Contacts of the helix formed by residues 303 - 317 (chain G) 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 THR 303 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G LEU* 3.4 33.4 - - + -
32G PHE* 6.4 0.9 - - + -
34G VAL* 4.1 8.5 - - + -
50G GLU* 2.7 30.4 + - - +
302G THR* 1.3 84.4 + - - +
304G GLY* 1.3 66.1 + - - +
305G ILE* 3.0 15.6 + - - +
306G THR* 3.2 11.6 + - - -
307G THR* 3.2 12.1 + - - -
328G TRP* 4.2 4.4 - - - -
331G VAL* 4.9 4.5 - - + -
334G ASP* 3.4 13.2 - - - +
335G ILE* 3.6 13.4 - - + +
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Residues in contact with GLY 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G THR* 1.3 74.5 - - - +
305G ILE* 1.3 59.4 + - - +
307G THR* 3.2 8.2 + - - -
308G CYS* 2.9 34.7 + - - -
328G TRP* 4.0 1.7 - - - +
334G ASP* 2.9 27.7 + - - -
336G VAL* 3.4 9.3 - - - +
341G LEU* 3.4 16.2 - - - -
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Residues in contact with ILE 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 3.6 31.0 - - + -
48G ILE* 4.1 13.0 - - + -
49G GLY* 4.0 8.5 - - - +
50G GLU* 3.7 11.2 - - + +
111G MSE 3.0 38.6 - - + +
303G THR* 3.0 9.8 - - - +
304G GLY* 1.3 78.1 - - - +
306G THR* 1.3 60.8 + - - +
308G CYS* 3.2 5.2 + - - +
309G ALA 3.1 11.1 + - - -
335G ILE* 3.8 7.9 - - + -
336G VAL* 3.6 3.7 - - + +
358G PHE* 3.7 24.4 - - + -
360G LEU* 3.7 32.5 - - + -
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Residues in contact with THR 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G GLU* 2.7 29.1 + - - +
111G MSE 4.0 12.6 - - - -
272G PRO* 4.9 6.5 - - + -
299G SER* 4.5 2.0 - - - +
300G SER* 4.1 7.0 - - - +
302G THR* 3.1 30.7 + - - +
303G THR 3.2 1.3 + - - -
305G ILE* 1.3 76.5 - - - +
307G THR* 1.3 61.3 + - - +
309G ALA* 3.1 2.7 + - - +
310G GLU* 2.8 65.7 + - + +
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Residues in contact with THR 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G TYR* 4.6 5.1 + - + +
303G THR 3.2 5.8 + - - -
304G GLY* 3.2 13.4 + - - -
306G THR* 1.3 79.8 - - - +
308G CYS* 1.3 57.1 + - - +
310G GLU* 3.5 10.4 + - - +
311G HIS* 3.0 27.0 + - + +
326G ILE* 4.1 18.2 - - + +
327G MSE 4.8 1.6 + - - -
328G TRP* 3.3 46.5 + - + +
341G LEU* 3.9 18.2 - - + -
348G LEU* 5.0 5.8 - - + -
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Residues in contact with CYS 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304G GLY 2.9 18.4 + - - -
305G ILE 3.6 7.6 - - - +
306G THR 3.2 0.2 - - - -
307G THR* 1.3 74.2 - - - +
309G ALA* 1.3 65.4 + - - +
311G HIS* 3.2 6.5 + - - +
312G HIS* 3.1 31.1 + - + -
336G VAL* 4.9 0.4 - - - -
339G PRO* 4.4 9.0 - - - -
341G LEU* 3.8 22.7 - - - -
351G PHE* 4.6 6.1 - - - -
356G LEU* 3.6 21.5 - - + +
358G PHE* 3.8 31.9 - - + -
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Residues in contact with ALA 309 (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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111G MSE 3.3 44.2 - - + -
272G PRO* 5.3 3.1 - - + -
278G ILE* 4.4 7.9 - - + +
305G ILE 3.1 5.9 + - - -
306G THR* 3.1 6.0 + - - +
308G CYS* 1.3 77.0 - - - +
310G GLU* 1.3 63.7 + - + +
311G HIS 3.2 0.3 + - - -
312G HIS* 3.2 4.2 + - - +
313G ILE* 3.0 31.4 + - + +
356G LEU* 3.6 17.6 - - + +
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Residues in contact with GLU 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G TYR* 5.0 5.4 - - + +
272G PRO* 3.6 25.5 - - + +
273G ARG* 5.6 0.9 + - - +
297G ILE* 3.1 34.4 - - + +
298G HIS 3.2 19.1 - - - +
299G SER* 2.9 29.9 + - - -
300G SER* 4.7 0.7 + - - -
306G THR* 2.8 43.8 + - + +
307G THR* 3.9 7.6 - - - +
309G ALA* 1.3 72.3 - - - +
311G HIS* 1.3 56.8 + - - +
313G ILE* 3.6 8.0 - - - +
314G GLY 2.9 23.0 + - - -
