Contacts of the helix formed by residues 300 - 320 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248H HIS* 3.8 4.8 - - - -
249H SER* 2.9 21.0 + - - -
250H GLU* 3.7 13.0 - - - +
298H LYS 3.9 2.4 + - - +
299H GLY* 1.3 73.2 - - - -
301H VAL* 1.3 65.6 + - - +
302H GLU* 3.2 7.6 + - + +
303H HIS* 3.4 40.3 + - + +
304H THR* 4.1 1.6 + - - -
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Residues in contact with VAL 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H MET* 3.8 29.6 - - - -
66H VAL* 3.6 25.4 - - + -
67H LEU* 4.4 3.1 - - + -
245H LEU* 4.1 15.5 - - + -
248H HIS* 3.4 35.7 - - + +
250H GLU* 2.9 29.6 + - + +
300H ASP* 1.3 69.8 - - - +
302H GLU* 1.3 68.6 + - - +
304H THR* 2.9 4.0 + - - -
305H ILE* 2.8 26.9 + - + +
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Residues in contact with GLU 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H VAL* 4.0 16.8 - - + +
69H LYS* 3.0 34.0 + - - -
70H PHE* 3.8 14.5 - - + -
250H GLU* 4.9 0.6 + - - +
300H ASP* 3.2 5.9 - - + +
301H VAL* 1.3 81.0 - - - +
303H HIS* 1.3 73.1 + - + +
305H ILE* 3.2 3.9 + - - +
306H ARG* 2.7 65.0 + - - +
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Residues in contact with HIS 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298H LYS 6.0 0.7 - - - -
300H ASP* 3.4 35.0 + - + +
301H VAL 3.2 0.8 - - - -
302H GLU* 1.3 89.6 - - + +
304H THR* 1.3 65.9 + - - +
306H ARG* 3.6 12.9 + - - +
307H ASP* 3.1 22.3 + - - +
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Residues in contact with THR 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244H MET* 3.7 24.0 - - + +
245H LEU* 4.4 6.3 - - + -
248H HIS* 2.6 30.7 + - + +
298H LYS* 5.1 2.9 + - - +
300H ASP 4.1 1.3 + - - -
301H VAL 2.9 7.4 + - - -
303H HIS* 1.3 77.6 - - - +
305H ILE* 1.3 65.2 + - - +
307H ASP* 3.1 8.8 + - + +
308H ILE* 3.0 39.2 + - + +
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Residues in contact with ILE 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H VAL* 5.1 0.2 - - + -
67H LEU* 3.8 30.5 - - + -
70H PHE* 3.7 37.7 - - + -
72H LEU* 4.0 22.0 - - + -
245H LEU* 3.8 24.9 - - + -
301H VAL* 2.8 22.5 + - + +
302H GLU* 3.2 8.3 + - - +
304H THR* 1.3 74.1 - - - +
306H ARG* 1.3 59.1 + - - +
308H ILE* 3.1 10.8 + - + +
309H LEU* 3.0 40.6 + - + +
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Residues in contact with ARG 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H LYS* 4.6 4.4 - - - +
70H PHE* 3.9 27.6 - - + -
302H GLU* 2.7 50.7 + - - +
303H HIS* 3.8 13.1 + - - +
305H ILE* 1.3 76.9 - - - +
307H ASP* 1.3 55.2 + - - +
309H LEU* 3.8 4.5 - - - +
310H GLY* 2.8 29.1 + - - -
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Residues in contact with ASP 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F LYS* 2.6 42.3 + - - +
287F ALA* 5.9 3.8 - - - +
288F SER* 4.9 4.0 + - - +
225H PRO* 3.6 18.2 - - - +
303H HIS 3.1 10.9 + - - +
304H THR* 3.1 12.4 + - + +
306H ARG* 1.3 79.8 - - - +
308H ILE* 1.3 62.9 + - - +
310H GLY* 3.9 0.6 - - - -
311H GLY* 3.1 20.1 + - - -
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Residues in contact with ILE 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ILE* 4.2 14.1 - - + -
72H LEU* 6.2 1.6 - - + -
225H PRO* 4.0 13.9 - - + +
228H VAL* 4.5 14.4 - - + -
241H LEU* 4.1 17.5 - - + -
244H MET* 3.7 28.3 - - + -
245H LEU* 4.4 9.2 - - + -
304H THR* 3.0 37.7 + - + +
305H ILE* 3.6 12.3 - - + +
307H ASP* 1.3 75.5 - - - +
309H LEU* 1.3 64.7 + - + +
311H GLY* 3.2 2.8 + - - -
312H ILE* 3.0 41.9 + - + +
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Residues in contact with LEU 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 3.7 19.7 - - + +
48H VAL* 3.9 13.2 - - + -
50H ILE* 3.8 28.7 - - + -
70H PHE* 4.1 21.5 - - + +
72H LEU* 4.2 13.0 - - + -
305H ILE* 3.0 35.6 + - + +
306H ARG* 4.0 4.7 - - - +
308H ILE* 1.3 75.2 - - + +
310H GLY* 1.3 57.1 + - - +
312H ILE* 3.2 2.4 + - + +
313H ARG* 2.9 58.2 + - - +
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Residues in contact with GLY 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ALA* 4.9 19.3 - - - +
306H ARG 2.8 21.8 + - - -
307H ASP* 3.9 1.1 - - - -
309H LEU* 1.3 72.8 - - - +
311H GLY* 1.3 61.7 + - - +
313H ARG* 3.5 10.2 + - - +
314H SER* 3.1 25.7 + - - -
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Residues in contact with GLY 311 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F LYS* 3.3 28.3 - - - -
