Contacts of the helix formed by residues 300 - 320 (chain G) in PDB entry 2BZN
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 ASP 300 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G HIS* 3.8 4.8 - - - -
249G SER* 2.9 23.2 + - - -
250G GLU* 3.6 12.8 - - - +
298G LYS 3.9 2.9 + - - +
299G GLY* 1.3 72.2 - - - -
301G VAL* 1.3 63.7 + - - +
302G GLU* 3.3 10.9 + - + +
303G HIS* 3.6 38.2 + - + +
304G THR* 4.3 1.4 + - - -
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Residues in contact with VAL 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G MET* 3.8 28.5 - - - -
66G VAL* 3.5 26.7 - - + -
67G LEU* 4.2 3.6 - - + -
245G LEU* 3.8 18.8 - - + -
248G HIS* 3.5 33.0 - - + +
250G GLU* 3.0 27.6 + - + +
299G GLY 3.7 0.6 + - - -
300G ASP* 1.3 70.6 - - - +
302G GLU* 1.3 68.1 + - - +
303G HIS 3.2 0.2 - - - -
304G THR* 3.1 4.9 + - - -
305G ILE* 2.9 25.0 + - + +
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Residues in contact with GLU 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G VAL* 4.1 20.6 - - + +
70G PHE* 4.1 13.6 - - + -
250G GLU* 4.8 0.6 + - - +
300G ASP* 3.2 10.0 - - + +
301G VAL* 1.3 80.7 - - - +
303G HIS* 1.3 94.6 + - + +
305G ILE* 3.4 4.2 + - - +
306G ARG* 2.9 60.2 + - - +
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Residues in contact with HIS 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298G LYS 5.8 1.6 - - - +
300G ASP* 3.6 37.3 + - + +
301G VAL 3.2 0.8 - - - -
302G GLU* 1.3 102.8 + - + +
304G THR* 1.3 61.9 + - - +
306G ARG* 3.4 9.2 + - - +
307G ASP* 2.9 27.6 + - - +
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Residues in contact with THR 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G MET* 3.8 22.2 - - + +
245G LEU* 4.6 4.7 - - + -
248G HIS* 2.8 26.3 + - + +
298G LYS* 5.0 4.1 + - + +
300G ASP 4.6 1.0 + - - -
301G VAL* 3.1 9.9 + - - -
303G HIS* 1.3 77.1 - - - +
305G ILE* 1.3 61.0 + - - +
307G ASP* 3.1 8.6 + - + +
308G ILE* 2.9 48.3 + - + +
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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
----------------------------------------------------------
50G ILE* 6.2 0.2 - - + -
67G LEU* 4.0 25.4 - - + -
70G PHE* 3.6 37.7 - - + -
72G LEU* 4.1 20.4 - - + -
241G LEU* 6.2 0.4 - - + -
245G LEU* 3.8 29.2 - - + -
301G VAL* 2.9 21.5 + - + +
302G GLU* 3.6 9.2 - - - +
304G THR* 1.3 74.6 - - - +
306G ARG* 1.3 63.8 + - - +
308G ILE* 3.3 11.6 + - + +
309G LEU* 3.0 37.5 + - + +
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Residues in contact with ARG 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G PHE* 3.9 30.6 - - + -
302G GLU* 2.9 49.0 + - - +
303G HIS* 3.7 8.3 - - - +
304G THR 3.2 0.2 - - - -
305G ILE* 1.3 74.4 - - - +
307G ASP* 1.3 57.6 + - - +
309G LEU* 4.0 5.0 - - + +
310G GLY* 2.9 29.5 + - - -
313G ARG* 5.4 0.3 + - - -
287H ALA* 5.4 1.6 - - - +
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Residues in contact with ASP 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225G PRO* 3.7 16.7 - - - +
