Contacts of the helix formed by residues 265 - 280 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A LEU* 4.6 1.3 - - + -
249A GLY 3.3 22.0 - - - +
251A VAL* 3.7 12.3 - - + +
260A GLY* 4.1 3.4 - - - -
261A ASP* 3.4 28.5 - - - +
262A SER 2.9 8.0 + - - +
263A PRO 2.9 1.4 + - - -
264A PHE* 1.3 77.7 - - - +
266A ALA* 1.3 66.7 + - - +
267A ASN 3.2 3.1 + - - -
268A ALA* 3.4 3.6 + - - +
269A LEU* 2.7 26.2 + - - +
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Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 3.7 31.6 - - + +
77A GLU* 3.8 15.9 - - + -
80A LEU* 4.1 3.6 - - + -
81A PRO* 3.3 19.3 - - + +
184A LEU* 3.9 12.3 - - - -
262A SER 3.7 2.8 + - - -
263A PRO 3.0 16.3 + - - +
265A ALA* 1.3 77.2 - - - +
267A ASN* 1.3 64.1 + - - +
269A LEU* 3.5 0.5 - - - +
270A GLY 3.1 16.8 + - - -
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Residues in contact with ASN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.7 26.0 - - + +
84A HIS* 3.0 35.5 + - - -
263A PRO 4.7 0.6 + - - -
264A PHE 5.1 2.9 + - - +
265A ALA 3.2 0.4 - - - -
266A ALA* 1.3 75.4 - - - +
268A ALA* 1.3 61.6 + - - +
269A LEU 2.9 3.1 - - - -
270A GLY* 2.7 25.6 + - - -
271A LYS* 3.0 28.7 + - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A GLY 4.6 8.7 - - - +
251A VAL* 3.8 19.9 - - + +
264A PHE 5.3 2.6 + - - +
265A ALA* 3.4 7.7 + - - +
267A ASN* 1.3 84.3 + - - +
269A LEU* 1.3 59.3 + - - +
271A LYS* 3.3 26.7 - - + +
272A LEU* 3.3 10.4 + - - +
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 4.8 7.2 - - + -
182A ILE* 4.1 18.8 - - + -
183A SER 3.8 7.4 - - - +
184A LEU* 3.6 44.4 - - + -
251A VAL* 3.5 13.0 - - + +
252A HIS 5.5 0.2 - - - +
258A LEU* 4.4 11.2 - - + -
259A THR* 3.7 29.8 - - - +
260A GLY 3.9 2.2 - - - +
265A ALA 2.7 23.3 + - - +
266A ALA 3.5 4.3 - - - +
268A ALA* 1.3 70.4 - - - +
270A GLY* 1.3 65.9 + - - +
271A LYS 3.1 1.6 - - - -
272A LEU* 3.0 5.8 + - + +
273A ALA* 2.9 22.4 + - + +
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Residues in contact with GLY 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 3.7 28.4 - - - +
84A HIS* 3.6 18.2 - - - +
85A LEU* 5.2 0.2 - - - +
266A ALA 3.1 7.4 + - - -
267A ASN 2.7 13.7 + - - -
269A LEU* 1.3 72.0 - - - +
271A LYS* 1.3 59.2 + - - -
273A ALA* 3.9 3.8 - - - +
274A ALA* 3.0 26.5 + - - +
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Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A HIS* 4.2 22.0 - - + +
267A ASN* 3.0 26.2 + - - +
268A ALA* 3.3 25.4 - - + +
270A GLY* 1.3 76.5 - - - +
272A LEU* 1.3 60.6 + - - +
274A ALA* 3.6 4.4 - - - +
275A GLN* 3.3 33.5 + - - +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A VAL* 3.9 24.2 - - + -
252A HIS* 4.7 5.4 - - - +
253A LYS* 4.1 17.3 - - + -
258A LEU* 3.8 36.3 - - + -
268A ALA 3.3 6.7 + - - +
269A LEU* 3.0 13.6 + - + +
271A LYS* 1.3 77.7 - - - +
273A ALA* 1.3 59.6 + - - +
274A ALA 3.1 1.8 - - - -
275A GLN* 3.3 5.5 + - + +
276A GLU* 2.9 47.0 + - + +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 5.4 1.3 - - + +
85A LEU* 4.2 23.1 - - + -
182A ILE* 4.4 22.2 - - + -
258A LEU* 3.7 20.6 - - + +
269A LEU* 2.9 14.6 + - + +
270A GLY* 4.0 6.5 - - - +
272A LEU* 1.3 76.6 - - - +
274A ALA* 1.3 60.1 + - - +
277A MET* 2.8 34.0 + - + +
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A HIS* 3.6 21.3 - - + +
85A LEU* 4.2 10.8 - - - +
88A ALA* 5.4 3.4 - - + -
90A PHE* 6.4 0.2 - - - -
270A GLY 3.0 18.0 + - - +
271A LYS* 3.6 6.7 - - - +
273A ALA* 1.3 73.7 - - - +
275A GLN* 1.3 57.4 + - - +
277A MET* 3.0 4.2 + - - +
278A LEU* 2.7 51.2 + - + +
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Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A LYS* 3.3 21.0 + - - +
272A LEU* 3.3 9.8 + - + +
274A ALA* 1.3 78.1 - - - +
276A GLU* 1.3 65.6 + - - +
278A LEU* 4.4 7.6 - - - +
279A ALA* 2.9 38.9 + - + +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PHE* 3.2 33.7 - - + -
253A LYS* 3.5 33.3 + - - +
255A ARG 5.3 0.9 - - - +
258A LEU* 3.9 13.5 - - + -
272A LEU* 2.9 42.8 + - + +
275A GLN* 1.3 81.2 - - + +
277A MET* 1.3 59.9 + - - +
279A ALA* 5.0 1.6 - - - +
280A ALA* 3.3 17.5 + - - +
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Residues in contact with MET 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE* 3.7 26.7 - - + -
85A LEU* 3.6 26.5 - - + -
90A PHE* 3.6 36.6 - - + -
147A ALA* 3.3 21.8 - - - +
180A PHE* 3.6 31.6 - - + -
182A ILE* 3.8 22.0 - - + -
258A LEU* 5.5 0.2 - - + -
273A ALA* 2.8 22.3 + - - +
274A ALA 3.0 3.2 + - - +
276A GLU* 1.3 76.3 - - - +
278A LEU* 1.3 65.2 + - - +
280A ALA* 3.2 16.6 + - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA* 3.8 43.1 - - + +
90A PHE* 5.1 5.8 - - + -
274A ALA* 2.7 31.2 + - + +
275A GLN* 3.6 6.7 - - - +
277A MET* 1.3 76.0 - - - +
279A ALA* 1.3 63.3 + - - +
280A ALA 3.2 5.9 + - - +
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A GLN* 2.9 19.7 + - + +
276A GLU* 5.0 2.0 - - - +
278A LEU* 1.3 77.8 - - - +
280A ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PHE* 4.5 13.5 - - + -
256A LYS* 5.1 9.4 - - - +
276A GLU 3.3 20.5 + - - +
277A MET 3.2 15.2 - - - +
278A LEU 3.2 5.5 - - - +
279A ALA* 1.3 82.8 - - - +
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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