Contacts of the helix formed by residues 265 - 279 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184C LEU* 4.6 1.3 - - + -
249C GLY* 3.3 25.4 - - - +
251C VAL* 3.8 13.0 - - + +
260C GLY* 3.8 4.0 - - - -
261C ASP* 3.5 29.4 - - - +
262C SER 3.0 9.2 + - - +
264C PHE* 1.3 79.2 - - - +
266C ALA* 1.3 65.6 + - - +
267C ASN 3.2 0.8 + - - -
268C ALA* 3.3 3.3 + - - +
269C LEU* 2.9 25.7 + - - +
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Residues in contact with ALA 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ILE* 3.7 32.3 - - + +
77C GLU* 3.9 10.1 - - - -
80C LEU* 4.2 7.6 - - + -
81C PRO* 3.5 15.0 - - + +
184C LEU* 3.9 13.0 - - + -
262C SER 3.6 2.8 + - - -
263C PRO 3.2 18.8 + - - +
264C PHE 3.1 1.4 - - - -
265C ALA* 1.3 79.3 - - - +
267C ASN* 1.3 64.2 + - - +
269C LEU* 3.6 0.9 + - - +
270C GLY* 3.3 13.5 + - - -
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Residues in contact with ASN 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 3.8 26.3 - - + +
84C HIS* 3.0 31.3 + - - -
264C PHE 4.2 5.1 + - - +
265C ALA 3.3 0.4 - - - -
266C ALA* 1.3 78.9 - - - +
268C ALA* 1.3 64.4 + - - +
270C GLY* 3.0 13.9 + - - -
271C LYS* 3.2 29.0 + - - +
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Residues in contact with ALA 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C GLY 4.8 6.1 - - - +
251C VAL* 4.1 19.4 - - + +
264C PHE 4.9 2.6 + - - +
265C ALA* 3.3 8.7 + - - +
267C ASN* 1.3 78.3 - - - +
269C LEU* 1.3 56.9 + - - +
271C LYS* 3.2 23.1 - - + +
272C LEU* 3.0 26.7 + - - +
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C PRO* 4.4 10.8 - - + -
150C PHE* 4.6 0.2 - - + -
182C ILE* 3.8 21.8 - - + -
183C SER 3.9 4.9 - - - +
184C LEU* 3.9 34.8 - - + -
251C VAL* 3.6 14.0 - - + +
258C LEU* 3.9 13.5 - - + -
259C THR* 3.5 40.4 - - - +
260C GLY* 5.0 0.4 - - - -
265C ALA 2.9 18.9 + - - +
266C ALA 3.8 2.5 - - - +
268C ALA* 1.3 73.8 - - - +
270C GLY* 1.3 60.2 + - - +
272C LEU* 3.3 6.2 + - + +
273C ALA* 2.8 30.1 + - + +
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Residues in contact with GLY 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO* 3.7 25.2 - - - +
84C HIS* 3.5 21.3 - - - +
85C LEU* 4.9 0.3 - - - +
266C ALA 3.3 4.6 + - - -
267C ASN 3.0 9.4 + - - -
269C LEU* 1.3 78.2 - - - +
271C LYS* 1.3 64.0 + - - +
273C ALA* 3.8 3.5 - - - +
274C ALA* 3.0 23.6 + - - +
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Residues in contact with LYS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C HIS* 3.7 24.7 - - + -
267C ASN* 3.2 25.7 + - - +
268C ALA* 3.2 23.8 - - + +
270C GLY* 1.3 77.9 - - - +
272C LEU* 1.3 64.3 + - - +
274C ALA* 3.5 2.8 - - - +
275C GLN* 2.8 44.6 + - - +
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C VAL* 3.9 26.2 - - + -
252C HIS* 3.8 28.0 - - - +
253C LYS* 4.4 8.1 - - + -
258C LEU* 3.6 20.2 - - + -
268C ALA 3.0 9.8 + - - +
269C LEU* 3.6 11.0 - - + +
271C LYS* 1.3 79.2 - - - +
273C ALA* 1.3 63.6 + - - +
275C GLN* 3.5 15.2 + - - +
276C GLU* 3.1 43.3 + - + +
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Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C PRO* 6.1 0.7 - - + -
85C LEU* 4.1 16.4 - - + -
182C ILE* 4.1 35.0 - - + -
258C LEU* 4.0 13.8 - - + +
269C LEU 2.8 21.6 + - - +
270C GLY* 3.8 4.9 - - - +
272C LEU* 1.3 73.3 - - - +
274C ALA* 1.3 58.3 + - - +
276C GLU* 4.0 0.5 - - - +
277C MET* 2.9 35.6 + - - +
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Residues in contact with ALA 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C HIS* 4.2 16.2 - - + +
85C LEU* 3.9 14.3 - - + +
88C ALA* 4.2 21.0 - - + +
270C GLY 3.0 16.5 + - - +
271C LYS* 3.0 5.0 + - - +
273C ALA* 1.3 76.3 - - - +
275C GLN* 1.3 64.3 + - + +
277C MET* 3.8 1.0 - - - +
278C LEU* 2.9 34.3 + - + +
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Residues in contact with GLN 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C LYS* 2.8 35.7 + - - +
272C LEU* 3.6 24.9 + - - +
274C ALA* 1.3 79.3 - - + +
276C GLU* 1.3 69.5 - - - +
278C LEU* 3.1 7.4 + - - +
279C ALA* 3.0 25.1 + - - +
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Residues in contact with GLU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C PHE* 3.7 23.8 - - + -
253C LYS* 3.3 34.7 + - + +
258C LEU* 3.7 16.4 - - + -
272C LEU* 3.1 29.7 + - + +
273C ALA 4.1 1.3 - - - +
275C GLN* 1.3 79.3 - - - +
277C MET* 1.3 62.8 + - - +
278C LEU 3.4 0.2 + - - -
279C ALA* 3.6 11.3 - - - +
280C ALA* 3.5 17.7 - - - +
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Residues in contact with MET 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ILE* 4.5 4.9 - - + -
85C LEU* 3.6 20.6 - - + -
90C PHE* 3.6 43.4 - - + -
147C ALA* 3.7 38.8 - - + +
148C ALA* 3.8 21.5 - - + -
180C PHE* 3.6 30.0 - - + -
182C ILE* 4.2 9.9 - - + -
273C ALA* 2.9 20.0 + - - +
274C ALA 4.1 1.6 - - - +
276C GLU* 1.3 74.6 - - - +
278C LEU* 1.3 59.0 + - - +
280C ALA* 3.2 20.8 + - - +
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Residues in contact with LEU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ALA* 3.9 38.8 - - + +
90C PHE* 4.7 6.5 - - + -
274C ALA* 2.9 27.6 + - + +
275C GLN* 3.4 6.5 - - - +
277C MET* 1.3 74.0 - - - +
279C ALA* 1.3 53.4 + - - +
280C ALA 2.5 26.5 + - - +
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C GLN 3.0 15.4 + - - +
276C GLU* 3.6 7.8 - - - +
278C LEU* 1.3 71.5 - - - +
280C ALA* 1.3 62.7 + - - +
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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