Contacts of the helix formed by residues 255 - 268 (chain B) in PDB entry 1XV9
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 GLN 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B GLN 4.0 1.0 + - - -
254B LEU* 1.3 80.9 - - - +
256B GLU* 1.3 67.7 + - - +
257B PRO* 3.3 7.1 - - + +
258B GLU* 2.8 33.9 + - + +
259B TYR 3.0 2.9 + - - -
295B TYR* 2.8 34.3 + - - -
300B GLN* 4.0 20.5 + - - +
304B ARG* 2.8 34.8 + - - +
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Residues in contact with GLU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.8 25.8 - - + +
121B HIS* 3.5 25.6 + - + -
122B THR* 4.0 8.4 + - - -
254B LEU 3.5 1.9 + - - -
255B GLN* 1.3 68.1 - - - +
257B PRO* 1.3 63.2 - - + +
259B TYR* 2.6 34.5 + - + +
260B VAL* 3.0 21.4 + - + +
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Residues in contact with PRO 257 (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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114B ILE* 4.1 21.9 - - + +
118B LEU* 4.7 9.4 - - + -
255B GLN* 3.6 6.7 - - + +
256B GLU* 1.3 97.6 - - + +
258B GLU* 1.3 63.7 + - - +
259B TYR 3.0 1.0 + - - -
260B VAL* 3.2 18.8 + - + +
261B LEU* 3.2 22.0 + - + +
295B TYR* 3.2 41.7 - - + +
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Residues in contact with GLU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLN 3.8 0.3 - - - +
254B LEU* 3.5 25.7 - - + +
255B GLN* 2.8 43.1 + - + +
257B PRO* 1.3 73.6 - - - +
259B TYR* 1.3 58.0 + - - +
261B LEU* 4.5 5.4 - - - -
262B LEU* 4.0 15.9 + - - +
292B LEU* 4.4 10.6 - - + +
295B TYR* 3.6 34.4 - - + +
296B ILE* 4.5 13.2 - - + +
299B GLN* 5.9 0.7 - - - +
304B ARG* 2.8 29.6 + - - -
308B LEU* 3.9 19.7 - - + +
312B LEU* 5.2 1.8 - - + +
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Residues in contact with TYR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ILE* 4.2 26.2 - - + +
205B VAL* 6.4 0.2 - - - -
207B ASN* 2.7 25.9 + - - -
208B THR* 3.3 31.2 - - + -
249B LEU* 3.7 27.5 + - + -
250B ARG* 3.7 22.6 + - - -
254B LEU* 3.2 41.9 + - + -
255B GLN 3.0 3.4 + - - -
256B GLU* 2.6 25.2 + - + +
258B GLU* 1.3 71.4 - - - +
260B VAL* 1.3 64.2 + - + +
262B LEU* 3.3 10.0 + - + +
263B ALA* 3.2 18.2 + - - +
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Residues in contact with VAL 260 (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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114B ILE* 6.2 0.2 - - + -
117B LEU* 3.2 48.7 - - + +
118B LEU* 3.5 24.0 - - + -
121B HIS* 4.4 23.6 - - + +
125B MET* 6.1 0.2 - - + -
175B PHE* 4.8 5.4 - - + -
256B GLU* 3.0 24.6 + - + +
257B PRO* 3.2 3.6 + - + +
259B TYR* 1.3 75.6 - - + +
261B LEU* 1.3 62.8 + - - +
263B ALA* 2.9 25.7 + - + +
264B ALA* 3.0 6.2 + - - +
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Residues in contact with LEU 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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113B LEU* 4.9 5.6 - - + -
114B ILE* 4.7 14.6 - - + -
117B LEU* 3.3 27.6 - - + -
257B PRO* 3.2 16.6 + - + +
258B GLU* 4.6 1.8 - - - +
260B VAL* 1.3 77.8 - - - +
262B LEU* 1.3 64.2 + - - +
264B ALA* 2.8 18.8 + - + +
265B MET* 2.9 15.4 + - + +
288B MET* 5.4 6.2 - - + +
291B THR* 4.2 22.0 - - + +
292B LEU* 3.3 54.3 - - + +
295B TYR* 4.8 10.8 - - + -
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Residues in contact with LEU 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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204B ILE* 4.2 22.0 - - + -
249B LEU* 4.7 11.7 - - + -
254B LEU* 4.5 20.6 - - + -
258B GLU 4.0 7.6 + - - +
