Contacts of the helix formed by residues 255 - 270 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ASN* 4.2 11.9 - - - +
253B THR 3.2 1.4 + - - -
254B LEU* 1.3 72.9 - - - +
256B ALA* 1.3 59.6 + - - +
257B GLY 3.3 2.9 - - - -
258B ASP* 3.3 21.3 + - - +
259B THR* 2.8 34.1 + - - -
288B LYS* 4.5 2.2 - - - -
294B PHE* 4.0 6.5 - - - -
299B ANP 4.2 5.5 + - - -
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B THR 3.1 17.7 + - - +
254B LEU 3.3 1.4 + - - -
255B GLY* 1.3 77.6 - - - +
257B GLY* 1.3 57.3 + - - +
259B THR* 3.2 4.8 + - - -
260B PHE* 2.8 29.8 + - - +
285B ALA* 3.7 5.6 - - - +
288B LYS* 4.2 10.9 - - + +
289B CYS* 3.7 23.6 - - - -
299B ANP 3.6 28.0 - - + +
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Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLU* 5.5 0.7 - - - -
256B ALA* 1.3 74.2 - - - +
258B ASP* 1.3 51.6 + - - +
260B PHE* 3.3 2.9 + - - +
261B ASN* 2.8 43.1 + - - +
299B ANP 2.8 47.8 + - - -
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Residues in contact with ASP 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASN* 2.9 46.1 - - - +
45B ASN* 2.9 42.4 + - + -
46B SER* 3.2 21.4 + - - +
49B VAL* 4.9 0.9 - - - -
171B GLU* 4.3 8.7 - - - +
255B GLY* 3.3 12.7 + - - +
257B GLY* 1.3 72.0 - - - +
259B THR* 1.3 64.5 + - - +
261B ASN* 4.4 4.5 + - - -
262B ALA* 3.1 22.3 + - - +
299B ANP 4.8 0.2 + - - -
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Residues in contact with THR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B VAL* 3.7 19.7 - - + +
255B GLY 2.8 20.8 + - - -
256B ALA* 3.2 8.3 + - - -
258B ASP* 1.3 74.0 - - - +
260B PHE* 1.3 64.6 + - - +
263B SER* 2.8 31.2 + - - -
284B VAL* 3.6 29.4 - - + +
285B ALA* 4.0 13.9 - - - -
288B LYS* 3.8 12.7 - - + +
294B PHE* 3.3 21.5 - - - -
297B ILE* 4.5 3.4 - - + -
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Residues in contact with PHE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B PHE* 4.3 2.2 - + - -
222B VAL* 3.8 20.0 - - + -
224B ALA* 3.9 17.0 - - + -
230B ALA* 3.5 31.2 - - + -
256B ALA 2.8 12.6 + - - +
257B GLY* 3.4 7.6 - - - +
259B THR* 1.3 77.6 - - - +
261B ASN* 1.3 79.0 + - - +
263B SER* 3.2 2.8 + - - -
264B VAL* 2.9 45.0 + - + +
278B LEU* 3.8 13.7 - - + -
281B GLY* 3.5 29.2 - - - -
282B CYS* 3.9 11.0 - - - -
285B ALA* 4.0 6.4 - - + +
299B ANP 4.0 19.3 - - - -
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Residues in contact with ASN 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 4.4 6.6 + - - +
137B HIS* 4.9 5.8 + - - +
171B GLU* 2.9 39.6 + - - +
190B PHE* 3.2 41.5 - - + +
257B GLY* 2.8 28.7 + - - +
258B ASP* 3.9 8.9 + - - +
259B THR 3.4 0.2 - - - -
260B PHE* 1.3 80.9 - - - +
262B ALA* 1.3 62.4 + - - +
264B VAL* 3.3 2.4 + - - +
265B ILE* 3.0 31.7 + - + +
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 3.5 31.1 + - - +
49B VAL* 3.7 17.9 - - + -
50B LEU* 3.4 18.0 - - + +
53B LEU* 4.4 0.9 - - - -
258B ASP 3.1 17.7 + - - +
259B THR 4.0 0.2 - - - +
261B ASN* 1.3 76.2 - - - +
263B SER* 1.3 58.4 + - - +
265B ILE* 3.5 8.4 + - - +
266B PHE* 2.8 30.0 + - - +
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Residues in contact with SER 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 4.0 0.9 - - - +
