Contacts of the helix formed by residues 297 - 319 (chain A) in PDB entry 2PA3
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 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 2.6 34.7 + - - +
293A ILE 5.5 0.7 - - - +
294A GLY 5.4 0.4 - - - +
295A GLY 3.5 3.8 + - - -
296A SER* 1.3 81.1 - - - +
298A GLN* 1.3 64.4 + - - +
299A GLU* 3.5 15.8 + - - +
300A ALA* 3.0 15.2 + - - +
301A GLN* 3.0 26.9 + - - +
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Residues in contact with GLN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 4.3 9.2 + - + +
297A THR* 1.3 73.4 - - - +
299A GLU* 1.3 64.0 + - - +
301A GLN* 3.1 10.0 + - + +
302A GLU* 3.0 39.3 + - - +
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A SER* 5.2 1.8 - - - +
297A THR* 3.3 16.7 - - - +
298A GLN* 1.3 78.7 + - - +
300A ALA* 1.3 66.2 + - - +
302A GLU* 3.1 20.5 + - - +
303A ASN* 3.0 32.3 + - - +
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER 4.2 1.8 - - - -
108A ASN* 3.6 21.1 - - + +
111A SER* 4.1 4.2 + - - +
295A GLY 3.3 26.2 - - - +
297A THR* 3.0 20.4 + - - +
299A GLU* 1.3 75.5 - - - +
301A GLN* 1.3 65.9 + - + +
303A ASN* 3.2 11.2 + - - +
304A ILE* 3.0 31.3 + - + +
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Residues in contact with GLN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 4.9 0.3 - - - +
19A VAL* 5.2 1.0 - - - -
20A HIS* 3.6 32.5 + - + +
60A ARG* 3.5 39.0 + - - +
82A PHE 5.3 3.9 + - - +
296A SER* 5.9 3.6 - - - +
297A THR 3.0 20.2 + - - +
298A GLN* 3.1 11.4 + - + +
300A ALA* 1.3 78.1 - - - +
302A GLU* 1.3 63.3 + - - +
304A ILE* 3.4 23.6 + - - +
305A GLY* 3.0 18.5 + - - -
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 3.1 36.3 + - + +
22A LYS* 3.7 30.2 - - + +
298A GLN* 3.0 26.3 + - - +
299A GLU* 3.1 20.6 + - - +
301A GLN* 1.3 76.1 - - - +
303A ASN* 1.3 66.2 + - - +
305A GLY* 3.3 0.9 + - - -
306A LEU* 3.1 28.6 + - + +
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Residues in contact with ASN 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER* 2.9 38.0 + - - +
108A ASN* 5.1 0.2 - - - +
110A ARG* 6.3 1.0 - - - +
299A GLU* 3.0 23.0 + - - +
300A ALA* 3.2 3.3 + - - +
302A GLU* 1.3 78.9 - - - +
304A ILE* 1.3 52.9 + - - +
306A LEU* 3.2 11.2 + - - +
307A GLU* 2.8 36.3 + - + +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PHE* 3.3 41.0 - - + +
83A ALA* 3.9 20.2 - - - +
84A ILE* 4.9 1.8 - - + +
104A ALA* 4.1 13.0 - - + +
107A SER* 3.7 20.6 - - - -
108A ASN* 4.5 15.7 - - - +
300A ALA* 3.0 22.1 + - + +
301A GLN* 3.7 25.8 - - - +
303A ASN* 1.3 75.5 - - - +
305A GLY* 1.3 63.8 + - - +
308A VAL* 3.1 24.9 + - - +
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Residues in contact with GLY 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A HIS* 4.8 6.7 - - - -
