Contacts of the helix formed by residues 261 - 278 (chain B) in PDB entry 2PMW
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 VAL 261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 5.5 2.2 - - + -
144A GLU* 4.3 3.6 - - - +
146A ASP* 3.4 9.4 + - - +
147A SER* 2.9 37.9 + - - +
148A SER 4.9 0.7 - - - +
149A VAL* 4.1 16.6 - - + +
260B THR* 1.3 69.1 - - - +
262B SER* 1.3 60.8 + - - +
264B THR* 3.1 7.9 + - - -
265B LEU* 2.8 33.0 + - + +
291B GLY* 6.2 0.7 - - - -
292B GLY 5.8 1.3 - - - +
294B SER* 3.9 18.8 - - - +
296B VAL* 3.9 28.5 - - + -
297B LEU* 4.1 15.5 - - + -
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Residues in contact with SER 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 4.3 4.9 - - - -
115A PHE* 4.8 2.6 - - - -
123A LEU* 3.7 36.5 - - - +
146A ASP* 2.6 34.0 + - - -
207B ASN* 5.0 2.8 + - - -
260B THR* 3.2 4.3 + - - -
261B VAL* 1.3 75.3 - - - +
263B GLY* 1.3 67.2 + - - +
265B LEU* 3.1 13.8 + - - +
266B ILE* 2.9 30.1 + - - +
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Residues in contact with GLY 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PHE* 4.3 2.6 - - - -
207B ASN* 3.4 34.3 - - - -
252B VAL* 3.9 12.4 - - - +
260B THR* 2.9 17.8 + - - -
262B SER* 1.3 78.1 + - - +
264B THR* 1.3 55.6 + - - +
266B ILE* 3.2 4.4 + - - +
267B GLY* 3.0 24.4 + - - -
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Residues in contact with THR 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A VAL* 3.8 15.2 - - - +
185B LEU* 4.2 6.5 - - + +
252B VAL* 4.4 13.9 - - - +
260B THR 2.9 14.5 + - - -
261B VAL* 3.1 9.3 + - - -
263B GLY* 1.3 72.7 - - - +
265B LEU* 1.3 67.3 + - - +
267B GLY* 3.3 1.0 + - - -
268B LEU* 2.9 26.6 + - + +
287B LEU* 4.2 24.7 - - + -
289B LEU* 4.4 18.0 - - + +
297B LEU* 4.0 21.3 - - + -
327B PRO* 6.1 0.4 - - + -
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 4.1 21.3 - - + -
115A PHE* 3.9 21.9 - - + -
118A LEU* 5.3 1.0 - - - +
119A LEU* 5.5 3.4 - - + -
261B VAL* 2.8 22.1 + - + +
262B SER* 3.2 9.0 - - - +
264B THR* 1.3 78.0 - - - +
266B ILE* 1.3 61.6 + - - +
268B LEU* 3.3 6.0 + - + +
269B GLU* 3.0 22.7 + - - +
296B VAL* 3.5 38.6 - - + +
297B LEU* 3.9 14.8 - - + -
300B ALA* 3.4 33.0 - - + -
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Residues in contact with ILE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A HIS* 3.9 43.7 - - + +
115A PHE* 3.8 18.2 - - + -
123A LEU* 4.5 13.2 - - + -
205B PHE* 3.5 22.9 - - + -
207B ASN* 3.5 23.1 - - - +
262B SER 2.9 21.2 + - - +
263B GLY 3.2 6.5 + - - +
265B LEU* 1.3 75.2 - - - +
267B GLY* 1.3 58.4 + - - +
269B GLU* 3.2 10.5 + - - +
270B PHE* 2.9 26.0 + - - +
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Residues in contact with GLY 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 4.2 9.4 - - - -
205B PHE* 3.5 22.1 - - - -
250B LEU* 3.4 12.7 - - - +
252B VAL* 4.7 0.4 - - - -
263B GLY 3.0 12.9 + - - -
264B THR 3.3 3.7 + - - -
266B ILE* 1.3 78.7 - - - +
268B LEU* 1.3 61.9 + - - +
270B PHE* 3.1 12.4 + - - +
271B ILE* 3.1 17.7 + - - +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.9 15.6 - - + +
185B LEU* 4.1 17.5 - - + +
264B THR* 2.9 24.1 + - + +
265B LEU* 3.3 4.9 + - - +
267B GLY* 1.3 74.9 - - - +
269B GLU* 1.3 63.7 + - - +
271B ILE* 3.2 9.6 + - + +
272B ARG* 3.2 20.8 + - - +
285B VAL* 4.3 12.8 - - + -
287B LEU* 4.2 16.2 - - + -
297B LEU* 4.2 15.7 - - + -
300B ALA* 4.3 16.8 - - + +
301B CYS* 4.1 27.4 - - - +
304B LEU* 4.0 21.0 - - + +
311B LEU* 5.0 1.1 - - + -
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Residues in contact with GLU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A HIS* 2.9 27.2 + - - -
