Contacts of the helix formed by residues 265 - 280 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184F LEU* 4.5 2.2 - - + -
249F GLY* 3.6 20.3 - - - +
250F ARG 3.8 1.3 - - - +
251F VAL* 3.8 3.4 - - + -
260F GLY* 3.8 11.4 - - - -
261F ASP* 3.6 32.1 - - - +
262F SER 2.8 11.5 + - - +
264F PHE* 1.3 78.0 - - - +
266F ALA* 1.3 64.7 + - - +
267F ASN 3.4 0.7 - - - -
268F ALA* 3.3 4.6 + - - +
269F LEU* 2.8 25.9 + - - +
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Residues in contact with ALA 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F ILE* 3.9 19.1 - - + +
77F GLU* 4.1 9.9 - - - -
80F LEU* 3.8 22.0 - - + -
81F PRO* 3.6 10.5 - - + +
184F LEU* 4.2 11.4 - - - -
262F SER 3.6 2.4 + - - -
263F PRO* 3.3 18.5 + - + +
264F PHE 3.1 2.0 - - - -
265F ALA* 1.3 77.9 - - - +
267F ASN* 1.3 63.6 + - - +
269F LEU* 3.3 3.8 + - - +
270F GLY* 3.1 16.1 + - - -
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Residues in contact with ASN 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F GLY 3.6 21.8 + - - +
80F LEU* 3.8 25.2 - - + +
84F HIS* 2.9 32.2 + - - -
264F PHE 4.5 3.8 + - - +
265F ALA 3.4 0.2 - - - -
266F ALA* 1.3 74.7 - - - +
268F ALA* 1.3 68.2 + - - +
270F GLY* 2.8 13.9 + - - +
271F LYS* 3.1 27.1 + - - +
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Residues in contact with ALA 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F GLY 4.3 9.4 - - - +
251F VAL* 3.7 24.2 - - + +
264F PHE 5.0 2.8 + - - +
265F ALA* 3.3 11.3 + - - +
267F ASN* 1.3 78.0 + - - +
269F LEU* 1.3 61.8 + - - +
271F LYS* 3.6 14.2 + - - +
272F LEU* 3.1 22.7 + - - +
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Residues in contact with LEU 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F PRO* 4.8 6.7 - - + -
150F PHE* 4.7 2.9 - - + -
182F ILE* 3.8 28.3 - - + -
183F SER 3.5 23.3 - - - +
184F LEU* 3.8 26.2 - - + -
251F VAL* 3.5 10.3 - - + +
258F LEU* 4.1 25.6 - - + -
259F THR 4.1 7.9 - - - +
260F GLY 4.1 2.2 - - - +
265F ALA 2.8 17.6 + - - +
266F ALA 3.5 5.6 - - - +
268F ALA* 1.3 75.6 - - - +
270F GLY* 1.3 59.2 + - - +
272F LEU* 3.3 7.4 + - + -
273F ALA* 2.8 34.8 + - + +
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Residues in contact with GLY 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F PRO* 3.7 28.2 - - - +
84F HIS* 3.7 17.3 - - - +
85F LEU* 4.9 1.0 - - - +
266F ALA 3.1 7.4 + - - -
267F ASN 2.8 7.5 + - - -
269F LEU* 1.3 75.6 - - - +
271F LYS* 1.3 57.2 + - - +
273F ALA* 3.9 3.1 - - - +
274F ALA* 2.8 32.7 + - - +
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Residues in contact with LYS 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F GLY* 3.9 23.8 - - - +
41F TYR* 3.4 19.3 - - + +
84F HIS* 3.9 10.2 - - + -
267F ASN* 3.1 27.3 + - - +
268F ALA* 3.7 17.1 - - - +
270F GLY* 1.3 74.4 - - - +
272F LEU* 1.3 64.6 + - - +
274F ALA* 3.1 2.4 + - - +
275F GLN* 2.8 38.6 + - - +
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Residues in contact with LEU 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F VAL* 4.3 13.5 - - + -
252F HIS* 3.7 39.7 - - - +
253F LYS* 4.3 9.0 - - + +
258F LEU* 4.2 20.4 - - + -
268F ALA 3.1 16.2 + - - +
269F LEU* 3.3 7.4 + - + +
271F LYS* 1.3 77.5 - - - +
273F ALA* 1.3 60.1 + - - +
275F GLN* 3.7 5.1 - - + +