22A LYS* 5.3 0.4 - - - -
23A ALA* 3.5 20.6 - - - +
82A PHE* 3.7 16.3 - - - -
301A GLN 3.0 16.3 + - - -
302A GLU 3.8 1.6 - - - -
304A ILE* 1.3 78.5 - - - +
306A LEU* 1.3 56.9 + - - +
309A ALA* 3.1 31.7 + - - +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 3.8 39.5 - - + +
25A GLU* 6.2 0.2 - - + -
26A SER* 3.2 25.9 + - - +
302A GLU* 3.1 18.2 + - + +
303A ASN* 3.5 12.3 - - - +
305A GLY* 1.3 73.4 - - - +
307A GLU* 1.3 66.5 + - - +
309A ALA* 3.9 1.0 - - - +
310A GLY* 2.9 20.6 + - - -
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ALA* 3.7 17.0 - - + -
105A PRO* 4.1 5.4 - - - +
106A PHE* 5.0 3.0 + - - -
107A SER* 3.5 22.4 + - - +
303A ASN* 2.8 19.1 + - + +
304A ILE 4.0 2.2 - - - +
306A LEU* 1.3 71.2 - - - +
308A VAL* 1.3 62.1 + - + +
310A GLY* 2.8 19.5 + - - -
311A LYS* 2.9 42.1 + - - +
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY* 3.8 20.2 - - - -
81A ALA 3.9 8.7 - - - +
82A PHE* 3.5 35.7 - - + -
102A PHE* 4.9 4.9 - - + +
103A ASN 3.3 33.9 - - - +
104A ALA* 3.6 15.3 - - + -
304A ILE 3.1 12.9 + - - +
307A GLU* 1.3 80.1 - - - +
309A ALA* 1.3 63.5 + - - +
311A LYS* 3.2 7.8 + - - +
312A LEU* 3.1 23.7 + - + +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.8 27.8 - - + +
26A SER* 4.2 8.7 - - - -
27A LEU* 4.0 13.2 - - + +
82A PHE* 4.0 8.8 - - + -
305A GLY 3.1 23.2 + - - +
306A LEU 3.9 1.8 - - - +
308A VAL* 1.3 78.6 - - - +
310A GLY* 1.3 57.2 + - - +
312A LEU* 3.1 8.8 + - - +
313A ILE* 2.8 34.3 + - - +
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Residues in contact with GLY 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 5.1 2.8 - - - -
306A LEU 2.9 12.0 + - - -
307A GLU 2.8 8.8 + - - -
309A ALA* 1.3 75.6 - - - +
311A LYS* 1.3 55.4 + - - -
313A ILE* 3.1 11.5 + - - +
314A LYS* 2.7 48.7 + - - +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PHE* 3.8 32.5 - - + -
103A ASN* 2.9 33.9 + - - +
105A PRO* 4.1 10.1 - - - +
307A GLU* 2.9 44.2 + - - +
308A VAL* 3.6 7.0 - - - +
309A ALA 3.2 0.2 - - - -
310A GLY* 1.3 75.3 - - - +
312A LEU* 1.3 57.6 + - - +
314A LYS* 3.7 11.0 - - + +
315A TYR* 2.8 31.7 + - - +
320A SER 4.9 0.5 - - - +
322A LEU 4.7 1.6 - - - +
323A SER* 3.0 33.0 + - - +
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 4.3 23.3 - - + -
15A LEU* 5.9 1.3 - - + -
27A LEU* 5.5 1.3 - - + -
56A PHE* 3.9 24.5 - - + -
57A ILE 4.8 4.0 - - - +
58A GLY* 5.2 0.4 - - - +
78A ALA* 4.6 5.8 - - + -
79A ILE 4.1 5.4 - - - +
80A GLY* 4.0 31.0 - - - +
82A PHE* 4.3 16.4 - - + -
102A PHE* 3.6 27.1 - - + -
308A VAL 3.1 14.6 + - - +
309A ALA* 3.4 9.4 - - - +
311A LYS* 1.3 77.8 - - - +
313A ILE* 1.3 64.1 + - - +
315A TYR* 3.3 4.8 + - - +
316A SER* 2.9 25.6 + - - -
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Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 5.4 1.8 - - + -
