Contacts of the helix formed by residues 265 - 279 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184E LEU* 4.4 1.1 - - + -
249E GLY* 3.3 22.5 - - - +
250E ARG 3.5 5.4 - - - +
251E VAL* 3.5 3.9 - - + +
260E GLY* 3.7 8.3 - - - -
261E ASP* 3.4 31.4 - - - +
262E SER 2.9 9.8 + - - +
264E PHE* 1.3 77.4 - - - +
266E ALA* 1.3 64.8 + - - +
267E ASN 3.5 0.9 - - - -
268E ALA* 3.4 3.1 + - - +
269E LEU* 2.9 25.3 + - - +
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Residues in contact with ALA 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ILE* 3.8 32.8 - - + +
77E GLU* 4.1 10.3 - - - -
80E LEU* 4.1 8.3 - - + -
81E PRO* 3.8 11.7 - - + +
184E LEU* 4.0 11.2 - - + -
262E SER 3.7 1.8 + - - -
263E PRO 3.2 18.1 + - - +
264E PHE 3.2 1.8 - - - -
265E ALA* 1.3 79.4 - - - +
267E ASN* 1.3 64.3 + - - +
269E LEU* 3.6 2.9 - - - +
270E GLY* 3.1 17.0 + - - -
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Residues in contact with ASN 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ASP* 3.4 14.3 - - + +
36E LEU* 3.7 7.3 - - - +
37E ASP* 3.1 45.0 + - - +
80E LEU* 3.8 16.1 - - + +
84E HIS* 2.8 35.2 + - - -
264E PHE 4.6 4.3 + - - +
265E ALA 3.5 0.4 - - - -
266E ALA* 1.3 78.3 - - - +
268E ALA* 1.3 63.4 + - - +
270E GLY* 3.1 4.9 + - - -
271E LYS* 3.0 30.1 + - - +
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Residues in contact with ALA 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E GLY 4.8 6.3 - - - +
251E VAL* 3.7 24.6 - - + +
264E PHE 5.2 1.9 + - - +
265E ALA* 3.4 4.9 + - - +
266E ALA 3.4 0.4 - - - -
267E ASN* 1.3 75.9 + - - +
269E LEU* 1.3 55.0 + - - +
271E LYS* 3.1 18.5 + - - +
272E LEU* 2.8 34.5 + - - +
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Residues in contact with LEU 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E PRO* 4.5 10.3 - - + -
150E PHE* 4.7 0.2 - - + -
182E ILE* 3.9 20.9 - - + -
183E SER 3.8 6.1 - - - +
184E LEU* 3.7 43.3 - - + -
251E VAL* 3.5 8.6 - - + +
258E LEU* 3.8 34.8 - - + +
259E THR 3.9 10.5 - - - +
260E GLY* 4.3 0.9 - - - +
265E ALA 2.9 19.2 + - - +
266E ALA 3.6 4.5 - - - +
268E ALA* 1.3 72.9 - - - +
270E GLY* 1.3 60.4 + - - +
272E LEU* 4.2 8.3 - - + -
273E ALA* 2.8 30.0 + - - +
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Residues in contact with GLY 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E PRO* 3.7 28.1 - - - +
84E HIS* 3.4 18.4 - - - +
85E LEU* 4.9 0.2 - - - +
266E ALA 3.1 7.8 + - - -
267E ASN 3.1 8.4 + - - -
269E LEU* 1.3 76.4 - - - +
271E LYS* 1.3 61.2 + - - +
273E ALA* 3.9 3.0 - - - +
274E ALA* 3.0 26.2 + - - +
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Residues in contact with LYS 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ASP* 3.8 25.1 + - - +
38E GLY* 4.5 9.7 - - - +
84E HIS* 3.5 26.0 + - + +
267E ASN* 3.0 29.5 + - - +
268E ALA* 3.3 20.2 - - - +
270E GLY* 1.3 75.2 - - - +
272E LEU* 1.3 65.7 + - - +
274E ALA* 3.7 3.8 - - - +
275E GLN* 3.0 41.2 + - - +
