Contacts of the helix formed by residues 265 - 281 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D LEU* 4.4 1.3 - - + -
249D GLY* 3.7 17.9 - - - +
250D ARG 3.6 24.0 - - - +
251D VAL* 3.9 2.7 - - + -
260D GLY* 3.8 8.7 - - - -
261D ASP* 3.7 12.1 - - - +
262D SER 2.9 12.5 + - - +
264D PHE* 1.3 77.6 - - - +
266D ALA* 1.3 58.4 + - - +
267D ASN 3.4 0.9 - - - -
268D ALA* 3.3 3.7 + - - -
269D LEU* 2.8 33.1 + - - +
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Residues in contact with ALA 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ILE* 3.9 29.8 - - + +
77D GLU* 3.9 13.2 - - - -
80D LEU* 4.1 7.4 - - + -
81D PRO* 3.2 17.6 - - + +
184D LEU* 3.9 11.7 - - + -
262D SER 3.8 2.4 + - - -
263D PRO 3.2 17.4 + - - +
264D PHE 3.2 1.8 - - - -
265D ALA* 1.3 77.7 - - - +
267D ASN* 1.3 61.8 + - - +
269D LEU* 3.6 0.5 - - - +
270D GLY 3.1 16.6 + - - -
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Residues in contact with ASN 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.3 19.9 - - - +
37D ASP* 3.2 37.2 + - - +
80D LEU* 3.9 18.6 - - + +
84D HIS* 2.8 32.9 + - - -
263D PRO 4.9 0.2 + - - -
264D PHE 4.5 5.1 + - - +
265D ALA 3.4 0.2 - - - -
266D ALA* 1.3 75.9 - - - +
268D ALA* 1.3 67.4 + - - +
270D GLY* 3.0 11.8 + - - -
271D LYS* 3.0 19.9 + - - +
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Residues in contact with ALA 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D GLY 4.6 6.5 - - - +
251D VAL* 3.8 25.4 - - + +
264D PHE 4.9 2.4 + - - +
265D ALA* 3.3 13.3 + - - +
267D ASN* 1.3 78.6 + - - +
269D LEU* 1.3 57.8 + - - +
271D LYS* 3.0 14.8 + - - +
272D LEU* 2.9 27.4 + - - +
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Residues in contact with LEU 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PRO* 4.7 5.2 - - + -
150D PHE* 4.9 2.9 - - + -
182D ILE* 3.7 28.9 - - + -
183D SER 3.3 26.2 - - - +
184D LEU* 3.8 23.3 - - + -
251D VAL* 3.4 9.7 - - + +
258D LEU* 4.0 25.1 - - + +
259D THR 4.1 8.3 - - - +
260D GLY 4.0 4.3 - - - +
265D ALA 2.8 21.3 + - - +
266D ALA 3.6 5.4 - - - +
268D ALA* 1.3 72.5 - - - +
270D GLY* 1.3 53.7 + - - +
272D LEU* 3.2 7.5 + - + -
273D ALA* 2.7 38.6 + - - +
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Residues in contact with GLY 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D PRO* 3.6 22.1 - - - +
84D HIS* 3.4 31.2 - - - +
85D LEU* 4.8 0.3 - - - +
266D ALA 3.1 7.9 + - - -
267D ASN 3.0 8.6 + - - -
269D LEU* 1.3 75.7 - - - +
271D LYS* 1.3 61.9 + - - +
273D ALA* 3.7 3.2 - - - +
274D ALA* 3.1 19.2 + - - +
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Residues in contact with LYS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ASP 3.4 21.0 + - - +
38D GLY* 3.8 21.3 - - - +
41D TYR* 3.7 11.0 - - + +
84D HIS* 3.7 17.5 - - + -
267D ASN* 3.0 16.0 + - - +
268D ALA* 3.0 13.8 + - - +
270D GLY* 1.3 74.7 - - - +
272D LEU* 1.3 61.0 + - - +
274D ALA* 3.3 2.1 + - - +
275D GLN* 2.8 40.8 + - - +
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D VAL* 4.1 22.9 - - + -
252D HIS 3.8 30.3 - - - +
253D LYS* 4.5 9.9 - - + +
258D LEU* 4.2 21.1 - - + -
268D ALA 2.9 12.3 + - - +
269D LEU* 3.6 10.8 - - + +
271D LYS* 1.3 75.9 - - - +
273D ALA* 1.3 63.4 + - - +
275D GLN* 3.1 7.9 + - + +
276D GLU* 2.9 44.1 + - + +
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D PRO* 6.0 0.7 - - + -
