Contacts of the helix formed by residues 265 - 281 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184G LEU* 4.5 1.6 - - + -
249G GLY 3.7 10.5 - - - +
250G ARG 3.6 15.7 - - - +
251G VAL* 3.7 3.4 - - + +
260G GLY* 3.8 7.6 - - - -
261G ASP* 3.4 26.2 - - - +
262G SER 2.9 14.5 + - - +
264G PHE* 1.3 79.7 - - - +
266G ALA* 1.3 63.3 + - - +
267G ASN 3.3 2.0 + - - -
268G ALA* 3.3 4.4 + - - -
269G LEU* 2.9 23.9 + - - +
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Residues in contact with ALA 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G ILE* 3.6 28.5 - - + +
77G GLU* 4.1 10.3 - - - -
80G LEU* 3.8 15.7 - - + -
81G PRO* 3.6 11.3 - - + +
184G LEU* 4.2 10.5 - - + -
262G SER 3.9 1.2 + - - -
263G PRO 3.0 17.9 + - - +
264G PHE 3.4 0.4 - - - -
265G ALA* 1.3 78.6 - - - +
267G ASN* 1.3 63.0 + - - +
269G LEU* 3.3 3.4 + - - +
270G GLY* 3.1 17.7 + - - -
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Residues in contact with ASN 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G ASP* 3.9 23.2 - - - +
36G LEU* 3.6 35.2 + - - +
80G LEU* 3.9 11.5 - - + +
84G HIS* 3.2 30.1 + - - -
264G PHE 4.9 2.8 + - - +
265G ALA 3.3 0.4 - - - -
266G ALA* 1.3 78.3 - - - +
268G ALA* 1.3 59.9 + - - +
270G GLY* 3.1 3.6 + - - -
271G LYS* 3.0 42.3 + - - +
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Residues in contact with ALA 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G GLY 4.6 9.6 - - - +
251G VAL* 3.7 28.5 - - + +
264G PHE 5.3 2.0 + - - +
265G ALA* 3.3 6.0 + - - +
267G ASN* 1.3 77.9 - - - +
269G LEU* 1.3 57.1 + - - +
271G LYS* 3.5 12.1 - - - +
272G LEU* 2.9 26.7 + - - +
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Residues in contact with LEU 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G PRO* 4.6 6.1 - - + -
150G PHE* 4.8 2.5 - - + -
182G ILE* 3.8 22.0 - - + -
183G SER 3.4 23.6 - - - +
184G LEU* 3.8 26.0 - - + -
251G VAL* 3.6 6.3 - - + +
258G LEU* 4.2 15.0 - - + -
259G THR 4.0 26.5 - - - +
260G GLY* 4.1 3.4 - - - +
265G ALA 2.9 16.7 + - - +
266G ALA* 3.5 5.6 - - - +
267G ASN 3.1 0.2 - - - -
268G ALA* 1.3 76.9 - - - +
270G GLY* 1.3 56.8 + - - +
271G LYS 3.2 0.2 - - - -
272G LEU* 4.4 6.1 - - + -
273G ALA* 2.7 38.5 + - + +
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Residues in contact with GLY 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G PRO* 3.6 20.3 - - - +
84G HIS* 3.6 26.9 - - - +
85G LEU* 4.8 0.9 - - - +
266G ALA 3.1 7.6 + - - -
267G ASN 3.1 7.2 + - - -
269G LEU* 1.3 74.8 - - - +
271G LYS* 1.3 57.3 + - - +
273G ALA* 4.0 3.2 - - - +
274G ALA* 2.9 31.7 + - - +
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Residues in contact with LYS 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G LEU 5.7 1.4 + - - -
84G HIS* 3.8 28.8 - - + -
267G ASN* 3.0 28.3 + - - +
268G ALA* 3.5 13.9 - - - +
269G LEU 3.2 0.2 - - - -
270G GLY* 1.3 76.1 - - - +
272G LEU* 1.3 62.7 + - - +
274G ALA* 3.4 4.3 - - - +
275G GLN* 3.1 45.6 + - - +
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Residues in contact with LEU 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251G VAL* 4.4 13.7 - - + -
252G HIS* 3.6 37.7 - - - +
253G LYS* 4.5 7.9 - - + -
258G LEU* 3.9 20.9 - - + -
268G ALA 2.9 17.4 + - - +
269G LEU* 3.1 8.0 + - + +
271G LYS* 1.3 76.7 - - - +
273G ALA* 1.3 66.0 + - - +
275G GLN* 3.3 12.0 + - - +
276G GLU* 3.0 44.7 + - + +
