Contacts of the helix formed by residues 265 - 281 (chain B) in PDB entry 1PV2
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 ALA 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B LEU* 4.7 1.1 - - + -
249B GLY 3.3 28.7 - - - +
250B ARG 3.6 12.3 - - - +
251B VAL* 3.8 6.5 - - + -
260B GLY* 3.9 4.7 - - - -
261B ASP* 3.7 10.8 - - - +
262B SER 2.9 12.7 + - - +
264B PHE* 1.3 77.2 - - - +
266B ALA* 1.3 59.4 + - - +
267B ASN 3.2 3.0 + - - -
268B ALA* 3.3 5.3 + - - -
269B LEU* 2.8 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
----------------------------------------------------------
76B ILE* 3.7 25.4 - - + +
77B GLU* 4.0 13.9 - - - -
80B LEU* 3.8 14.8 - - + +
81B PRO* 3.7 11.8 - - + +
184B LEU* 4.0 11.9 - - + -
262B SER 3.9 2.2 + - - -
263B PRO 3.2 16.0 + - - +
264B PHE 3.5 0.4 - - - -
265B ALA* 1.3 77.0 - - - +
267B ASN* 1.3 62.4 + - - +
269B LEU* 3.4 3.4 + - - +
270B GLY* 3.1 17.5 + - - -
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Residues in contact with ASN 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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80B LEU* 3.6 22.7 - - + +
84B HIS* 2.8 34.8 + - - -
264B PHE 5.0 2.5 + - - +
265B ALA 3.3 0.4 - - - -
266B ALA* 1.3 76.1 - - - +
268B ALA* 1.3 61.5 + - - +
270B GLY* 3.1 3.8 + - - -
271B LYS* 2.8 39.0 + - - +
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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
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249B GLY 4.6 7.6 - - - +
251B VAL* 3.8 24.2 - - + +
264B PHE 5.4 1.7 + - - +
265B ALA* 3.3 8.6 + - - +
267B ASN* 1.3 78.3 + - - +
269B LEU* 1.3 56.8 + - - +
271B LYS* 3.4 14.9 + - + +
272B LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 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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81B PRO* 4.8 7.0 - - + -
150B PHE* 4.9 0.4 - - + -
182B ILE* 4.1 19.3 - - + -
183B SER 3.4 24.2 - - - +
184B LEU* 3.5 29.2 - - + -
251B VAL* 3.7 8.7 - - + +
258B LEU* 4.2 12.8 - - + -
259B THR 3.9 29.4 - - - +
260B GLY 4.0 2.0 - - - +
265B ALA 2.8 17.7 + - - +
266B ALA 3.6 6.1 - - - +
268B ALA* 1.3 73.7 - - - +
270B GLY* 1.3 61.1 + - - +
272B LEU* 3.2 5.5 + - + +
273B ALA* 2.8 29.7 + - - +
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Residues in contact with GLY 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PRO* 3.7 27.1 - - - +
84B HIS* 3.4 18.3 - - - +
85B LEU* 4.6 0.2 - - - +
266B ALA 3.1 8.0 + - - -
267B ASN 3.1 6.7 + - - -
269B LEU* 1.3 73.3 - - - +
271B LYS* 1.3 64.3 + - - +
273B ALA* 4.0 5.2 - - - +
274B ALA* 3.0 26.7 + - - +
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Residues in contact with LYS 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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84B HIS* 3.6 25.5 + - + -
267B ASN* 2.8 23.9 + - - +
268B ALA* 3.4 16.6 - - + +
270B GLY* 1.3 77.0 - - - +
272B LEU* 1.3 59.8 + - - +
274B ALA* 4.0 2.7 - - - +
275B GLN* 3.3 43.4 + - - +
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Residues in contact with LEU 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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251B VAL* 4.7 15.7 - - + -
252B HIS 3.9 17.9 - - - +
253B LYS* 4.6 8.3 - - + -
258B LEU* 3.8 33.4 - - + -
268B ALA 2.9 17.1 + - - +
269B LEU* 3.5 10.8 - - + +
271B LYS* 1.3 76.1 - - - +
273B ALA* 1.3 65.2 + - - +
275B GLN* 3.3 2.8 + - + -
276B GLU* 3.0 49.7 + - + +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PRO* 5.8 1.3 - - + -
85B LEU* 3.7 20.4 - - + -
182B ILE* 3.8 29.2 - - + -
258B LEU* 3.7 15.8 - - + +
269B LEU 2.8 20.0 + - - +
270B GLY* 4.0 4.9 - - - +
272B LEU* 1.3 72.9 - - - +
274B ALA* 1.3 65.8 + - - +
277B MET* 3.1 28.6 + - - +