85D LEU* 3.8 26.9 - - + -
182D ILE* 4.3 21.5 - - + -
258D LEU* 3.8 14.1 - - + +
269D LEU* 2.7 22.1 + - + +
270D GLY* 3.7 5.6 - - - +
272D LEU* 1.3 72.9 - - - +
274D ALA* 1.3 57.4 + - - +
276D GLU* 3.5 0.5 + - - +
277D MET* 2.9 35.8 + - - +
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Residues in contact with ALA 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D TYR* 3.4 38.6 - - + +
84D HIS* 4.6 3.6 - - + +
85D LEU* 3.8 12.2 - - + +
88D ALA* 4.0 16.4 - - + -
270D GLY 3.1 11.3 + - - +
271D LYS 3.7 0.2 - - - +
273D ALA* 1.3 78.5 - - - +
275D GLN* 1.3 55.7 + - - +
277D MET* 4.5 1.1 - - - -
278D LEU* 2.8 41.1 + - - +
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Residues in contact with GLN 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D TYR* 3.7 22.6 + - - -
271D LYS* 2.8 31.5 + - - +
272D LEU* 3.4 10.5 - - + +
274D ALA* 1.3 75.2 - - - +
276D GLU* 1.3 68.4 - - + +
278D LEU* 3.9 6.3 - - - +
279D ALA* 3.2 21.4 + - - +
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Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D PHE* 3.5 29.6 - - + -
253D LYS* 3.3 41.3 + - + +
255D ARG 5.2 1.1 - - - +
258D LEU* 4.1 10.5 - - + -
272D LEU* 2.9 39.3 + - + +
275D GLN* 1.3 79.9 - - - +
277D MET* 1.3 61.2 + - - +
279D ALA* 3.6 5.6 + - - +
280D ALA* 3.2 18.9 + - - +
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Residues in contact with MET 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ILE* 4.7 4.3 - - + -
85D LEU* 3.7 22.0 - - - -
90D PHE* 3.8 31.5 - - + -
147D ALA* 3.5 35.4 - - + +
148D ALA* 3.9 24.5 - - + -
180D PHE* 3.6 28.7 - - + -
182D ILE* 4.1 10.3 - - - -
273D ALA* 2.9 23.6 + - - +
274D ALA 4.0 0.9 - - - +
276D GLU* 1.3 74.5 - - - +
278D LEU* 1.3 64.9 + - - +
280D ALA 3.7 0.3 + - - -
281D TYR* 3.3 31.0 + - + +
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Residues in contact with LEU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D TYR* 3.5 38.6 - - + -
43D LYS 3.4 22.0 - - - +
44D PRO* 4.3 0.7 - - + -
45D TYR* 4.2 7.6 - - + +
88D ALA* 3.4 36.1 - - + +
90D PHE* 4.5 6.5 - - + -
274D ALA 2.8 28.7 + - - +
275D GLN* 3.9 7.4 - - - +
277D MET* 1.3 73.0 - - - +
279D ALA* 1.3 63.8 + - - +
281D TYR* 3.2 21.0 + - - -
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Residues in contact with ALA 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D GLN 3.2 13.9 + - - +
276D GLU* 4.0 6.3 - - - +
277D MET 3.3 0.2 - - - -
278D LEU* 1.3 78.2 - - - +
280D ALA* 1.3 63.8 + - - +
281D TYR 3.3 5.9 + - - +
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Residues in contact with ALA 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D PHE* 4.1 21.3 - - + -
256D LYS* 5.2 8.5 - - - +
276D GLU 3.2 16.4 + - - +
277D MET 4.1 1.8 - - - +
279D ALA* 1.3 79.1 - - - +
281D TYR* 1.3 67.4 + - + +
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Residues in contact with TYR 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D TYR* 3.6 41.3 - + + -
49D HIS* 2.8 37.0 + + - -
90D PHE* 4.0 12.3 - + + -
147D ALA* 3.5 34.2 - - + +
179D ARG* 4.6 9.9 + - - -
180D PHE* 5.0 8.1 - + - -
277D MET* 3.3 26.5 + - + +
278D LEU* 3.2 17.4 + - - +
279D ALA 3.1 5.3 - - - +
280D ALA* 1.3 87.5 - - + +
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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