192F THR* 3.7 5.0 - - - +
225H PRO* 4.5 1.3 - - - -
307H ASP 3.1 14.8 + - - -
308H ILE 3.7 3.4 - - - -
310H GLY* 1.3 76.0 - - - +
312H ILE* 1.3 63.0 + - - +
314H SER* 3.2 7.1 + - - -
315H THR* 3.0 23.3 + - - -
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Residues in contact with ILE 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 3.8 22.4 - - + -
50H ILE* 3.8 22.0 - - + -
225H PRO 4.2 13.9 - - - +
228H VAL* 3.4 30.1 - - + -
229H ALA* 4.4 12.8 - - + +
232H PHE* 4.0 8.7 - - + -
308H ILE* 3.0 25.3 + - + +
309H LEU* 3.2 6.3 + - + +
311H GLY* 1.3 73.4 - - - +
313H ARG* 1.3 65.4 + - - +
315H THR* 3.2 9.0 + - - -
316H CYS* 3.1 23.9 + - - -
324H LEU* 4.3 17.3 - - + -
327H LEU* 5.1 2.0 - - + -
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Residues in contact with ARG 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H GLU* 3.6 26.4 + - - -
30H VAL* 3.1 47.7 + - + +
31H ASP* 5.6 0.2 - - - +
32H LEU* 3.7 27.9 - - + +
309H LEU* 2.9 48.3 + - - +
310H GLY* 3.7 9.0 - - - +
312H ILE* 1.3 76.2 - - - +
314H SER* 1.3 56.9 + - - +
316H CYS 3.4 0.9 + - - -
317H THR* 2.9 31.3 + - - -
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Residues in contact with SER 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192F THR* 3.4 8.3 - - - +
289F GLU* 2.7 27.7 + - - -
310H GLY 3.1 17.9 + - - -
311H GLY* 3.6 4.9 - - - -
312H ILE 3.1 0.4 - - - -
313H ARG* 1.3 76.1 - - - +
315H THR* 1.3 58.3 + - - +
317H THR* 3.3 8.4 + - - -
318H TYR* 2.9 41.1 + - - -
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Residues in contact with THR 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192F THR* 2.6 34.1 + - - +
194F VAL* 4.1 14.4 - - + -
17H LEU* 3.9 24.7 - - + -
229H ALA* 3.4 24.2 - - + +
311H GLY 3.0 14.9 + - - -
312H ILE* 3.4 8.1 - - - -
314H SER* 1.3 76.4 - - - +
316H CYS* 1.3 62.7 + - - +
318H TYR* 3.2 3.6 + - - +
319H VAL* 3.0 23.3 + - + +
327H LEU* 4.1 9.9 - - + -
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Residues in contact with CYS 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H VAL* 3.8 20.0 - - + -
32H LEU* 4.5 0.2 - - - -
312H ILE* 3.1 19.1 + - - -
313H ARG 3.5 8.1 - - - +
315H THR* 1.3 76.8 - - - +
317H THR* 1.3 63.3 + - - +
319H VAL* 3.3 8.9 + - - +
320H GLY 3.0 5.0 + - - -
321H ALA* 2.8 52.8 + - + +
324H LEU* 4.3 28.3 - - - -
327H LEU* 4.3 14.4 - - - -
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Residues in contact with THR 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ASN* 3.7 20.2 + - + +
135F SER* 6.3 1.3 - - - -
22H SER* 3.8 12.8 + - - +
24H LEU* 3.8 24.0 - - + +
30H VAL* 3.7 12.1 - - - +
313H ARG 2.9 16.4 + - - -
314H SER* 3.6 11.0 - - - -
315H THR 3.2 0.2 - - - -
316H CYS* 1.3 76.5 - - - +
318H TYR* 1.3 62.8 + - - +
320H GLY* 3.2 9.7 + - - -
321H ALA 4.2 0.2 + - - -
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Residues in contact with TYR 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F ALA* 3.7 27.1 + - + +
132F ASN* 3.7 39.2 + - + +
180F ILE* 4.1 14.0 - - + +
188F THR* 3.8 13.6 + - + +
192F THR* 4.1 10.8 - - - -
194F VAL* 3.7 33.7 - - + -
289F GLU* 2.7 25.9 + - - -
19H PRO* 3.3 10.9 - - + +
20H LYS 2.8 28.8 + - - +
314H SER* 2.9 43.2 + - - -
315H THR 3.2 6.7 + - - +
317H THR* 1.3 77.5 - - - +
319H VAL* 1.3 58.3 + - - +
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Residues in contact with VAL 319 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F VAL* 4.8 2.0 - - + -
17H LEU* 4.3 23.3 - - + -
18H ARG 3.4 24.0 - - - +
19H PRO* 4.5 0.4 - - + -
20H LYS* 3.6 22.8 - - + +
21H ARG 4.8 0.3 - - - +
315H THR 3.0 19.3 + - - +
316H CYS* 3.6 8.1 - - - +
318H TYR* 1.3 80.4 - - + +
320H GLY* 1.3 59.3 + - - +
321H ALA* 4.2 5.4 - - + +
327H LEU* 3.6 24.2 - - + -
330H ARG* 3.7 38.8 + - + +
331H THR* 5.4 0.4 - - - -
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Residues in contact with GLY 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ARG 4.4 3.6 - - - -
22H SER* 3.6 30.1 - - - -
24H LEU* 4.2 9.8 - - - +
316H CYS 3.0 3.9 + - - -
317H THR 3.2 5.5 + - - -
318H TYR 3.5 0.4 - - - -
319H VAL* 1.3 78.8 - - - +
321H ALA* 1.3 59.6 + - - +
322H ALA 3.8 2.3 + - - -
326H GLU* 4.0 0.2 - - - +
330H ARG* 3.2 25.1 + - - -
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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