53B LEU* 3.8 16.2 - - - +
259B THR 2.8 22.6 + - - -
260B PHE 3.6 3.4 - - - -
262B ALA* 1.3 75.6 - - - +
264B VAL* 1.3 64.6 + - - +
266B PHE* 3.7 0.3 - - - +
267B SER* 3.0 24.6 + - - -
280B PHE* 3.7 14.3 - - - -
281B GLY* 3.7 20.2 - - - -
284B VAL* 3.3 28.9 - - - +
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Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B VAL* 5.3 0.4 - - + -
190B PHE* 4.0 18.2 - - + -
222B VAL* 5.3 8.5 - - + -
260B PHE* 2.9 52.3 + - + +
261B ASN 3.8 3.4 - - - +
263B SER* 1.3 73.4 - - - +
265B ILE* 1.3 67.2 + - - +
267B SER* 3.2 2.8 + - - -
268B LEU* 2.9 42.1 + - + +
274B VAL* 6.6 0.4 - - + -
277B ALA* 3.6 32.3 - - + +
278B LEU* 4.5 3.4 - - + +
281B GLY* 4.2 1.1 - - - -
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Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.1 22.2 - - + -
8B CYS* 5.6 4.0 - - - -
46B SER* 6.0 1.1 - - - +
50B LEU* 4.4 3.6 - - + -
135B TRP* 3.8 39.8 - - + +
137B HIS* 3.5 43.7 - - + +
169B SER* 3.6 11.7 - - - +
190B PHE* 4.1 11.7 - - + -
261B ASN 3.0 25.4 + - - +
262B ALA* 3.6 9.0 - - - +
264B VAL* 1.3 75.6 - - - +
266B PHE* 1.3 58.8 + - - +
268B LEU* 3.3 1.7 + - - +
269B SER* 2.8 29.3 + - - -
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Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.7 0.7 - - + -
50B LEU* 4.1 5.4 - - + -
53B LEU* 3.6 45.3 - - + -
54B GLY 4.4 3.1 - - - -
55B ALA* 3.7 38.8 - - + -
262B ALA 2.8 21.3 + - - +
263B SER 3.7 4.3 - - - +
264B VAL 3.2 0.2 - - - -
265B ILE* 1.3 76.3 - - - +
267B SER* 1.3 65.1 + - - +
269B SER* 2.7 25.6 + - - -
270B GLN* 3.0 49.9 + - + +
280B PHE* 4.2 16.4 - + - -
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Residues in contact with SER 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B SER 3.0 17.3 + - - -
266B PHE* 1.3 80.0 - - - +
268B LEU* 1.3 62.8 + - - +
270B GLN* 3.0 12.8 + - - +
272B ARG* 3.1 48.2 + - - +
276B GLU* 4.2 2.1 + - - +
277B ALA* 3.4 28.1 + - - -
280B PHE* 4.1 15.2 - - - +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TRP* 3.8 22.5 - - + -
188B VAL* 4.0 29.2 - - + -
220B VAL* 6.2 1.8 - - + -
264B VAL* 2.9 36.6 + - + +
265B ILE* 5.1 0.2 - - - -
267B SER* 1.3 76.7 - - - +
269B SER* 1.3 57.8 + - - +
271B GLY* 2.8 20.8 + - - -
272B ARG 3.6 20.9 - - - +
274B VAL* 3.9 27.6 - - + +
277B ALA* 3.8 18.2 - - + -
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Residues in contact with SER 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 3.9 19.9 - - - +
134B LYS* 4.3 25.3 + - - +
135B TRP* 3.9 20.6 - - - -
265B ILE 2.8 19.2 + - - -
266B PHE* 2.7 24.6 + - - -
268B LEU* 1.3 72.9 - - - +
270B GLN* 1.3 68.8 + - - +
271B GLY 3.1 1.1 + - - -
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Residues in contact with GLN 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LYS* 4.6 9.4 + - - -
266B PHE* 3.0 54.1 + - + +
267B SER* 3.4 10.3 - - - +
268B LEU 3.0 0.4 - - - -
269B SER* 1.3 85.0 + - - +
271B GLY* 1.3 58.1 + - - +
272B ARG* 3.4 12.4 + - + -
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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