Contacts of the helix formed by residues 226 - 244 (chain A) in PDB entry 1NVP
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 SER 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE* 3.2 16.5 - - - +
224A ALA* 4.1 0.3 - - - +
225A LYS* 1.3 80.5 - - - +
227A GLU* 1.3 69.8 + - - +
228A GLU* 3.6 6.9 + - - +
229A GLN* 2.8 38.7 + - - +
230A SER* 2.9 19.1 + - - -
318A ARG* 4.4 10.1 - - - +
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Residues in contact with GLU 227 (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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165A LEU* 4.8 0.2 - - - -
168A ILE* 3.6 5.1 - - + +
226A SER* 1.3 71.2 - - - +
228A GLU* 1.3 63.4 + - - +
230A SER* 3.2 6.2 + - - -
231A ARG* 3.0 23.7 + - - +
253A PHE* 4.7 3.5 - - - -
255A ILE* 4.9 20.9 - - + -
258A MET* 3.8 19.9 - - + +
318A ARG* 2.8 58.3 + - - +
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Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A SER* 3.2 6.3 + - - +
227A GLU* 1.3 81.6 + - - +
229A GLN* 1.3 61.4 + - + +
231A ARG* 3.3 17.0 + - - +
232A LEU* 2.9 29.8 + - + +
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Residues in contact with GLN 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU* 5.4 4.9 + - - +
207A PRO* 3.5 31.8 - - + +
224A ALA* 3.9 9.5 - - + +
225A LYS* 3.4 24.9 + - - +
226A SER* 2.8 32.5 + - - +
228A GLU* 1.3 76.0 - - + +
230A SER* 1.3 58.1 + - - +
232A LEU* 4.4 4.3 - - + -
233A ALA* 2.9 32.1 + - - +
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE* 3.7 23.1 + - - +
170A SER* 2.8 32.7 + - - -
221A CYS* 3.9 7.8 - - - -
224A ALA* 3.6 12.7 - - - +
226A SER 2.9 13.6 + - - -
227A GLU* 3.5 9.2 - - - -
228A GLU 3.2 0.4 - - - -
229A GLN* 1.3 78.8 - - - +
231A ARG* 1.3 61.4 + - - +
233A ALA* 3.9 3.3 - - - +
234A ALA* 3.1 23.7 + - - +
253A PHE* 3.9 6.5 - - - -
255A ILE* 5.0 0.9 - - - -
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Residues in contact with ARG 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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227A GLU 3.0 14.0 + - - +
228A GLU* 4.0 15.0 - - - +
230A SER* 1.3 73.6 - - - +
232A LEU* 1.3 65.9 + - - +
234A ALA* 3.4 2.4 + - - +
235A ARG* 2.9 45.4 + - + +
250A PHE* 4.0 25.8 + - + -
253A PHE* 3.2 57.3 + - + +
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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
----------------------------------------------------------
206A GLU* 5.7 2.5 - - + +
207A PRO* 4.0 19.7 - - + -
228A GLU* 2.9 20.8 + - + +
229A GLN* 3.8 6.5 - - + +
231A ARG* 1.3 76.1 - - - +
233A ALA* 1.3 65.0 + - - +
235A ARG* 2.9 23.5 + - + +
236A LYS* 3.0 41.1 + - + +
239A ARG* 5.6 5.6 - - - +
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Residues in contact with ALA 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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204A ILE* 5.0 1.6 - - + -
207A PRO* 3.9 17.6 - - + +
209A THR* 3.4 29.2 - - + +
221A CYS* 3.8 13.9 - - - -
229A GLN 2.9 18.4 + - - +
232A LEU* 1.3 75.9 - - - +
234A ALA* 1.3 63.1 + - - +
236A LYS* 3.0 17.5 + - - +
237A TYR* 3.0 21.1 + - + -
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Residues in contact with ALA 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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172A VAL* 4.4 3.4 - - + -
219A MET* 3.6 15.7 - - + +
221A CYS* 4.2 12.7 - - + -
230A SER 3.1 16.6 + - - +
231A ARG 3.7 4.3 - - - +
233A ALA* 1.3 78.6 - - - +
235A ARG* 1.3 57.3 + - - +
237A TYR* 3.5 9.8 + - - -
238A ALA* 3.0 28.6 + - - +
250A PHE* 3.6 19.0 - - + -
253A PHE* 4.1 11.9 - - + -
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Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ARG* 2.9 36.5 + - + +
232A LEU* 2.9 17.3 + - + +
234A ALA* 1.3 75.4 - - - +
236A LYS* 1.3 57.7 + - - +
238A ALA* 3.3 4.4 + - - +
239A ARG* 2.9 53.4 + - - +
250A PHE* 3.6 47.3 - - + +