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B HIS* 4.2 22.4 - - + +
85B LEU* 3.5 11.1 - - + +
88B ALA* 4.3 12.1 - - + -
90B PHE* 5.8 0.4 - - - -
270B GLY 3.0 19.0 + - - +
271B LYS* 4.0 4.5 - - - +
273B ALA* 1.3 76.9 - - - +
275B GLN* 1.3 59.8 + - + +
276B GLU 2.8 7.1 + - - -
277B MET* 3.9 0.8 - - - +
278B LEU* 3.0 35.8 + - + +
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Residues in contact with GLN 275 (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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271B LYS* 3.3 34.7 + - - +
272B LEU* 3.3 4.2 + - - +
274B ALA* 1.3 77.6 - - + +
276B GLU* 1.3 66.2 + - + +
278B LEU* 4.5 13.0 - - + -
279B ALA* 4.4 12.7 - - - +
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Residues in contact with GLU 276 (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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180B PHE* 3.4 18.3 - - + -
253B LYS* 2.9 42.2 + - - +
258B LEU* 4.3 11.2 - - + -
272B LEU* 3.0 40.7 + - + +
273B ALA 4.1 1.3 - - - +
274B ALA 3.0 0.8 - - - -
275B GLN* 1.3 82.6 - - - +
277B MET* 1.3 62.8 + - - +
278B LEU 3.2 1.6 - - - -
279B ALA* 4.1 4.0 - - - +
280B ALA* 3.2 27.0 + - - +
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Residues in contact with MET 277 (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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51B ILE* 4.5 4.9 - - + -
85B LEU* 4.2 10.8 - - - -
90B PHE* 3.7 44.2 - - + -
147B ALA* 3.6 25.4 - - + +
148B ALA* 4.1 9.6 - - + -
180B PHE* 3.6 33.7 - - + -
182B ILE* 4.0 25.8 - - - -
258B LEU* 5.2 0.2 - - + -
273B ALA* 3.1 20.2 + - - +
274B ALA 4.2 0.2 - - - +
276B GLU* 1.3 74.2 - - - +
278B LEU* 1.3 59.6 + - - +
280B ALA 3.8 0.7 - - - -
281B TYR* 3.1 35.5 + - + +
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Residues in contact with LEU 278 (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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43B LYS 4.0 11.9 - - - +
44B PRO* 4.0 28.9 - - + +
45B TYR* 4.1 14.1 - - + +
88B ALA* 3.8 25.1 - - + +
90B PHE* 4.8 3.6 - - + -
274B ALA* 3.0 28.1 + - + +
275B GLN* 4.5 11.4 - - + +
277B MET* 1.3 78.3 - - - +
279B ALA* 1.3 60.6 + - - +
281B TYR* 3.4 4.1 + - - +
282B ALA* 3.2 27.5 + - - +
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Residues in contact with ALA 279 (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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275B GLN 4.4 14.3 + - - +
276B GLU* 3.9 5.8 + - - +
278B LEU* 1.3 77.2 - - - +
280B ALA* 1.3 63.4 + - - +
281B TYR 3.4 0.2 - - - -
282B ALA* 3.6 17.4 + - - +
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Residues in contact with ALA 280 (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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180B PHE* 3.5 27.1 - - + -
256B LYS* 4.7 10.8 - - - +
276B GLU 3.2 21.4 + - - +
277B MET 3.9 2.5 - - - +
278B LEU 3.2 0.6 - - - -
279B ALA* 1.3 80.9 - - - +
281B TYR* 1.3 60.4 + - + +
282B ALA 3.3 2.9 + - - -
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Residues in contact with TYR 281 (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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45B TYR* 3.6 42.1 - + + -
49B HIS* 2.4 41.6 + + + -
90B PHE* 3.8 8.7 - + - -
147B ALA* 3.3 27.5 - - + +
179B ARG* 4.0 10.1 - - - -
180B PHE* 4.6 16.4 - + - -
256B LYS* 6.3 0.2 - - - -
277B MET* 3.1 27.7 + - + +
278B LEU* 3.4 3.6 + - - +
279B ALA 3.4 0.2 - - - -
280B ALA* 1.3 81.1 - - + +
282B ALA* 1.3 60.6 + - - +
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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
------------------------------------------------------------
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