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Residues in contact with ALA 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G PRO* 5.9 0.9 - - + -
85G LEU* 3.8 27.8 - - + -
182G ILE* 4.4 20.0 - - + -
258G LEU* 3.6 19.5 - - + +
269G LEU* 2.7 22.1 + - + +
270G GLY* 4.0 1.8 - - - +
272G LEU* 1.3 72.7 - - - +
274G ALA* 1.3 62.9 + - - +
277G MET* 3.0 30.9 + - - +
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Residues in contact with ALA 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G HIS* 4.5 14.1 - - + +
85G LEU* 3.9 10.9 - - - +
88G ALA* 4.3 17.0 - - + +
270G GLY 2.9 21.0 + - - +
271G LYS* 3.4 7.2 - - - +
273G ALA* 1.3 76.9 - - - +
275G GLN* 1.3 58.2 + - + +
277G MET* 3.8 1.0 - - - +
278G LEU* 2.9 41.1 + - + +
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Residues in contact with GLN 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271G LYS* 3.1 42.7 + - - +
272G LEU* 3.9 11.7 - - - +
274G ALA* 1.3 80.8 - - + +
276G GLU* 1.3 71.2 + - + +
278G LEU* 3.2 7.6 + - - +
279G ALA* 3.0 26.0 + - - +
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Residues in contact with GLU 276 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G PHE* 3.4 30.0 - - + -
253G LYS* 3.3 36.4 + - - +
255G ARG 4.8 1.2 - - - +
258G LEU* 4.0 19.1 - - + -
272G LEU* 3.0 33.5 + - + +
275G GLN* 1.3 82.9 - - + +
277G MET* 1.3 61.7 + - - +
279G ALA* 3.6 5.2 + - - +
280G ALA* 3.5 16.6 + - - +
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Residues in contact with MET 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ILE* 4.5 3.4 - - + -
85G LEU* 3.6 20.2 - - + -
90G PHE* 3.4 40.3 - - + -
147G ALA* 3.6 37.0 - - + +
148G ALA* 3.8 22.2 - - + -
180G PHE* 3.4 32.1 - - + -
182G ILE* 4.1 10.8 - - - -
273G ALA* 3.0 20.0 + - - +
274G ALA 4.1 0.2 - - - +
276G GLU* 1.3 74.2 - - - +
278G LEU* 1.3 59.5 + - - +
281G TYR* 3.1 27.6 + - - +
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Residues in contact with LEU 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G PRO* 6.4 2.9 - - + -
43G LYS 3.4 27.4 - - - +
45G TYR* 3.7 29.8 - - + +
88G ALA* 3.8 27.6 - - + +
90G PHE* 4.7 1.6 - - + -
274G ALA* 2.9 26.4 + - + +
275G GLN* 3.2 7.4 + - + +
277G MET* 1.3 78.4 - - - +
279G ALA* 1.3 59.2 + - - +
281G TYR* 3.2 29.8 - - + +
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Residues in contact with ALA 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275G GLN 3.0 16.9 + - - +
276G GLU* 4.1 5.2 - - - +
277G MET 3.4 0.2 - - - -
278G LEU* 1.3 78.3 - - - +
280G ALA* 1.3 58.7 + - + +
281G TYR* 3.8 18.1 + - - -
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Residues in contact with ALA 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G PHE* 4.6 15.3 - - + -
256G LYS* 5.0 11.2 - - - +
276G GLU 3.5 14.2 + - - +
278G LEU 3.3 0.2 - - - -
279G ALA* 1.3 76.7 - - + +
281G TYR* 1.3 82.5 + - - +
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Residues in contact with TYR 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G TYR* 3.8 41.6 + + + -
49G HIS* 4.7 5.5 + - - -
90G PHE* 3.9 10.7 - - - -
147G ALA* 4.7 8.5 - - - +
180G PHE* 6.1 2.4 - - - -
277G MET* 3.1 22.0 + - - +
278G LEU* 3.2 25.6 - - + -
279G ALA* 3.8 15.6 + - - -
280G ALA* 1.3 91.1 - - - +
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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
------------------------------------------------------------
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