LEU* 3.3 3.7 + - + -
247A TYR* 3.3 18.7 + - - +
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Residues in contact with ASP 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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231A GLU* 5.4 0.9 - - - +
240A VAL* 3.5 19.9 + - - +
241A LYS* 3.3 36.5 + - + +
243A TYR* 1.3 81.8 - - - +
245A TRP* 1.3 64.9 + - + +
247A TYR* 3.3 6.8 - - - +
248A ARG* 2.9 39.0 + - - +
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Residues in contact with TRP 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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224A ALA* 3.9 26.1 - - + +
227A LYS* 3.4 56.1 + - + -
228A ALA* 3.9 10.5 - - - -
231A GLU* 2.7 27.3 + - + -
241A LYS* 3.0 26.2 + - + +
244A ASP* 1.3 78.3 - - + +
246A LEU* 1.3 59.4 + - - +
247A TYR 2.9 1.8 - - - -
248A ARG* 3.2 65.9 - - + +
249A ILE* 2.8 39.8 + - + +
253A VAL* 4.5 15.0 - - + -
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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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12A ARG* 3.0 20.8 + - - -
33A ALA* 3.9 36.1 - - + +
36A ALA* 3.5 14.8 - - + +
37A LEU* 3.6 14.8 - - + +
196A MET* 5.9 0.9 - - - -
200A LEU* 4.0 25.4 - - + -
220A THR* 4.2 19.1 - - + -
221A PHE* 4.2 16.8 - - + -
224A ALA* 3.9 18.1 - - + +
242A LEU* 3.0 25.4 + - + +
243A TYR* 3.3 8.9 + - + +
245A TRP* 1.3 77.0 - - - +
247A TYR* 1.3 57.1 + - - +
249A ILE* 3.5 4.9 - - - +
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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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12A ARG* 3.4 14.8 + - - +
35A LEU 5.3 1.8 - - - -
36A ALA* 3.1 28.7 + - + +
243A TYR 3.3 10.9 + - - +
244A ASP* 3.3 10.1 - - - +
245A TRP 2.9 0.2 - - - -
246A LEU* 1.3 80.2 - - - +
248A ARG* 1.3 73.0 + - + +
249A ILE 3.5 0.4 - - - +
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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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231A GLU* 4.2 12.7 + - - -
244A ASP* 2.9 27.6 + - - +
245A TRP* 3.2 53.4 + - + +
247A TYR* 1.3 85.4 - - + +
249A ILE* 1.3 69.1 + - - +
250A ASN* 3.2 16.5 + - - +
253A VAL* 4.7 0.9 - - - +
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Residues in contact with ILE 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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8A LEU* 4.0 4.9 - - + +
12A ARG* 2.7 51.3 + - - +
220A THR* 3.8 45.3 - - + +
223A ILE* 3.9 21.5 - - + -
224A ALA* 4.9 2.0 - - + +
245A TRP* 2.8 29.6 + - + +
246A LEU* 3.5 6.7 - - - +
248A ARG* 1.3 74.0 - - - +
250A ASN* 1.3 56.1 + - - +
253A VAL* 4.1 16.4 - - + -
254A ILE* 3.8 28.0 - - + -
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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