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Residues in contact with LEU 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E VAL* 4.0 25.1 - - + -
252E HIS 3.9 26.2 - - - +
253E LYS* 4.4 8.1 - - + -
258E LEU* 4.1 19.5 - - + -
268E ALA 2.8 19.4 + - - +
269E LEU* 3.6 9.4 - - + +
271E LYS* 1.3 73.3 - - - +
273E ALA* 1.3 64.6 + - - +
275E GLN* 3.1 6.8 + - + +
276E GLU* 2.9 46.8 + - + +
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Residues in contact with ALA 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E PRO* 6.0 1.3 - - + -
85E LEU* 3.8 22.0 - - + -
182E ILE* 4.1 28.0 - - + -
258E LEU* 3.8 14.8 - - + +
269E LEU* 2.8 22.1 + - + +
270E GLY* 3.9 3.1 - - - +
272E LEU* 1.3 72.5 - - - +
274E ALA* 1.3 65.7 - - - +
276E GLU* 3.9 0.2 - - - -
277E MET* 2.8 29.6 + - - +
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Residues in contact with ALA 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E HIS* 4.1 22.2 - - + +
85E LEU* 3.7 12.2 - - + +
88E ALA* 4.2 12.3 - - + -
90E PHE* 5.4 0.7 - - - -
270E GLY 3.0 17.6 + - - +
271E LYS* 3.7 5.4 - - - +
273E ALA* 1.3 77.2 - - - +
275E GLN* 1.3 59.0 + - - +
277E MET* 3.9 1.0 - - - +
278E LEU* 2.8 41.2 + - + +
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Residues in contact with GLN 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E LYS* 3.0 33.2 + - - +
272E LEU* 3.6 6.6 - - + +
274E ALA* 1.3 79.2 - - - +
276E GLU* 1.3 69.1 + - - +
278E LEU* 3.4 9.5 + - + +
279E ALA* 3.1 23.4 + - - +
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Residues in contact with GLU 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E PHE* 3.4 29.1 - - + -
253E LYS* 3.3 32.9 + - + +
255E ARG 5.2 0.9 - - - +
258E LEU* 4.0 18.6 - - + -
272E LEU* 2.9 34.3 + - + +
275E GLN* 1.3 82.9 - - - +
277E MET* 1.3 61.3 + - - +
279E ALA* 3.4 21.3 + - - +
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Residues in contact with MET 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ILE* 3.7 17.0 - - + -
85E LEU* 3.9 20.9 - - - -
90E PHE* 3.6 28.6 - - + -
147E ALA* 3.6 34.8 - - + +
148E ALA* 3.9 16.6 - - + -
180E PHE* 3.7 30.3 - - + -
182E ILE* 4.0 10.5 - - + -
273E ALA* 2.8 19.6 + - - +
274E ALA 4.0 0.2 - - - +
276E GLU* 1.3 73.3 - - - +
278E LEU* 1.3 67.1 + - - +
279E ALA 3.2 0.4 - - - -
280E ALA* 3.5 7.4 + - - +
281E TYR 3.6 21.0 + - - +
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Residues in contact with LEU 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E ARG* 4.8 11.0 - - - +
88E ALA* 3.7 38.6 - - + +
90E PHE* 4.1 11.0 - - + -
274E ALA* 2.8 26.4 + - + +
275E GLN* 3.7 9.2 - - + +
277E MET* 1.3 75.9 - - - +
279E ALA* 1.3 52.3 + - - +
280E ALA* 2.5 22.0 + - - -
281E TYR 3.8 1.0 + - - -
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Residues in contact with ALA 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E GLN 3.1 16.2 + - - +
276E GLU* 3.4 14.0 + - - +
277E MET 3.2 0.6 - - - -
278E LEU* 1.3 71.9 - - - +
280E ALA* 1.3 61.2 + - - +
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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