Contacts of the helix formed by residues 277 - 291 (chain B) in PDB entry 2PGW
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 GLY 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B SER* 3.6 17.4 - - - +
110B ASP* 3.6 7.2 - - - -
111B MSE 5.7 0.2 - - - -
272B PRO* 2.8 24.9 + - - +
275B ILE* 3.7 0.3 - - - +
276B GLY* 1.3 76.9 - - - +
278B ILE* 1.3 62.2 + - - +
280B PRO* 3.5 3.8 - - - -
281B MSE 3.2 29.3 + - - +
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Residues in contact with ILE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASP* 2.7 12.5 + - - +
111B MSE 4.1 22.4 - - + +
114B TRP* 4.1 24.0 - - + -
125B VAL* 4.3 7.9 - - + -
129B LEU* 3.7 31.0 - - + -
272B PRO* 5.5 0.9 - - + -
277B GLY* 1.3 70.6 - - - -
279B GLN* 1.3 66.3 + - - +
281B MSE 3.1 19.4 + - - +
282B MSE 3.4 7.4 + - - +
309B ALA* 4.5 9.2 - - + +
313B ILE* 3.7 30.8 - - + +
356B LEU* 3.7 28.9 - - + -
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Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU 3.0 30.5 + - - -
130A GLY* 4.0 1.1 - - - -
79B VAL* 4.3 3.8 - - - +
80B ALA* 3.6 25.0 - - - +
110B ASP* 3.1 4.9 + - - +
114B TRP* 3.7 33.1 - - + +
129B LEU* 5.3 4.3 - - + +
278B ILE* 1.3 78.9 - - - +
280B PRO* 1.4 72.8 - - + +
282B MSE 3.0 27.6 + - + +
283B LYS* 3.3 17.4 + - + +
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Residues in contact with PRO 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 6.4 0.9 - - + -
110B ASP* 3.7 7.6 - - - +
253B LEU* 5.0 0.3 - - - +
275B ILE* 3.3 40.9 - - + +
276B GLY* 3.4 19.3 - - - +
277B GLY* 3.5 10.1 - - - -
278B ILE 3.4 4.5 - - - +
279B GLN* 1.4 95.2 - - + +
281B MSE 1.3 54.8 + - - +
283B LYS* 3.1 17.0 + - + +
284B ALA 3.0 23.4 + - - -
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Residues in contact with MSE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 3.1 40.4 - - - +
271B GLY* 3.6 16.4 - - - +
272B PRO* 4.0 4.3 - - + -
275B ILE* 3.5 13.2 - - + -
277B GLY 3.2 20.0 - - - +
278B ILE 3.1 12.8 + - - +
280B PRO* 1.3 80.4 - - - +
282B MSE 1.3 55.6 + - - +
284B ALA* 3.3 4.7 + - - +
285B ALA* 2.9 30.9 + - - +
295B ILE* 4.1 13.2 - - + +
297B ILE* 3.3 28.5 - - + -
313B ILE* 3.8 27.8 - - + -
317B ILE* 4.3 5.2 - - + +
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Residues in contact with MSE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLN* 5.3 3.6 - - - +
283A LYS* 5.7 1.0 - - - +
129B LEU* 4.0 37.0 - - + +
278B ILE 3.6 13.9 - - - +
279B GLN* 3.0 18.2 + - + +
281B MSE 1.3 76.7 - - - +
283B LYS* 1.3 59.1 + - + +
285B ALA* 3.6 6.0 + - + +
286B ALA* 3.1 25.6 + - - +
313B ILE* 4.5 6.1 - - - +
316B ALA* 3.3 44.6 - - + +
317B ILE* 4.1 16.4 - - + +
318B PRO* 5.4 3.4 - - + -
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Residues in contact with LYS 283 (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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282A MSE 5.6 1.6 - - - +
286A ALA* 3.9 27.8 - - + +
289A GLU* 2.7 37.2 + - - -
318A PRO* 4.6 10.7 - - - +
253B LEU* 3.8 18.2 - - + +
279B GLN* 3.7 22.9 - - + +
280B PRO* 3.1 15.0 + - + +
282B MSE 1.3 76.1 - - + +
284B ALA* 1.3 65.7 + - - +
286B ALA* 3.1 5.6 + - - +
287B VAL* 3.1 25.1 + - - +
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.8 10.5 - - + +