303G HIS 2.9 14.9 + - - +
304G THR* 3.1 11.4 + - + +
306G ARG* 1.3 76.2 - - - +
308G ILE* 1.3 63.4 + - + +
310G GLY* 3.9 1.0 - - - -
311G GLY* 3.1 19.4 + - - -
191H LYS* 3.0 40.7 + - - +
287H ALA* 5.7 6.5 - - - +
288H SER* 5.1 6.8 + - - -
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Residues in contact with ILE 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G ILE* 4.1 15.0 - - + -
225G PRO* 4.0 13.1 - - + +
228G VAL* 4.6 13.2 - - + -
241G LEU* 4.0 17.3 - - + -
244G MET* 3.8 29.2 - - + -
245G LEU* 4.6 3.4 - - + -
304G THR* 2.9 38.3 + - + +
305G ILE* 3.7 15.7 - - + +
307G ASP* 1.3 77.6 - - + +
309G LEU* 1.3 64.0 + - + +
311G GLY* 3.3 2.8 + - - -
312G ILE* 3.1 40.7 + - + +
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Residues in contact with LEU 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 3.7 15.8 - - + +
48G VAL* 3.9 20.0 - - + -
50G ILE* 3.8 27.8 - - + -
70G PHE* 4.1 24.9 - - + +
72G LEU* 4.1 7.6 - - + -
305G ILE* 3.0 37.4 + - + +
306G ARG* 4.1 4.3 - - - +
308G ILE* 1.3 72.6 - - + +
310G GLY* 1.3 59.8 + - - +
312G ILE* 3.3 3.4 + - + -
313G ARG* 2.9 60.2 + - - +
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Residues in contact with GLY 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G ARG 2.9 18.1 + - - -
307G ASP 3.9 1.1 - - - -
309G LEU* 1.3 75.3 - - - +
311G GLY* 1.3 59.9 + - - +
313G ARG* 3.4 14.0 + - - +
314G SER* 3.0 26.9 + - - -
287H ALA* 4.1 23.0 - - - +
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Residues in contact with GLY 311 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225G PRO* 4.3 2.5 - - - -
307G ASP 3.1 15.6 + - - -
308G ILE 3.3 3.3 + - - -
309G LEU 3.3 0.2 - - - -
310G GLY* 1.3 75.3 - - - +
312G ILE* 1.3 56.3 + - - +
314G SER* 3.1 7.4 + - - -
315G THR* 3.0 26.8 + - - -
191H LYS* 3.1 29.8 - - - -
192H THR* 3.6 6.4 - - - +
287H ALA* 5.0 0.6 - - - +
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Residues in contact with ILE 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 3.7 21.8 - - + -
50G ILE* 3.8 20.0 - - + -
225G PRO* 4.2 14.3 - - - +
228G VAL* 3.6 27.6 - - + -
229G ALA* 4.3 10.1 - - + +
232G PHE* 4.1 9.9 - - + -
308G ILE* 3.1 22.3 + - + +
309G LEU* 3.8 6.5 - - + +
311G GLY* 1.3 71.9 - - - +
313G ARG* 1.3 65.1 + - - +
315G THR* 3.1 9.1 + - - -
316G CYS* 3.0 25.0 + - - -
324G LEU* 4.2 17.9 - - + -
327G LEU* 4.9 5.6 - - + -
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Residues in contact with ARG 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G GLU* 4.2 26.4 + - - -
30G VAL* 3.5 39.2 + - + +
32G LEU* 3.6 29.8 - - + +
48G VAL* 6.3 1.0 - - - +
306G ARG 5.4 0.6 + - - -
309G LEU* 2.9 51.3 + - - +
310G GLY* 3.6 11.2 - - - +
312G ILE* 1.3 71.1 - - - +
314G SER* 1.3 58.6 + - - +
316G CYS* 3.4 3.3 + - - +
317G THR* 3.0 31.4 + - - -
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Residues in contact with SER 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G GLY 3.0 14.0 + - - -
