Contacts of the helix formed by residues 230 - 246 (chain A) in PDB entry 2HRC
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A TRP* 3.5 19.4 + - + +
228A PRO 3.7 0.6 - - - -
229A THR* 1.3 75.1 - - - +
231A HIS* 1.3 77.8 + + - +
232A LEU* 3.1 41.3 + - + -
233A LEU* 3.0 28.4 + - + +
234A ILE* 3.0 11.1 + - - +
380A ALA* 3.9 16.2 - - - +
383A ASP* 2.7 31.2 + - - +
384A LEU* 3.3 38.3 + - + +
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Residues in contact with HIS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR 3.1 5.9 + - - -
230A HIS* 1.3 83.8 + + - +
232A LEU* 1.3 85.3 + - + +
234A ILE* 3.5 5.0 + - - +
235A GLN* 3.0 26.3 + - - +
286A LYS* 4.3 11.7 - - - +
290A ARG* 5.6 1.0 - - - -
383A ASP* 3.4 28.4 - - - -
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Residues in contact with LEU 232 (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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230A HIS* 3.1 16.4 + - + -
231A HIS* 1.3 100.6 - - + +
233A LEU* 1.3 66.6 + - - +
235A GLN* 3.5 23.6 - - - +
236A CYS* 3.0 27.5 + - - -
376A LEU* 4.3 16.1 - - + +
379A LYS* 3.9 32.8 - - + +
380A ALA* 3.6 29.2 - - + +
383A ASP* 4.3 6.3 - - + -
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Residues in contact with LEU 233 (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 PRO* 3.7 21.1 - - + -
227A TRP* 3.7 42.0 - - + +
228A PRO 4.2 12.1 - - - +
230A HIS* 3.0 20.3 + - + +
232A LEU* 1.3 77.2 - - - +
234A ILE* 1.3 64.6 + - + +
236A CYS* 3.2 7.4 + - - +
237A PHE* 3.1 53.7 + - + -
283A THR* 4.9 2.5 - - + -
338A THR* 4.4 5.2 - - + -
371A LEU* 3.6 20.2 - - + -
377A PHE* 4.2 4.5 - - + -
380A ALA* 4.1 6.4 - - + +
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Residues in contact with ILE 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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228A PRO 3.9 11.2 - - - +
229A THR* 3.9 1.6 - - - +
230A HIS 3.0 13.4 + - - +
231A HIS* 3.6 7.4 - - - +
233A LEU* 1.3 81.2 - - + +
235A GLN* 1.3 56.0 + - - +
237A PHE* 3.3 3.0 + - - +
238A ALA* 2.9 27.2 + - - +
283A THR* 3.8 29.6 - - + +
286A LYS* 3.5 66.2 - - + +
287A VAL* 3.8 12.6 - - + +
290A ARG* 4.3 12.6 - - + -
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A HIS* 3.0 17.0 + - - +
232A LEU* 3.5 25.6 - - - +
234A ILE* 1.3 76.7 - - - +
236A CYS* 1.3 57.7 + - - +
238A ALA* 3.3 0.7 + - - +
239A ASP* 2.8 46.5 + - - +
290A ARG* 3.3 43.8 + - - +
376A LEU* 3.8 22.5 - - + +
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Residues in contact with CYS 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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232A LEU 3.0 21.7 + - - -
233A LEU 3.2 8.0 + - - +
235A GLN* 1.3 76.3 - - - +
237A PHE* 1.3 63.9 + - - +
239A ASP* 3.3 5.8 + - - +
240A HIS* 3.0 28.9 + - - +
371A LEU* 3.8 23.3 - - + -
374A ASN* 4.2 8.7 - - - +
376A LEU* 3.7 21.1 - - - -
377A PHE* 3.6 40.8 - - - -
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Residues in contact with PHE 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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192A PRO* 5.6 2.0 - - + -
193A GLN* 5.4 0.4 - - - -
233A LEU* 3.1 50.2 + - + -
234A ILE* 3.3 6.0 + - - +
236A CYS* 1.3 77.5 - - - +
238A ALA* 1.3 63.9 + - - +
240A HIS* 3.3 4.8 + - + +
241A ILE* 2.9 31.7 + - + +
283A THR* 4.2 6.1 - - + -
287A VAL* 3.8 20.4 - - + -
333A VAL* 4.8 5.8 - - + -
334A PRO 3.5 20.2 - - - -
335A ILE* 3.7 43.7 - - + -
337A PHE 4.2 13.2 - - - -
338A THR* 5.1 1.3 - - + -
369A GLU 6.2 0.2 - - - -
370A SER* 6.5 0.4 - - - -
371A LEU* 4.1 23.1 - - + -
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Residues in contact with ALA 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 ILE 2.9 16.8 + - - +
235A GLN 3.6 4.3 - - - +
237A PHE* 1.3 77.7 - - - +
239A ASP* 1.3 64.6 + - - +