256B VAL* 3.9 22.8 - - + +
270B ILE* 4.8 13.7 - - + -
275B ILE* 4.2 19.7 - - + -
280B PRO 3.0 12.3 + - - +
281B MSE 3.3 11.2 + - - +
283B LYS* 1.3 76.4 - - - +
285B ALA* 1.3 62.6 + - - +
287B VAL* 3.2 4.4 + - - +
288B ALA* 3.0 23.0 + - - +
295B ILE* 4.2 2.9 - - + +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B MSE 2.9 16.4 + - - +
282B MSE 3.7 6.5 - - + +
283B LYS 3.2 0.2 - - - -
284B ALA* 1.3 78.4 - - - +
286B ALA* 1.3 56.5 + - - +
288B ALA 3.4 0.3 + - - -
289B GLU* 2.9 26.4 + - - +
295B ILE* 3.7 15.6 - - + +
317B ILE* 3.9 39.7 - - + -
318B PRO* 5.6 2.2 - - + -
319B ASN* 3.0 13.6 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 4.0 3.6 - - - +
283A LYS* 3.8 46.4 - - + +
286A ALA* 4.8 1.8 - - + -
287A VAL* 4.6 2.0 - - + -
282B MSE 3.1 15.2 + - - +
283B LYS* 3.1 11.2 + - - +
285B ALA* 1.3 74.7 - - - +
287B VAL* 1.3 59.6 + - - +
289B GLU* 3.3 12.2 + - - +
290B ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TYR* 4.7 3.7 - - + -
286A ALA* 4.2 4.7 - - + +
287A VAL* 4.1 30.7 - - + -
290A ALA* 4.3 5.2 - - + -
253B LEU* 3.9 18.6 - - + +
256B VAL* 4.2 4.7 - - + -
257B TYR* 3.9 41.7 - - + +
260B CYS* 4.2 9.4 - - + -
283B LYS 3.1 13.9 + - - +
284B ALA 3.2 6.7 + - - +
286B ALA* 1.3 76.2 - - - +
288B ALA* 1.3 62.3 + - - +
290B ALA* 3.3 4.5 + - - +
291B ALA* 3.1 20.4 + - - +
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Residues in contact with ALA 288 (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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256B VAL* 4.5 0.6 - - + +
260B CYS* 4.0 11.9 - - - -
268B ILE* 4.6 9.6 - - + -
284B ALA 3.0 12.7 + - - +
285B ALA 3.6 7.2 - - - +
287B VAL* 1.3 76.2 - - - +
289B GLU* 1.3 61.5 + - - +
291B ALA* 2.9 9.9 + - - +
293B LEU* 2.8 44.5 + - + +
294B LYS 4.7 0.4 - - - +
295B ILE* 3.8 22.2 - - + -
319B ASN* 3.8 1.3 - - - +
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Residues in contact with GLU 289 (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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253A LEU* 4.2 10.3 - - + +
254A TYR* 3.4 27.7 + - - +
283A LYS* 2.8 37.4 + - - -
285B ALA 2.9 16.0 + - - +
286B ALA* 3.5 6.2 - - - +
288B ALA* 1.3 77.5 - - - +
290B ALA* 1.3 58.3 + - - +
292B GLY* 2.8 20.6 + - - +
293B LEU 3.8 2.9 - - - +
318B PRO* 4.0 19.7 - - - +
319B ASN* 3.3 20.3 - - + +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.7 23.1 - - + +
254A TYR* 3.4 26.2 - - - -
257A TYR* 3.6 36.2 - - + +
287A VAL* 4.1 10.3 - - + -
286B ALA 2.9 17.6 + - - +
287B VAL 3.3 6.5 + - - +
289B GLU* 1.3 75.9 - - - +
291B ALA* 1.3 56.5 + - - +
292B GLY 3.4 0.2 - - - -
229G SER* 4.6 3.1 + - - -
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Residues in contact with ALA 291 (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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257A TYR* 3.7 15.9 - - + +
260B CYS* 3.5 38.4 - - + -
263B ARG* 2.6 38.7 + - - +
287B VAL 3.1 4.9 + - - +
288B ALA 2.9 9.6 + - - +
290B ALA* 1.3 76.1 - - - +
292B GLY* 1.3 62.9 + - - +
293B LEU* 3.5 3.5 + - + +
229G SER* 3.9 5.4 + - - -
232G ALA* 4.0 0.2 - - - +
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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