Contacts of the helix formed by residues 255 - 270 (chain A) in PDB entry 3NBV
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 GLY 255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASN* 4.3 10.1 - - - -
254A LEU* 1.3 74.3 - - - +
256A ALA* 1.3 57.9 + - - +
257A GLY 3.4 1.8 - - - -
258A ASP* 3.3 17.6 + - - +
259A THR* 2.8 33.9 + - - -
288A LYS* 4.5 1.1 - - - -
294A PHE* 4.1 7.4 - - - -
299A ANP 2.4 23.1 + - - -
300A FRU 4.3 0.9 - - - -
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 3.1 18.3 + - - +
254A LEU 3.3 1.4 + - - -
255A GLY* 1.3 75.9 - - - +
257A GLY* 1.3 59.2 + - - +
259A THR* 3.0 9.2 + - - -
260A PHE* 2.8 30.0 + - - +
285A ALA* 3.8 6.2 - - - +
288A LYS* 4.4 5.8 - - + +
289A CYS* 3.8 24.2 - - - -
299A ANP 3.5 29.4 + - + +
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Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU* 5.6 0.9 - - - -
256A ALA* 1.3 73.8 - - - +
258A ASP* 1.3 58.2 + - - -
260A PHE* 3.4 3.1 + - - +
261A ASN* 3.0 36.9 + - - +
299A ANP 2.8 46.3 + - - -
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Residues in contact with ASP 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASN* 3.3 38.9 + - - +
45A ASN* 3.0 38.4 + - + +
46A SER* 3.5 15.3 + - - +
49A VAL* 4.7 2.0 - - - -
171A GLU* 4.4 4.3 - - - +
173A GLU* 5.0 1.2 - - - +
255A GLY* 3.3 7.4 + - - +
256A ALA 3.2 0.4 - - - -
257A GLY* 1.3 75.8 - - - +
259A THR* 1.3 66.1 + - - +
261A ASN* 4.5 5.2 + - - +
262A ALA* 3.0 26.7 + - - +
299A ANP 5.1 0.9 + - - -
300A FRU 2.9 23.1 + - - -
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Residues in contact with THR 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 3.8 17.2 - - + +
255A GLY 2.8 18.6 + - - -
256A ALA* 3.0 10.3 + - - -
258A ASP* 1.3 78.6 - - - +
260A PHE* 1.3 59.9 + - - +
262A ALA* 3.6 1.7 + - - +
263A SER* 2.9 29.6 + - - -
284A VAL* 3.6 39.9 - - + +
285A ALA* 3.8 8.7 - - - -
288A LYS* 3.9 13.3 - - + +
294A PHE* 3.5 19.2 - - - -
297A ILE* 4.4 3.1 - - + -
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Residues in contact with PHE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 4.3 1.6 - + - -
222A VAL* 3.8 19.1 - - + -
224A ALA* 3.7 19.5 - - + -
230A ALA* 3.5 30.7 - - + -
256A ALA 2.8 12.5 + - - +
257A GLY* 3.5 7.4 - - - +
258A ASP 3.3 0.2 - - - -
259A THR* 1.3 73.2 - - - +
261A ASN* 1.3 81.0 + - - +
263A SER* 3.1 3.3 + - - -
264A VAL* 2.9 45.6 + - + +
278A LEU* 3.8 28.5 - - + -
281A GLY* 3.4 26.9 - - - -
282A CYS* 3.7 2.9 - - - -
285A ALA* 3.9 8.2 - - + +
299A ANP 4.0 19.5 - - - -
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Residues in contact with ASN 261 (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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46A SER* 4.6 6.0 + - - +
137A HIS* 4.8 6.6 + - - +
171A GLU* 3.2 35.0 + - - +
190A PHE* 3.2 43.5 - - + +
257A GLY 3.0 24.3 + - - +
258A ASP* 4.0 8.1 + - - +
260A PHE* 1.3 80.2 - - - +
262A ALA* 1.3 64.5 + - - +
264A VAL* 3.2 2.9 + - - +
265A ILE* 2.9 33.5 + - + +
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Residues in contact with ALA 262 (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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46A SER* 3.6 22.1 + - - +
49A VAL* 3.5 29.2 - - + -
50A LEU* 3.6 15.0 - - + +
53A LEU* 4.7 1.1 - - - -
258A ASP 3.0 18.8 + - - +
261A ASN* 1.3 76.8 - - - +
263A SER* 1.3 57.3 + - - +
265A ILE* 3.4 8.1 + - - +
266A PHE* 2.9 30.4 + - - +
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 4.1 0.9 - - - +
53A LEU* 3.9 15.1 - - - +
259A THR 2.9 21.8 + - - -
260A PHE 3.1 4.0 + - - -