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Residues in contact with LYS 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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204A ILE* 5.3 15.9 - - + -
206A GLU* 2.6 37.6 + - - +
207A PRO* 4.5 4.9 - - + +
232A LEU* 3.0 41.6 + - + +
233A ALA* 3.0 8.0 + - - +
235A ARG* 1.3 73.4 - - - +
237A TYR* 1.3 66.8 + - - +
239A ARG* 2.9 22.6 + - - +
240A VAL* 2.8 29.5 + - + +
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Residues in contact with TYR 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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202A MET* 3.5 40.6 + - + +
204A ILE* 2.6 33.2 + - + +
209A THR* 2.4 47.8 + - - -
210A THR 3.4 0.5 + - - -
211A ALA* 3.6 27.8 - - + -
213A ILE* 4.9 3.4 - - + -
219A MET* 3.6 20.9 - - - -
221A CYS* 4.3 7.4 - - + -
233A ALA* 3.0 33.3 + - + -
234A ALA* 3.8 7.2 - - - +
236A LYS* 1.3 74.9 - - - +
238A ALA* 1.3 63.8 + - - +
240A VAL* 3.2 9.0 + - + +
241A VAL* 3.1 26.9 + - - +
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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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174A LEU* 3.5 37.2 - - + -
219A MET* 4.4 0.2 - - - +
234A ALA 3.0 18.4 + - - +
235A ARG* 3.5 5.4 - - - +
236A LYS 3.1 0.2 - - - -
237A TYR* 1.3 78.6 - - - +
239A ARG* 1.3 56.6 + - - +
241A VAL* 3.6 2.8 + - - +
242A GLN* 2.9 27.7 + - - +
248A ALA* 4.0 5.9 - - + +
249A LYS 4.5 3.8 - - - +
250A PHE* 4.0 12.8 - - + -
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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* 5.6 4.6 - - - +
235A ARG* 2.9 46.2 + - - +
236A LYS* 2.9 26.4 + - - +
238A ALA* 1.3 74.3 - - - +
240A VAL* 1.3 61.4 + - - +
242A GLN* 3.3 20.6 + - - +
243A LYS* 2.8 61.1 + - + +
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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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187A ALA* 4.2 18.2 - - + -
188A ARG 5.9 0.2 - - - +
202A MET* 4.0 27.1 - - + -
204A ILE* 5.5 8.5 - - + -
236A LYS* 2.8 19.8 + - + +
237A TYR* 3.4 10.3 - - - +
239A ARG* 1.3 75.6 - - - +
241A VAL* 1.3 65.9 + - + +
243A LYS* 3.1 18.6 + - + +
244A LEU* 3.1 18.4 + - + +
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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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174A LEU* 4.2 19.1 - - + -
178A LEU* 3.8 32.1 - - + -
183A ILE* 4.3 20.4 - - + -
202A MET* 5.1 0.4 - - + -
213A ILE* 4.4 18.6 - - + -
219A MET* 6.0 0.2 - - - -
237A TYR 3.1 15.7 + - - +
238A ALA 3.8 4.0 - - - +
240A VAL* 1.3 82.5 - - + +
242A GLN* 1.3 64.0 + - - +
244A LEU* 3.2 16.1 + - - +
246A PHE* 3.5 29.5 + - + -
248A ALA* 4.3 5.4 - - + -
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Residues in contact with GLN 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 2.9 19.8 + - - +
239A ARG* 3.3 21.9 + - + +
240A VAL 3.1 0.2 - - - -
241A VAL* 1.3 77.3 - - - +
243A LYS* 1.3 58.8 + - + +
245A GLY* 3.1 18.0 + - - -
246A PHE 3.3 22.7 + - - +
247A PRO* 5.3 1.3 - - + -
248A ALA* 3.1 28.6 + - + +
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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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186A ARG* 4.7 4.2 + - - -
239A ARG* 2.8 48.4 + - + +
240A VAL* 3.1 8.5 + - + +
242A GLN* 1.3 71.4 - - + +
244A LEU* 1.3 58.8 - - + +
245A GLY* 3.0 9.7 + - - -
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Residues in contact with LEU 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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182A THR* 5.1 0.8 - - + +
183A ILE* 3.9 36.8 - - + +
186A ARG* 2.8 70.0 + - + +
187A ALA* 3.9 21.3 - - + +
240A VAL* 3.1 21.6 + - + +
241A VAL* 3.7 10.1 - - - +
242A GLN 3.2 1.0 - - - -
243A LYS* 1.3 78.6 - - + +
245A GLY* 1.3 59.3 + - - +
246A PHE* 3.7 15.9 - - + -
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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
------------------------------------------------------------
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