259B TYR* 3.3 13.3 + - + +
261B LEU* 1.3 77.2 - - - +
263B ALA* 1.3 63.9 + - - +
265B MET* 3.0 11.7 + - + +
266B ALA* 2.9 22.0 + - - +
292B LEU* 3.9 7.6 - - + +
312B LEU* 4.4 30.3 - - + +
313B LEU* 6.4 0.2 - - + -
315B LEU* 5.8 5.2 - - + -
316B LEU* 3.7 36.8 - - + -
319B LEU* 5.7 2.9 - - + -
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Residues in contact with ALA 263 (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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125B MET* 5.4 5.8 - - + -
175B PHE* 5.1 11.7 - - + -
201B ILE* 4.3 18.8 - - + +
204B ILE* 3.8 22.4 - - + +
205B VAL* 5.6 2.7 - - + -
259B TYR 3.2 6.4 + - - +
260B VAL* 2.9 22.1 + - + +
262B LEU* 1.3 76.8 - - - +
264B ALA* 1.3 62.6 + - - +
266B ALA* 2.9 15.8 + - - +
267B LEU* 3.0 12.5 + - - +
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Residues in contact with ALA 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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117B LEU* 4.0 21.7 - - + +
175B PHE* 5.8 3.3 - - - -
260B VAL 3.0 6.3 + - - +
261B LEU* 2.8 15.4 + - + +
263B ALA* 1.3 79.8 - - - +
265B MET* 1.3 55.1 + - - +
267B LEU* 3.1 12.0 + - - +
268B PHE* 2.9 38.5 + - + +
288B MET* 4.0 24.5 - - + -
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Residues in contact with MET 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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420A LEU* 4.1 14.4 - - + -
261B LEU 2.9 16.9 + - - +
262B LEU* 3.0 12.7 + - - +
264B ALA* 1.3 70.0 - - - +
266B ALA* 1.3 68.5 + - - +
268B PHE 3.8 10.5 - - - +
269B SER* 3.3 10.7 + - - -
285B GLN* 5.1 7.7 - - + +
288B MET* 3.8 23.3 - - + -
289B ALA* 3.8 24.0 - - + +
292B LEU* 4.5 15.0 - - + -
309B TYR* 3.8 29.2 - - - +
313B LEU* 4.2 7.4 - - + -
316B LEU* 3.7 31.1 - - + +
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Residues in contact with ALA 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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197B ALA* 4.0 0.9 - - + -
200B GLU* 4.1 17.0 - - + +
201B ILE* 4.3 9.9 - - + -
204B ILE* 3.8 24.9 - - + -
262B LEU 2.9 5.2 + - - +
263B ALA 2.9 9.7 + - - +
265B MET* 1.3 74.7 - - - +
267B LEU* 1.3 57.7 + - - +
269B SER* 2.9 15.5 + - - -
272B ARG* 2.6 28.1 + - - +
316B LEU* 4.0 16.5 - - + +
320B ARG* 5.8 0.9 - - - +
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Residues in contact with LEU 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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175B PHE* 5.3 6.1 - - + -
176B THR* 4.0 18.8 - - + -
179B LEU* 4.4 8.1 - - + -
182B PHE* 4.0 25.6 - - + -
193B LEU* 3.5 36.5 - - + +
194B LEU* 3.9 19.7 - - + -
197B ALA* 3.3 16.6 - - + +
201B ILE* 4.0 10.5 - - + +
263B ALA 3.0 7.9 + - - +
264B ALA* 3.2 12.3 - - - +
266B ALA* 1.3 81.2 - - - +
268B PHE* 1.3 72.5 + - + +
269B SER* 2.7 16.5 + - - -
272B ARG* 4.1 1.6 + - - -
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Residues in contact with PHE 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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179B LEU* 5.0 5.8 - - + -
181B VAL* 4.4 18.4 - - + -
182B PHE* 3.7 37.0 - + + -
185B LEU* 3.8 14.1 - - + -
193B LEU* 4.0 12.8 - - + -
264B ALA* 2.9 22.6 + - + +
265B MET* 3.8 7.8 - - - +
267B LEU* 1.3 84.0 - - + +
269B SER* 1.3 60.3 + - - +
270B PRO 4.0 0.7 - - - -
281B ILE* 4.0 7.9 - - + -
284B LEU* 4.0 31.6 - - + -
285B GLN* 3.3 29.6 - - - +
288B MET* 4.2 26.5 - - + -
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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