Contacts of the helix formed by residues 230 - 244 (chain A) in PDB entry 7EHH
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 ASP 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A LEU* 4.6 0.3 - - - +
224A VAL* 4.1 9.1 - - - +
229A GLY* 1.3 74.6 - - - +
231A ALA* 1.3 65.9 + - - +
232A LYS* 4.1 11.3 - - - +
233A LEU* 3.0 26.5 + - - +
234A PHE* 3.0 22.2 + - - +
705A SO4 3.5 26.3 + - - +
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Residues in contact with ALA 231 (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 VAL* 4.4 8.9 - - + +
230A ASP* 1.3 75.6 - - - +
232A LYS* 1.3 57.7 + - - +
234A PHE 3.2 1.0 + - - -
235A LYS* 2.9 26.7 + - - +
332A TYR* 4.9 5.6 - - - +
333A TRP* 6.0 0.9 - - + -
337A PHE* 3.3 33.4 - - + -
705A SO4 3.2 22.8 + - - +
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Residues in contact with LYS 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 ASP* 3.3 11.7 + - - +
231A ALA* 1.3 77.4 - - - +
233A LEU* 1.3 57.9 + - - +
235A LYS* 3.4 7.2 + - - +
236A GLN* 2.9 29.4 + - - +
705A SO4 4.9 0.6 + - - -
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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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184A LEU* 3.9 26.2 - - + -
185A GLN* 3.5 37.9 - - + +
188A LEU* 4.1 11.4 - - + -
228A PHE 4.1 1.3 - - - +
229A GLY* 4.1 17.7 - - - -
230A ASP* 3.0 22.2 + - - +
232A LYS* 1.3 76.0 - - - +
234A PHE* 1.3 58.0 + - - +
236A GLN* 3.3 22.9 + - - +
237A LEU* 2.9 27.7 + - + +
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Residues in contact with PHE 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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184A LEU* 3.9 19.2 - - + +
204A LEU* 4.3 9.9 - - + -
207A ILE* 3.5 25.6 - - + -
224A VAL* 4.1 8.3 - - + -
230A ASP 3.0 15.8 + - - +
231A ALA 3.2 3.8 + - - +
233A LEU* 1.3 75.2 - - - +
235A LYS* 1.3 60.0 + - - +
237A LEU* 3.2 11.6 + - + +
238A VAL* 2.9 53.1 + - + +
248A VAL* 4.7 2.2 - - + -
250A LEU* 3.6 29.2 - - + -
333A TRP* 3.9 20.0 - + - -
337A PHE* 3.4 36.6 - + + -
339A ILE* 4.0 7.2 - - + -
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Residues in contact with LYS 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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231A ALA 2.9 17.9 + - - +
232A LYS* 3.7 6.3 - - - +
234A PHE* 1.3 76.6 - - - +
236A GLN* 1.3 63.9 + - - +
238A VAL* 3.3 5.1 + - - +
239A GLN* 2.9 55.5 + - - +
336A GLU 3.1 27.9 + - - -
337A PHE* 3.9 27.2 + - + +
338A ASP* 5.4 3.6 - - - +
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Residues in contact with GLN 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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185A GLN* 5.4 0.4 - - - +
188A LEU* 3.6 25.8 - - + +
232A LYS 2.9 14.3 + - - +
233A LEU* 3.5 23.0 - - - +
234A PHE 3.3 0.2 - - - -
235A LYS* 1.3 78.3 - - - +
237A LEU* 1.3 58.2 + - - +
239A GLN* 3.4 6.9 + - - +
240A ALA* 2.9 29.0 + - + +
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Residues in contact with LEU 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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184A LEU* 4.0 32.5 - - + +
187A ILE* 3.9 30.5 - - + -
188A LEU* 4.0 32.7 - - + +
191A LEU* 4.3 10.3 - - + -
202A ILE* 5.6 1.8 - - + -
204A LEU* 4.5 12.1 - - + -
233A LEU* 2.9 16.5 + - + +
234A PHE* 3.2 17.7 + - + +
236A GLN* 1.3 77.0 - - - +
238A VAL* 1.3 59.3 + - + +
240A ALA* 3.3 1.0 + - - +
241A ALA* 2.9 31.7 + - + +
248A VAL* 6.0 3.8 - - + -
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Residues in contact with VAL 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 PHE* 2.9 54.8 + - + +
235A LYS* 3.9 4.5 - - - +
237A LEU* 1.3 76.0 - - + +
239A GLN* 1.3 60.9 + - + +
241A ALA* 3.3 1.9 + - - +
242A HIS* 2.9 54.9 + - + +
248A VAL* 4.4 21.8 - - + -
337A PHE* 3.2 26.9 - - + +
338A ASP* 4.2 4.0 - - + +
339A ILE* 4.6 2.5 - - + +
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Residues in contact with GLN 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 LYS* 2.9 51.0 + - - +
236A GLN* 4.0 5.9 - - - +
238A VAL* 1.3 81.0 - - + +
240A ALA* 1.3 56.1 + - - +
242A HIS* 3.4 8.7 + - - +
243A GLU* 2.9 28.9 + - - +
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Residues in contact with ALA 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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188A LEU* 3.7 13.0 - - + -
191A LEU* 3.6 21.3 - - + -
236A GLN* 2.9 19.8 + - + +
237A LEU 3.8 0.4 - - - +
239A GLN* 1.3 74.1 - - - +
241A ALA* 1.3 64.8 + - - +
243A GLU* 3.2 9.4 + - - +
244A ARG* 3.0 29.0 + - - +
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Residues in contact with ALA 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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191A LEU* 4.0 11.1 - - + +
202A ILE* 4.7 9.0 - - + -
237A LEU* 2.9 19.2 + - + +
238A VAL 3.6 4.7 - - - +
240A ALA* 1.3 76.5 - - - +
242A HIS* 1.3 57.5 + - - +
244A ARG* 3.0 9.9 + - - -
246A ILE* 2.7 54.9 + - + +
248A VAL* 3.9 16.4 - - + -
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Residues in contact with HIS 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 VAL* 2.9 35.3 + - + +
239A GLN* 3.8 8.4 - - - +
241A ALA* 1.3 75.5 - - - +
243A GLU* 1.3 63.0 + - - +
245A GLY* 2.9 13.9 + - - -
246A ILE 3.3 20.4 - - - +
247A ARG* 4.1 5.1 - - + -
248A VAL* 4.4 2.4 + - + -
338A ASP* 3.1 43.1 + - - +
340A ASP* 2.7 32.0 + - - -
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Residues in contact with GLU 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 GLN 2.9 18.2 + - - +
240A ALA* 3.4 10.5 - - - +
242A HIS* 1.3 77.2 - - - +
244A ARG* 1.3 61.5 + - + +
245A GLY 3.3 2.8 + - - -
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Residues in contact with ARG 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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188A LEU 5.9 0.4 + - - -
191A LEU* 3.7 32.5 - - - +
192A ASP* 3.2 47.1 - - - +
195A GLN* 2.6 60.9 + - - +
240A ALA* 3.0 16.4 + - - +
241A ALA* 3.0 9.7 + - - +
243A GLU* 1.3 78.4 - - + +
245A GLY* 1.3 61.0 + - - +
246A ILE* 3.3 17.3 + - + +
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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