276F GLU* 2.9 51.4 + - + +
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Residues in contact with ALA 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F PRO* 6.1 0.9 - - + -
85F LEU* 4.0 13.7 - - + -
182F ILE* 4.0 29.2 - - + -
258F LEU* 3.5 22.9 - - + +
269F LEU* 2.8 23.1 + - + +
270F GLY* 3.9 3.6 - - - +
272F LEU* 1.3 73.5 - - - +
274F ALA* 1.3 62.3 + - - +
276F GLU 4.0 0.2 - - - -
277F MET* 3.1 30.3 + - - +
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Residues in contact with ALA 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F TYR* 3.4 31.2 - - + +
84F HIS 4.0 13.7 - - - +
85F LEU* 3.8 12.5 - - + +
88F ALA* 4.1 8.3 - - + -
90F PHE* 4.8 0.9 - - - -
270F GLY 2.8 22.6 + - - +
271F LYS 3.5 0.2 - - - +
273F ALA* 1.3 74.2 - - - +
275F GLN* 1.3 56.9 + - - +
277F MET* 3.9 1.0 - - - +
278F LEU* 2.9 36.2 + - - +
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Residues in contact with GLN 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ASP 5.3 1.4 + - - -
41F TYR* 3.7 26.3 - - - -
271F LYS* 2.8 34.9 + - - +
272F LEU* 3.7 6.1 - - + +
274F ALA* 1.3 74.2 - - - +
276F GLU* 1.3 66.2 + - + +
278F LEU* 3.2 8.6 + - - +
279F ALA* 3.1 25.6 + - - +
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Residues in contact with GLU 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F PHE* 3.3 30.8 - - + -
253F LYS* 3.3 41.4 + - + +
255F ARG 4.9 1.9 - - - +
258F LEU* 4.2 11.2 - - + -
272F LEU* 2.9 36.4 + - + +
273F ALA 4.1 2.0 - - - +
275F GLN* 1.3 77.5 - - + +
277F MET* 1.3 60.0 + - - +
279F ALA* 3.8 5.3 + - - +
280F ALA* 3.5 15.1 + - - +
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Residues in contact with MET 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ILE* 3.8 11.4 - - + -
85F LEU* 3.8 21.3 - - - -
90F PHE* 3.6 42.0 - - + -
147F ALA* 3.6 22.7 - - + +
148F ALA* 4.0 20.0 - - + -
180F PHE* 3.5 31.2 - - + -
182F ILE* 4.2 9.2 - - - -
273F ALA* 3.1 16.2 + - - +
274F ALA 4.0 0.7 - - - +
276F GLU* 1.3 75.8 - - - +
278F LEU* 1.3 64.5 + - - +
280F ALA 3.3 4.0 + - - -
281F TYR* 2.9 28.8 - - + -
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Residues in contact with LEU 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F TYR* 3.7 32.1 - - + -
43F LYS 3.2 27.1 - - - +
44F PRO 3.9 1.6 - - - -
45F TYR* 3.9 13.2 - - + +
88F ALA* 3.8 29.8 - - + +
90F PHE* 4.6 4.9 - - + -
274F ALA 2.9 23.1 + - - +
275F GLN* 3.5 10.3 - - + +
277F MET* 1.3 78.4 - - - +
279F ALA* 1.3 60.8 + - - +
280F ALA 3.4 0.7 + - - -
281F TYR* 3.4 20.8 + - - +
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Residues in contact with ALA 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F GLN 3.1 15.3 + - - +
276F GLU* 4.3 5.6 - - - +
277F MET 3.3 0.2 - - - -
278F LEU* 1.3 78.1 - - - +
280F ALA* 1.3 59.2 + - - +
281F TYR 3.2 4.9 + - - -
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Residues in contact with ALA 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F PHE* 4.0 20.2 - - + -
256F LYS* 5.2 7.6 - - - +
276F GLU 3.5 16.2 + - - +
277F MET 3.3 6.2 + - - +
278F LEU 3.2 1.2 - - - -
279F ALA* 1.3 78.4 - - - +
281F TYR* 1.3 69.1 + - + +
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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