241A ILE* 3.2 3.3 + - - +
242A LEU* 3.0 31.6 + - + +
287A VAL* 4.4 9.6 - - + +
290A ARG* 3.6 29.8 - - + +
291A LEU* 3.9 20.5 - - + +
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Residues in contact with ASP 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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235A GLN* 2.8 38.0 + - - +
236A CYS* 3.6 5.8 - - - +
238A ALA* 1.3 75.8 - - - +
240A HIS* 1.3 64.3 + - + +
242A LEU* 3.3 11.3 + - - +
243A LYS* 3.0 44.4 + - - +
290A ARG* 5.0 3.5 + - - -
374A ASN* 5.4 3.3 - - - +
376A LEU* 3.8 20.1 - - - +
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Residues in contact with HIS 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 CYS 3.0 19.5 + - - +
237A PHE* 3.8 7.0 - - + +
239A ASP* 1.3 81.0 - - + +
241A ILE* 1.3 62.6 + - - +
243A LYS* 3.6 16.0 + - + +
244A GLU* 3.2 24.1 + - - +
368A ALA* 4.0 10.2 - - + +
369A GLU* 2.7 52.5 + - + +
370A SER 3.3 19.6 + - - -
371A LEU* 3.8 17.4 + - + -
374A ASN* 3.1 31.6 + - + +
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Residues in contact with ILE 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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237A PHE* 2.9 20.7 + - + +
238A ALA 3.6 4.0 - - - +
240A HIS* 1.3 74.4 - - - +
242A LEU* 1.3 61.4 + - - +
244A GLU* 3.2 3.6 + - - +
245A LEU* 2.9 39.1 + - + +
258A ILE* 4.2 7.4 - - + -
260A PHE* 3.9 19.5 - - + -
287A VAL* 3.6 31.6 - - + -
291A LEU* 3.8 20.9 - - + -
331A LEU* 3.8 18.5 - - + +
333A VAL* 3.7 28.7 - - + -
368A ALA* 4.5 4.3 - - + -
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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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238A ALA* 3.0 22.2 + - + +
239A ASP* 3.8 11.2 - - - +
241A ILE* 1.3 78.0 - - - +
243A LYS* 1.3 62.1 + - + +
245A LEU* 3.3 13.7 + - + +
246A ASP* 3.2 21.7 + - - +
253A ARG* 4.0 24.6 + - - +
291A LEU* 3.5 24.7 - - + -
294A CYS* 4.9 5.6 - - - -
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Residues in contact with LYS 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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239A ASP* 3.0 30.2 + - - +
240A HIS* 3.9 15.9 + - + +
241A ILE 3.3 0.2 - - - -
242A LEU* 1.3 77.3 - - + +
244A GLU* 1.3 61.8 + - - +
246A ASP* 3.5 17.3 + - - +
247A HIS* 3.4 21.0 + - - +
369A GLU* 6.0 2.0 - - - +
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Residues in contact with GLU 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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240A HIS 3.2 17.8 + - - +
241A ILE 3.7 3.6 - - - +
243A LYS* 1.3 74.6 - - - +
245A LEU* 1.3 62.5 + - - +
246A ASP 3.1 1.8 - - - -
247A HIS* 2.9 38.2 + - - +
248A PHE* 3.4 10.8 - - - -
331A LEU* 3.5 29.6 - - + -
366A ARG* 3.0 36.5 + - + +
367A ARG 3.5 23.1 - - - +
368A ALA* 4.0 3.8 - - - -
369A GLU* 4.3 11.1 + - - +
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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
----------------------------------------------------------
241A ILE* 2.9 33.1 + - + +
242A LEU* 3.6 22.2 - - + +
244A GLU* 1.3 77.1 - - - +
246A ASP* 1.3 61.3 + - - +
247A HIS 3.1 1.0 + - - -
248A PHE* 3.1 24.0 + - + +
253A ARG* 4.0 33.3 - - + +
256A VAL* 3.7 38.4 - - + -
258A ILE* 5.0 2.5 - - + -
294A CYS* 4.4 7.4 - - - -
295A ASN* 3.8 24.7 - - - +
331A LEU* 3.9 13.7 - - + -
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Residues in contact with ASP 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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242A LEU 3.2 11.5 + - - +
243A LYS* 3.5 14.4 - - - +
244A GLU 3.1 0.4 - - - -
245A LEU* 1.3 78.8 - - - +
247A HIS* 1.3 66.2 + - - +
248A PHE 3.4 5.2 - - - +
253A ARG* 5.2 6.0 - - - +
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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