325G GLN 4.4 6.8 - - - +
326G ILE* 5.3 1.0 - - - -
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Residues in contact with HIS 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G VAL* 3.7 15.0 - - + +
139G TYR* 3.3 25.7 + - - +
307G THR 3.0 18.0 + - - +
308G CYS* 3.4 9.9 - - - +
309G ALA 3.1 0.4 - - - -
310G GLU* 1.3 74.7 - - - +
312G HIS* 1.3 63.8 + - - +
314G GLY* 3.2 2.3 + - - -
315G LEU* 3.0 51.7 + - + +
348G LEU* 3.4 29.2 + - + -
349G ASP 3.5 5.5 + - - -
350G ALA* 3.5 2.1 - - - -
351G PHE* 3.1 58.5 - + + +
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Residues in contact with HIS 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G PRO* 3.6 19.3 - - + -
125G VAL* 4.0 20.0 - - + -
126G HIS* 3.1 44.8 + + - +
129G LEU* 4.5 2.8 - - - +
278G ILE* 5.9 0.4 - - + -
308G CYS* 3.1 25.1 + - - -
309G ALA 3.2 5.8 + - - +
311G HIS* 1.3 78.4 - - - +
313G ILE* 1.3 66.8 + - + +
315G LEU* 3.3 6.4 + - - +
316G ALA* 3.2 23.2 + - - +
351G PHE* 3.6 21.4 - + + +
353G LYS 4.7 1.1 - - - -
355G GLY 3.7 4.9 - - - -
356G LEU* 3.2 39.3 + - + -
357G GLY* 4.9 0.2 - - - -
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Residues in contact with ILE 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G LEU* 5.0 3.8 - - - -
272G PRO* 4.0 24.0 - - + -
278G ILE* 3.7 46.0 - - + +
281G MSE 3.7 33.4 - - + -
282G MSE 4.6 3.5 - - - +
297G ILE* 4.4 4.7 - - + -
309G ALA* 3.0 26.6 + - + +
310G GLU* 3.6 9.6 - - - +
312G HIS* 1.3 75.5 - - - +
314G GLY* 1.3 64.4 + - - +
316G ALA* 3.1 14.4 + - - +
317G ILE* 3.3 29.6 + - + +
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Residues in contact with GLY 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G ARG* 2.7 29.2 + - - -
137G VAL* 4.4 6.3 - - - -
297G ILE* 3.5 20.9 - - - -
310G GLU 2.9 12.1 + - - -
311G HIS 3.2 4.5 + - - -
313G ILE* 1.3 78.2 - - - +
315G LEU* 1.3 51.6 + - - +
317G ILE* 3.4 6.1 + - - +
320G LEU* 3.2 21.3 - - - +
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Residues in contact with LEU 315 (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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126G HIS* 3.4 33.4 - - + +
132G ALA* 3.1 10.7 - - + -
133G HIS* 2.7 31.2 + - - -
134G ARG* 3.5 34.5 + - + +
136G ALA 4.7 2.9 - - - +
137G VAL* 3.8 16.8 - - + +
311G HIS* 3.0 41.8 + - + +
312G HIS* 3.6 7.6 - - - +
313G ILE 3.2 0.4 - - - -
314G GLY* 1.3 78.0 - - - +
316G ALA* 1.3 58.8 + - - +
317G ILE 3.5 0.7 + - - -
350G ALA* 3.8 23.1 - - + -
351G PHE 4.3 0.7 - - - +
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Residues in contact with ALA 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E GLN* 5.8 0.9 + - - -
126G HIS* 4.4 5.1 - - + +
129G LEU* 3.7 35.0 - - + +
131G GLY 3.6 13.2 - - - +
133G HIS* 3.5 17.1 + - - -
282G MSE 3.1 29.8 - - + +
312G HIS 3.2 14.0 + - - +
313G ILE 3.1 3.1 + - - +
315G LEU* 1.3 76.4 - - - +
317G ILE* 1.3 56.8 - - - +
318G PRO* 3.6 1.9 - - - +
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Residues in contact with ILE 317 (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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133G HIS* 4.0 1.3 - - - -
134G ARG* 2.8 31.5 + - - -
281G MSE 4.2 17.3 - - + +
282G MSE 4.1 11.7 - - + -
285G ALA* 3.7 26.7 - - + -
295G ILE* 4.6 4.7 - - + -
313G ILE* 3.3 34.3 + - + +
314G GLY 3.4 4.2 + - - +
315G LEU 3.3 1.6 - - - -
316G ALA* 1.3 78.8 - - - +
318G PRO* 1.3 60.9 - - - +
319G ASN* 3.2 40.2 - - - +
320G LEU* 3.7 18.2 - - + +
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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
------------------------------------------------------------
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