311G GLY* 3.1 8.4 + - - -
313G ARG* 1.3 74.7 - - - +
315G THR* 1.3 65.2 + - - +
317G THR* 3.3 8.6 + - - -
318G TYR* 2.9 33.9 + - - -
192H THR* 3.7 8.3 - - - -
287H ALA* 5.6 3.5 - - - +
289H GLU* 3.4 25.6 + - - -
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Residues in contact with THR 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G LEU* 3.8 28.0 - - + -
229G ALA* 3.4 19.8 - - + +
311G GLY 3.0 14.5 + - - -
312G ILE* 3.1 8.6 + - - -
314G SER* 1.3 75.5 - - - +
316G CYS* 1.3 63.0 + - - +
318G TYR* 3.0 13.3 + - - +
319G VAL* 3.1 14.7 + - + +
327G LEU* 4.0 12.6 - - + -
192H THR* 2.6 31.5 + - - +
194H VAL* 4.2 12.1 - - + -
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Residues in contact with CYS 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G VAL* 3.5 26.0 - - + -
32G LEU* 4.5 3.1 - - - -
312G ILE* 3.0 17.2 + - - -
313G ARG 3.6 2.9 - - - +
315G THR* 1.3 73.8 - - - +
317G THR* 1.3 59.0 + - - +
319G VAL* 3.3 3.3 + - - +
320G GLY 2.8 10.9 + - - -
321G ALA* 2.7 56.7 + - + +
324G LEU* 4.4 20.4 - - - -
327G LEU* 4.4 20.4 - - - -
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Residues in contact with THR 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G SER* 3.9 11.2 + - - +
24G LEU* 3.8 18.6 - - + +
30G VAL* 3.6 12.1 - - - +
313G ARG* 3.0 16.3 + - - +
314G SER* 3.5 12.0 - - - -
315G THR 3.2 0.2 - - - -
316G CYS* 1.3 76.5 - - - +
318G TYR* 1.3 62.1 + - + +
319G VAL 3.3 0.9 + - - -
320G GLY* 3.4 8.1 + - - -
321G ALA 4.1 0.2 + - - -
132H ASN* 3.6 22.1 + - + +
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Residues in contact with TYR 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G PRO* 3.4 10.0 - - + +
20G LYS 2.8 28.6 + - - +
314G SER* 2.9 29.8 + - - -
315G THR 3.0 6.7 + - - +
317G THR* 1.3 75.4 - - - +
319G VAL* 1.3 60.0 + - + +
131H ALA* 3.6 37.1 + - + +
132H ASN* 3.8 30.3 + - + +
180H ILE* 4.2 12.4 - - + +
188H THR* 3.8 21.3 + - + +
192H THR* 4.1 4.7 - - + -
194H VAL* 3.7 35.9 - - + -
289H GLU* 2.8 36.3 + - - -
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Residues in contact with VAL 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G LEU* 4.3 24.9 - - + -
18G ARG 3.6 21.1 - - - +
20G LYS* 3.7 22.8 - - + +
21G ARG 4.8 0.5 - - - +
315G THR* 3.1 16.4 + - + +
316G CYS 3.6 8.5 - - - +
318G TYR* 1.3 81.6 - - + +
320G GLY* 1.3 60.1 + - - +
321G ALA* 4.1 7.0 - - + -
327G LEU* 3.9 20.6 - - + -
330G ARG* 3.6 42.3 + - + +
331G THR* 5.4 0.7 - - - -
194H VAL* 4.9 0.4 - - + -
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Residues in contact with GLY 320 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ARG 4.6 0.7 - - - -
22G SER* 3.4 31.9 - - - -
24G LEU* 4.3 10.3 - - - +
316G CYS 2.8 4.1 + - - -
317G THR 3.4 5.3 + - - -
318G TYR 3.5 0.2 - - - -
319G VAL* 1.3 79.6 - - - +
321G ALA* 1.3 61.7 + - - +
322G ALA 3.7 1.4 + - - -
326G GLU* 3.8 0.2 - - - +
330G ARG* 3.0 29.3 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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