Contacts of the helix formed by residues 263 - 273 (chain B) in PDB entry 1V40
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 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B LYS* 6.1 2.4 - - - +
252B PRO 3.9 6.3 + - - -
262B HIS* 1.3 92.7 - - + +
264B SER* 1.3 67.3 + - - +
265B LEU* 3.3 3.0 + - - +
266B ALA* 3.0 14.8 + - + +
267B ILE* 3.0 22.4 + - - +
3400B GSH 3.1 37.3 + - - +
490C ALA* 3.3 23.1 - - - +
493C ASP* 3.6 19.2 - - + +
494C THR* 3.3 22.6 + - - +
497C ASP* 3.1 21.4 + - - -
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Residues in contact with SER 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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214B ARG* 3.2 32.6 + - - +
217B ILE* 4.6 1.5 - - - +
218B ILE* 4.0 16.9 - - - +
252B PRO* 3.8 14.0 - - - +
263B GLN* 1.3 71.5 - - - +
265B LEU* 1.3 69.3 + - - +
267B ILE* 3.5 2.3 + - - +
268B ALA* 2.8 29.1 + - - +
352B TYR* 5.2 1.7 + - - -
3400B GSH 2.5 34.2 + - - -
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE* 4.7 3.8 - - + -
263B GLN* 3.3 2.7 + - - +
264B SER* 1.3 85.8 + - - +
266B ALA* 1.3 61.5 + - - +
268B ALA* 3.7 3.1 - - - +
269B ARG* 2.9 43.5 + - - +
292B VAL* 3.6 33.2 - - + -
293B ASP* 3.7 16.4 - - - +
296B ASP* 3.5 30.7 - - + +
348B TRP* 4.0 12.2 - - + -
352B TYR* 4.0 23.1 - - + +
3400B GSH 4.6 2.0 + - - +
493C ASP* 4.0 16.8 - - - +
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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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262B HIS 3.8 9.2 - - - +
263B GLN* 3.0 15.6 + - + +
265B LEU* 1.3 78.2 - - - +
267B ILE* 1.3 58.0 + - - +
269B ARG* 3.5 14.1 + - - +
270B TYR* 3.0 27.2 + - - +
486C CYS* 3.6 14.9 - - - +
489C ASP* 3.6 11.1 - - + +
490C ALA 3.6 27.1 - - - +
493C ASP* 4.6 2.7 + - - +
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ILE* 3.6 24.9 - - + -
252B PRO 4.3 4.3 - - - +
253B ILE 4.2 3.6 - - - -
254B LEU* 3.6 41.3 - - + +
261B LEU* 3.7 36.6 - - + +
262B HIS* 3.7 14.6 - - - +
263B GLN 3.0 20.7 + - - +
264B SER 3.6 5.8 - - - +
266B ALA* 1.3 74.7 - - - +
268B ALA* 1.3 66.9 + - - +
270B TYR* 3.1 8.7 + - + +
271B LEU* 3.0 29.7 + - + +
486C CYS* 4.2 2.2 - - - -
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Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE* 4.2 12.1 - - + -
218B ILE* 4.7 3.8 - - + -
221B ILE* 3.5 22.6 - - + +
264B SER 2.8 20.4 + - - +
265B LEU* 3.7 2.7 - - - +
267B ILE* 1.3 79.6 - - - +
269B ARG* 1.3 61.2 + - - +
271B LEU* 3.4 2.1 + - - +
272B THR* 3.0 29.3 + - - +
348B TRP* 3.6 27.6 - - + -
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Residues in contact with ARG 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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265B LEU* 2.9 26.9 + - - +
266B ALA* 3.8 8.0 - - - +
268B ALA* 1.3 73.8 - - - +
270B TYR* 1.3 66.9 + - - +
272B THR* 3.2 8.5 + - - +
273B LYS* 3.0 28.2 + - + +
289B ASP* 2.8 38.5 + - - +
292B VAL* 5.5 0.8 - - - +
293B ASP* 4.9 9.7 + - - -
348B TRP* 4.1 21.2 - - + +
469C ARG* 3.4 37.1 - - - +
473C LYS* 5.9 0.9 - - - +
489C ASP* 3.0 35.2 + - - +
493C ASP* 5.4 3.0 + - - -
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Residues in contact with TYR 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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204B TYR* 4.8 7.8 + + - -
254B LEU* 5.1 1.8 - - + -
256B VAL* 4.5 17.3 - - + +
261B LEU* 3.9 19.5 - - + -
266B ALA 3.0 15.6 + - - +
267B ILE* 3.1 8.7 + - - +
269B ARG* 1.3 78.2 - - - +
271B LEU* 1.3 83.0 + - + +
273B LYS* 3.5 19.3 + - + +
482C GLU* 3.7 45.2 - - + +
483C MET* 3.7 29.0 - - + +
486C CYS* 3.9 17.7 - - + -
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Residues in contact with LEU 271 (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 TYR* 4.2 18.8 - - + +
218B ILE* 3.9 20.2 - - + -
221B ILE* 3.7 24.0 - - + -
222B PHE* 3.8 39.3 - - + -
225B LEU* 3.6 11.5 - - + +
227B ILE* 5.7 3.8 - - + -
254B LEU* 4.3 2.5 - - + -
267B ILE* 3.0 28.3 + - + +
268B ALA* 3.9 3.8 - - - +
270B TYR* 1.3 93.6 - - + +
272B THR* 1.3 61.1 + - - +
273B LYS 3.4 1.6 + - - +
275B THR* 3.5 13.9 - - - +
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Residues in contact with THR 272 (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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221B ILE* 3.6 30.7 - - + -
225B LEU* 5.1 0.2 - - - -
268B ALA 3.0 18.7 + - - +
269B ARG* 3.2 9.4 + - - +
271B LEU* 1.3 74.6 - - - +
273B LYS* 1.3 67.1 + - - +
274B ASN 3.3 0.3 + - - -
275B THR* 2.5 29.9 + - - -
277B LEU* 4.0 19.3 - - + -
278B ALA* 3.5 11.7 - - - +
348B TRP* 3.5 33.1 + - + -
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Residues in contact with LYS 273 (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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269B ARG* 3.0 20.3 + - + +
270B TYR* 3.6 14.1 - - + +
271B LEU 3.4 3.4 - - - +
272B THR* 1.3 79.5 + - - +
274B ASN* 1.3 89.9 + - - +
275B THR* 3.3 6.1 + - - +
278B ALA* 4.6 6.1 - - - -
473C LYS* 6.3 3.1 - - - +
482C GLU* 4.5 22.1 + - + +
485C GLN* 2.2 39.8 + - - +
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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