115A PHE* 3.1 21.1 - - + +
116A HIS 2.9 45.1 + - - +
117A GLY* 5.0 2.9 - - - +
118A LEU* 4.0 15.9 + - + +
265B LEU 3.0 14.1 + - - +
266B ILE* 3.4 10.9 - - - +
267B GLY 3.2 0.2 - - - -
268B LEU* 1.3 76.9 - - - +
270B PHE* 1.3 57.7 + - - +
272B ARG* 3.3 4.0 + - - +
273B LYS* 3.0 50.6 + - - +
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Residues in contact with PHE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 5.4 3.4 - + - -
203B THR* 4.0 35.0 - - + -
205B PHE* 3.5 36.6 - + + -
250B LEU* 3.8 15.3 - - + -
266B ILE 2.9 13.1 + - - +
267B GLY 3.1 9.6 + - - +
269B GLU* 1.3 74.9 - - - +
271B ILE* 1.3 65.9 + - - +
273B LYS* 3.4 11.3 + - + +
274B SER* 2.9 44.5 + - - -
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Residues in contact with ILE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 3.7 53.4 + - + -
185B LEU* 3.7 30.3 - - + -
250B LEU* 4.0 8.1 - - + -
267B GLY 3.1 11.8 + - - +
268B LEU* 3.2 13.7 + - + +
270B PHE* 1.3 79.2 - - - +
272B ARG* 1.3 61.7 + - - +
274B SER* 3.4 6.3 + - - -
275B GLN* 3.1 22.1 + - - +
283B LEU* 4.3 12.4 - - + +
285B VAL* 4.0 20.0 - - + -
304B LEU* 5.0 7.0 - - + -
309B VAL* 5.6 1.3 - - + -
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Residues in contact with ARG 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLY* 4.0 26.2 + - - +
118A LEU* 4.1 11.6 - - + +
268B LEU 3.2 9.9 + - - +
269B GLU 3.7 7.2 - - - +
270B PHE 3.3 0.2 - - - -
271B ILE* 1.3 81.8 - - - +
273B LYS* 1.3 61.9 + - - +
275B GLN* 2.7 40.4 + - - +
276B LEU* 3.1 53.4 + - + +
304B LEU* 4.1 21.3 - - + -
307B ALA* 3.7 33.1 + - - +
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Residues in contact with LYS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A HIS* 4.8 4.9 - - - -
116A HIS* 3.3 54.6 + - - +
117A GLY* 5.4 2.7 - - - -
269B GLU* 3.0 46.2 + - + +
270B PHE* 3.8 11.2 - - + +
272B ARG* 1.3 75.0 - - + +
274B SER* 1.3 64.1 + - - +
276B LEU* 3.2 13.0 + - + +
277B VAL* 2.9 31.7 + - + +
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 3.9 18.7 + - - -
270B PHE* 2.9 39.1 + - - -
271B ILE 3.6 5.2 - - - -
272B ARG 3.3 0.2 - - - -
273B LYS* 1.3 75.7 - - - +
275B GLN* 1.3 58.3 + - - +
277B VAL* 3.3 6.7 + - - +
278B GLN* 2.8 32.2 + - - +
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Residues in contact with GLN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR* 5.4 0.6 + - - -
271B ILE 3.1 10.3 + - - +
272B ARG* 2.7 42.8 + - - +
273B LYS 3.2 0.4 - - - -
274B SER* 1.3 80.6 - - - +
276B LEU* 1.3 60.0 + - + +
278B GLN 4.3 4.7 - - - -
279B PRO* 3.1 37.1 - - + +
280B VAL* 5.1 6.3 - - + +
281B GLY 4.8 6.5 + - - -
283B LEU* 3.7 33.6 - - + +
307B ALA 5.2 3.0 + - - -
308B GLY 5.3 2.8 + - - -
309B VAL* 4.0 18.0 - - - +
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLY* 5.5 7.4 - - - +
272B ARG* 3.1 58.2 + - + +
273B LYS* 3.6 12.1 - - + +
275B GLN* 1.3 77.7 - - - +
277B VAL* 1.3 64.1 + - + +
279B PRO* 3.9 10.0 - - - +
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LYS* 2.9 23.8 + - + +
274B SER* 3.7 6.5 - - - +
276B LEU* 1.3 80.3 - - + +
278B GLN* 1.3 64.2 + - + +
279B PRO* 3.9 3.0 - - - +
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Residues in contact with GLN 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ARG* 5.8 4.6 - - - +
274B SER 2.8 15.6 + - - +
275B GLN* 3.4 6.0 - - - +
277B VAL* 1.3 85.2 - - + +
279B PRO* 1.3 69.6 - - + +
280B VAL* 3.5 14.4 + - + +
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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
------------------------------------------------------------
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