26A SER* 3.5 35.4 - - - +
27A LEU* 3.7 25.4 - - + -
30A ALA* 3.6 23.1 - - + -
32A TYR* 4.4 9.4 - - + -
309A ALA 2.8 18.9 + - - +
310A GLY* 3.3 10.3 - - - +
312A LEU* 1.3 70.6 - - - +
314A LYS* 1.3 55.6 + - + +
316A SER* 3.0 6.4 + - - -
317A ASP* 2.7 53.0 + - - +
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLY* 2.7 33.7 + - - +
311A LYS* 3.7 9.5 - - + +
313A ILE* 1.3 74.4 - - + +
315A TYR* 1.3 57.0 + - - +
317A ASP* 3.0 3.8 + - - +
318A ASN* 2.7 51.1 + - - +
319A GLY 3.2 2.4 + - - -
320A SER* 4.4 13.5 - - - +
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Residues in contact with TYR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A PHE* 4.2 3.4 - + - -
77A VAL* 3.4 32.3 + - + +
78A ALA* 3.7 15.5 - - + -
98A GLY 4.3 4.9 + - - -
100A PRO* 3.4 28.7 - - + +
102A PHE* 3.9 11.0 - + + -
311A LYS 2.8 21.1 + - - +
312A LEU* 3.7 3.8 - - - +
314A LYS* 1.3 72.2 - - - +
316A SER* 1.3 62.4 + - - +
319A GLY* 3.1 17.9 + - - +
320A SER 3.2 26.1 + - - +
321A THR* 3.3 24.0 - - + -
327A PHE* 4.7 3.1 - - - -
341A MET* 3.2 18.5 - - + +
343A ILE* 4.6 3.6 - - - +
378A TYR* 3.8 11.4 - + - -
405A ARG* 5.7 1.0 - - - -
407A ARG* 3.0 29.1 + - - -
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Residues in contact with SER 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 4.5 7.4 - - - +
13A PHE* 5.2 0.7 - - - -
32A TYR* 2.7 33.0 + - - -
56A PHE* 3.6 27.4 - - - -
312A LEU 2.9 17.8 + - - -
313A ILE* 3.5 3.1 - - - -
315A TYR* 1.3 79.1 - - - +
317A ASP* 1.3 63.1 + - - +
407A ARG* 3.1 25.7 + - - +
409A LEU* 4.6 4.0 - - - +
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LYS* 4.1 15.2 + - - -
30A ALA* 4.8 5.7 - - - +
32A TYR* 2.7 26.0 + - - -
313A ILE* 2.7 38.6 + - + +
314A LYS* 3.9 3.1 - - - +
316A SER* 1.3 77.0 - - - +
318A ASN* 1.3 61.0 + - + +
409A LEU* 4.1 4.0 - - - +
410A TYR* 3.5 26.3 - - - -
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Residues in contact with ASN 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LYS* 2.7 32.0 + - - +
317A ASP* 1.3 77.6 - - + +
319A GLY* 1.3 57.5 + - - +
320A SER* 2.9 32.2 - - - +
331A SER* 5.2 2.0 + - - -
332A LEU 5.3 7.5 + - - +
339A ARG* 3.9 34.5 + - - +
380A VAL* 4.6 2.4 - - - +
409A LEU* 3.6 12.1 - - - +
410A TYR* 4.6 6.1 - - + -
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Residues in contact with GLY 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LYS 3.2 0.8 + - - -
315A TYR* 3.1 24.1 + - - -
318A ASN* 1.3 77.7 - - - +
320A SER* 1.3 66.2 + - - +
321A THR* 3.3 7.1 + - - +
330A VAL 3.9 2.0 - - - +
331A SER* 5.9 0.4 - - - -
378A TYR* 2.6 32.7 + - - -
380A VAL* 4.4 4.5 - - - +
407A ARG* 4.7 0.9 - - - -
409A LEU* 3.6 12.6 - - - +
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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