262A ALA* 1.3 75.4 - - - +
264A VAL* 1.3 61.7 + - - +
266A PHE* 3.7 1.0 - - - +
267A SER* 3.0 30.0 + - - -
280A PHE* 3.7 18.3 - - - -
281A GLY* 3.6 19.1 - - - -
284A VAL* 3.3 24.8 - - - +
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Residues in contact with VAL 264 (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 VAL* 5.1 2.2 - - + -
190A PHE* 3.9 20.4 - - + -
222A VAL* 5.2 6.7 - - + -
260A PHE* 2.9 50.3 + - + +
261A ASN 3.2 5.8 + - - +
263A SER* 1.3 72.3 - - - +
265A ILE* 1.3 61.3 + - - +
267A SER* 3.2 1.9 + - - -
268A LEU* 2.8 51.3 + - + +
277A ALA* 3.8 27.8 - - + +
278A LEU* 4.7 2.9 - - + -
281A GLY* 4.2 0.9 - - - -
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Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.3 23.3 - - + -
8A CYS* 5.7 3.4 - - - -
46A SER* 5.9 1.6 - - - +
50A LEU* 4.6 4.5 - - + -
135A TRP* 3.9 38.6 - - + +
137A HIS* 3.6 42.0 - - + +
169A SER* 3.6 12.6 - - - +
190A PHE* 4.2 9.2 - - + -
261A ASN* 2.9 25.3 + - + +
262A ALA* 3.6 8.3 - - - +
264A VAL* 1.3 75.6 - - - +
266A PHE* 1.3 60.0 + - - +
268A LEU* 3.7 1.1 - - - +
269A SER* 2.8 30.3 + - - -
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Residues in contact with PHE 266 (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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6A ILE* 5.0 0.7 - - + -
50A LEU* 4.0 5.4 - - + -
53A LEU* 3.6 48.5 - - + -
54A GLY 5.0 1.1 - - - -
55A ALA* 3.8 32.8 - - + -
262A ALA 2.9 17.6 + - - +
263A SER 3.7 3.4 - - - +
265A ILE* 1.3 79.3 - - - +
267A SER* 1.3 67.0 + - - +
269A SER* 3.0 22.9 + - - -
270A GLN* 3.0 48.9 + - + +
280A PHE* 4.0 18.4 - + - -
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Residues in contact with SER 267 (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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263A SER 3.0 18.0 + - - -
264A VAL 3.2 0.2 + - - -
266A PHE* 1.3 81.5 - - - +
268A LEU* 1.3 62.9 + - - +
270A GLN* 3.0 12.3 + - - +
271A GLY 3.4 0.3 + - - -
272A ARG* 3.2 40.8 + - - +
276A GLU* 4.3 1.2 + - - +
277A ALA* 3.5 30.8 + - - -
280A PHE* 4.1 17.8 - - - +
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Residues in contact with LEU 268 (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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135A TRP* 3.8 17.9 - - + -
188A VAL* 3.8 31.0 - - + -
190A PHE* 6.0 0.2 - - + -
220A VAL* 6.1 2.7 - - + -
222A VAL* 6.3 0.4 - - + -
264A VAL* 2.8 34.3 + - + +
265A ILE 3.8 2.5 - - - +
267A SER* 1.3 75.9 - - - +
269A SER* 1.3 56.3 + - - +
271A GLY* 2.8 22.5 + - - -
272A ARG 3.6 20.5 - - - +
273A SER 4.1 3.8 - - - +
274A VAL* 4.2 21.3 - - + +
277A ALA* 3.7 17.3 - - + -
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Residues in contact with SER 269 (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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6A ILE* 4.2 11.7 - - - +
134A LYS* 3.2 40.9 + - - +
135A TRP* 3.8 20.7 - - - -
167A ARG* 6.2 0.4 - - - -
265A ILE 2.8 21.2 + - - -
266A PHE* 3.0 18.2 + - - -
268A LEU* 1.3 71.5 - - - +
270A GLN* 1.3 62.5 + - - +
271A GLY 3.2 1.2 + - - -
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Residues in contact with GLN 270 (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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134A LYS* 4.7 6.9 + - - -
266A PHE* 3.0 56.6 + - + +
267A SER* 3.0 8.2 + - - +
268A LEU 3.0 1.4 - - - -
269A SER* 1.3 82.8 + - - +
271A GLY* 1.3 58.5 + - - +
272A ARG* 3.5 33.7 + - + +
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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