Contacts of the helix formed by residues 232 - 245 (chain A) in PDB entry 1HVD
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 ASN 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A GLU* 3.3 48.6 + - - +
111A THR* 4.7 0.9 + - - -
149A TYR* 3.4 35.7 - - + -
231A GLY* 1.3 71.9 - - - +
233A LEU* 1.3 61.7 + - - +
235A GLN* 3.5 22.8 + - - +
236A LEU 3.0 18.0 + - - -
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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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148A TYR* 3.8 43.5 - - + +
149A TYR* 3.9 17.3 - - + +
152A MET* 4.2 14.4 - - + -
187A TRP* 4.7 6.3 - - + +
191A GLU* 4.4 17.0 - - + +
194A PHE* 4.6 9.6 - - + -
195A ILE* 4.9 4.3 - - + -
231A GLY 3.3 1.0 - - - -
232A ASN* 1.3 77.8 - - - +
234A GLU* 1.3 63.9 + - + +
236A LEU* 3.1 4.5 + - + +
237A LEU* 2.9 49.9 + - + +
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Residues in contact with GLU 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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186A LYS 5.2 5.6 - - - +
187A TRP* 5.2 13.5 - - + -
225A ILE* 3.7 31.1 - - + +
227A ARG* 4.8 14.2 - - + +
230A SER 3.2 23.4 - - - +
231A GLY* 3.1 17.2 + - - +
233A LEU* 1.3 83.4 + - + +
235A GLN* 1.3 63.5 + - - +
237A LEU* 3.2 5.1 + - + +
238A LEU* 3.0 26.9 + - - +
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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
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107A GLU* 5.4 2.2 - - - +
108A LYS* 5.4 8.9 - - - +
111A THR* 3.9 12.9 + - + +
227A ARG 4.6 11.2 + - - +
228A GLU* 5.7 0.9 - - - -
229A THR* 3.7 8.6 - - - +
230A SER* 3.3 22.9 + - - -
231A GLY 3.0 19.7 + - - +
232A ASN* 3.6 25.6 + - - +
234A GLU* 1.3 76.5 - - - +
236A LEU* 1.3 61.5 + - - +
238A LEU* 3.4 11.6 + - - +
239A ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 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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111A THR* 3.7 23.8 - - + +
115A ALA* 4.1 13.0 - - + +
149A TYR* 3.8 17.9 - - + -
152A MET* 3.2 37.0 - - + -
153A LEU* 3.4 31.2 - - + +
156A LEU* 4.0 19.7 - - + -
232A ASN 3.0 14.5 + - - +
233A LEU* 3.1 8.0 + - + +
235A GLN* 1.3 74.6 - - - +
237A LEU* 1.3 66.1 + - - +
239A ALA* 3.0 4.5 + - - +
240A VAL* 2.9 24.4 + - + +
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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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152A MET* 3.8 27.1 - - - -
187A TRP* 4.0 27.8 - - + -
194A PHE* 3.9 26.2 - - + -
198A PHE* 4.1 21.7 - - + -
225A ILE* 3.9 18.4 - - + -
233A LEU* 2.9 39.9 + - + +
234A GLU* 3.5 7.6 - - + +
236A LEU* 1.3 72.1 - - - +
238A LEU* 1.3 57.3 + - - +
240A VAL* 3.4 6.8 + - - +
241A VAL* 2.9 33.4 + - - +
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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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222A GLU* 3.8 34.1 - - + +
225A ILE* 3.9 28.7 - - + +
226A ASP* 4.3 4.3 - - - +
227A ARG 3.9 23.3 - - - +
228A GLU* 4.0 22.4 - - + -
234A GLU 3.0 15.4 + - - +
235A GLN* 3.5 8.5 - - - +
237A LEU* 1.3 74.1 - - - +
239A ALA* 1.3 64.1 + - - +
241A VAL* 3.3 4.6 + - - +
242A LYS* 3.0 47.6 + - - +
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Residues in contact with ALA 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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111A THR* 3.7 11.7 - - + -
