Contacts of the helix formed by residues 235 - 244 (chain A) in PDB entry 2HD5
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 THR 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A CYS 2.8 17.4 + - - -
232A LEU* 3.0 22.1 + - - +
234A ASN* 1.3 74.2 - - - +
236A ARG* 1.3 68.0 + - - +
237A GLU 4.7 0.9 - - - +
238A LEU* 3.0 20.9 + - + +
239A ARG* 2.9 21.6 + - - +
323A LEU* 4.7 2.0 - - + -
324A PHE* 4.6 7.9 - - + -
401A ILE* 3.8 26.2 - - + -
451A TYR* 2.7 30.4 + - - +
517A PHE* 4.8 0.2 - - - -
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Residues in contact with ARG 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 ASN 3.4 4.4 + - - +
235A THR* 1.3 73.9 - - - +
237A GLU* 1.3 80.6 + - - +
239A ARG* 3.2 16.7 + - - +
240A ASP* 3.0 44.0 + - - +
401A ILE* 5.6 1.6 - - - +
451A TYR* 5.2 0.6 - - - -
472A PRO* 3.2 55.5 + - + +
473A GLY* 4.7 1.0 - - - +
519A GLU* 4.6 23.0 + - - +
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A THR* 3.4 2.0 - - + +
236A ARG* 1.3 103.8 - - - +
238A LEU* 1.3 58.5 + - - +
240A ASP* 3.9 11.0 - - - +
241A TYR* 3.1 27.0 + - - +
319A ARG* 3.7 27.9 + - - +
323A LEU* 3.7 26.6 - - + +
400A LYS* 6.5 0.2 - - + -
401A ILE* 5.4 8.1 - - + +
519A GLU* 5.6 1.2 - - - +
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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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232A LEU* 3.8 44.2 - - + +
235A THR* 3.0 15.0 + - - +
237A GLU* 1.3 78.6 - - - +
239A ARG* 1.3 66.4 + - - +
241A TYR* 3.3 13.0 + - + +
242A CYS* 3.3 21.4 + - - -
260A PHE* 4.0 24.0 - - + -
264A ILE* 6.2 0.2 - - + -
304A LEU* 4.9 6.1 - - + -
307A LEU* 5.2 0.4 - - + -
319A ARG* 6.4 0.4 - - + -
320A ILE* 3.7 29.6 - - + -
323A LEU* 3.5 19.1 - - + +
324A PHE* 4.5 12.3 - - + -
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Residues in contact with ARG 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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232A LEU 4.4 2.6 + - - -
233A SER 3.3 21.3 - - - +
235A THR 2.9 8.7 + - - +
236A ARG* 3.4 18.3 + - - +
238A LEU* 1.3 76.6 - - - +
240A ASP* 1.3 87.9 + - - +
242A CYS* 3.0 7.4 + - - +
243A LEU* 2.9 41.0 + - + +
264A ILE* 3.8 12.8 - - + -
268A TRP* 3.3 65.0 - - + +
472A PRO* 3.9 25.3 - - - +
473A GLY* 4.6 5.7 - - - +
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Residues in contact with ASP 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 ARG* 3.0 30.7 + - - +
237A GLU* 3.9 12.8 - - - +
239A ARG* 1.3 105.6 + - - +
241A TYR* 1.3 57.7 + - - +
243A LEU* 4.3 9.3 - - - +
244A GLN* 2.8 56.8 + - - +
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Residues in contact with TYR 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 GLU 3.1 16.1 + - - +
238A LEU* 3.3 15.9 - - + +
239A ARG 3.2 0.2 - - - -
240A ASP* 1.3 75.0 - - - +
242A CYS* 1.3 65.3 + - - +
244A LEU* 3.0 100.1 + + + -
245A ASP* 2.5 26.9 + - - -
257A VAL* 5.1 4.3 - - + -
311A VAL* 3.7 17.9 - - + +
319A ARG* 3.4 40.2 - - + +
320A ILE* 4.3 25.4 - - + -
323A LEU* 6.2 0.2 - - + -
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Residues in contact with CYS 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* 3.5 14.8 - - - -
239A ARG 3.0 8.1 + - - +
241A TYR* 1.3 86.3 - - - +
243A LEU* 1.3 62.1 + - - +
244A TYR* 3.2 16.8 + - - +
257A VAL* 6.3 1.3 - - - -
260A PHE* 3.7 30.3 - - - -
261A ALA* 3.8 27.1 - - + +
264A ILE* 4.0 17.3 - - + -
265A GLN* 2.8 26.1 + - + -
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Residues in contact with LEU 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 ARG* 2.9 51.0 + - + +
240A ASP* 3.1 8.9 + - - +
242A CYS* 1.3 72.3 - - - +
244A GLN* 1.3 78.6 + - + +
264A ILE* 4.2 4.7 - - + +
265A GLN* 3.6 39.5 + - + +
268A TRP* 4.1 20.9 - - + -
269A THR* 5.9 2.2 - - + -
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Residues in contact with GLN 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 ASP* 2.8 40.2 + - - +
243A LEU* 1.3 78.1 - - + +
244A ARG* 1.3 105.3 + - + +
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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