115A ALA* 3.6 18.6 - - + -
235A GLN 3.0 12.6 + - - +
236A LEU 3.0 7.9 + - - +
238A LEU* 1.3 74.7 - - - +
240A VAL* 1.3 58.0 + - - +
242A LYS* 3.5 1.0 + - - +
243A SER* 3.0 33.6 + - - -
250A TYR* 3.5 37.0 - - + +
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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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115A ALA* 3.9 15.0 - - + +
152A MET* 5.1 5.6 - - + -
156A LEU* 3.9 31.6 - - + -
161A ARG* 4.7 3.4 - - - +
198A PHE* 3.9 35.7 - - + +
206A LEU* 5.7 0.2 - - + -
236A LEU* 2.9 22.6 + - + +
237A LEU* 3.7 7.4 - - - +
239A ALA* 1.3 71.9 - - - +
241A VAL* 1.3 58.9 + - - +
243A SER* 3.2 2.8 + - - -
244A ILE* 2.8 53.1 + - + +
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Residues in contact with VAL 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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198A PHE* 3.8 29.2 - - + -
210A PHE* 3.7 17.6 - - + -
221A ILE* 3.6 23.3 - - + -
222A GLU* 3.3 29.4 - - + +
225A ILE* 3.9 15.0 - - + -
237A LEU 2.9 21.1 + - - +
238A LEU* 3.7 6.7 - - - +
240A VAL* 1.3 73.2 - - - +
242A LYS* 1.3 61.9 + - + +
244A ILE* 3.3 2.9 + - - +
245A ARG* 3.1 25.9 + - - +
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Residues in contact with LYS 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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222A GLU* 4.3 21.1 - - - +
226A ASP* 5.3 3.4 + - - -
228A GLU* 4.3 13.3 + - - +
238A LEU* 3.0 45.6 + - + +
239A ALA 3.8 0.2 - - - +
241A VAL* 1.3 76.2 - - - +
243A SER* 1.3 56.4 + - - +
245A ARG* 3.3 9.3 + - - +
246A SER* 2.9 31.1 + - - +
249A ALA* 5.3 1.4 - - - +
250A TYR* 3.8 34.0 + - + +
253A GLU* 2.9 38.0 + - - +
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Residues in contact with SER 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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115A ALA 3.4 23.8 + - - -
116A SER* 3.7 5.2 - - - -
203A VAL* 5.6 0.3 - - - +
207A ARG* 5.4 0.3 + - - -
239A ALA 3.0 19.7 + - - -
240A VAL* 3.8 2.2 - - - -
242A LYS* 1.3 72.4 - - - +
244A ILE* 1.3 68.6 + - - +
246A SER 3.5 13.4 + - - -
247A ILE* 3.5 26.9 + - - +
250A TYR* 3.2 24.0 - - - +
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Residues in contact with ILE 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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115A ALA 5.7 2.0 - - - +
161A ARG* 4.2 18.8 - - - +
203A VAL* 3.8 30.1 - - + +
206A LEU* 4.0 24.5 - - + -
207A ARG* 3.0 42.7 + - + -
210A PHE* 3.5 24.5 - - + -
240A VAL* 2.8 48.1 + - + +
241A VAL 3.7 4.5 - - - +
243A SER* 1.3 75.9 - - - +
245A ARG* 1.3 63.4 + - - +
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Residues in contact with ARG 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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207A ARG* 3.6 21.9 + - + +
210A PHE* 3.7 40.8 + - + +
211A ASP* 5.2 6.3 + - - -
220A GLN* 3.3 31.9 + - - +
221A ILE* 3.9 8.3 - - - +
222A GLU* 2.9 40.4 + - - -
241A VAL* 3.1 15.2 + - - +
242A LYS* 3.6 9.2 - - - +
244A ILE* 1.3 78.9 - - - +
246A SER* 1.3 65.2 + - - +
249A ALA* 6.4 0.2 - - + -
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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