Contacts of the helix formed by residues 304 - 316 (chain A) in PDB entry 4BKR
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 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A VAL* 3.8 12.9 - - - +
302A HIS* 5.0 1.0 + - - -
303A GLU* 1.3 74.6 - - - +
305A CYS* 1.3 65.9 + - - -
307A GLU* 2.9 18.6 + - - +
308A GLN* 3.2 23.9 + - - +
369A GLU* 5.2 10.1 - - - -
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Residues in contact with CYS 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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27A GLN* 4.9 5.4 - - - +
52A GLY* 3.8 33.2 - - - +
53A TYR* 3.7 18.6 - - + -
56A ALA* 3.8 5.2 - - + -
274A VAL* 3.8 25.1 - - - +
275A VAL 4.7 3.8 - - - -
276A THR* 3.9 11.7 - - - -
304A GLY* 1.3 71.4 - - - -
306A ILE* 1.3 64.1 + - - +
308A GLN* 3.3 2.3 + - - +
309A VAL* 3.0 28.4 + - - +
373A LEU* 6.2 1.8 - - - -
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Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 3.6 43.6 + - + +
30A TYR* 4.0 17.7 - - + -
31A VAL* 3.7 18.2 - - + -
56A ALA* 3.6 33.7 - - - +
59A ILE* 3.9 12.3 - - + -
60A THR* 3.7 12.3 - - - +
305A CYS* 1.3 79.1 - - - +
307A GLU* 1.3 79.3 + - - +
310A TYR* 2.9 34.2 + - - +
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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
----------------------------------------------------------
26A LYS* 6.0 1.9 - - - -
30A TYR* 3.5 43.0 + - + +
302A HIS 5.6 0.7 - - - +
303A GLU* 3.8 31.9 - - + +
304A GLY* 2.9 29.0 + - - +
306A ILE* 1.3 88.5 - - - +
308A GLN* 1.3 62.3 + - - +
310A TYR* 3.9 2.1 - - - +
311A SER* 3.2 25.1 + - - -
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Residues in contact with GLN 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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53A TYR* 3.5 27.8 - - + +
271A LEU* 3.6 11.6 - - + -
272A LYS* 2.8 48.6 + - - +
274A VAL* 5.5 0.4 - - + -
303A GLU* 3.6 10.0 + - - +
304A GLY 3.2 16.8 + - - +
305A CYS 3.6 2.9 - - - +
307A GLU* 1.3 80.6 - - - +
309A VAL* 1.3 56.5 + - - +
311A SER* 3.0 8.1 + - - -
312A LEU* 3.0 21.5 + - - +
332A ALA* 3.1 38.3 + - - +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.4 45.5 - - + +
56A ALA* 3.9 7.0 - - + -
57A ALA* 3.5 31.4 - - + +
60A THR* 3.7 6.1 - - - +
223A PHE* 4.8 6.3 - - + -
271A LEU* 4.6 8.7 - - + -
305A CYS 3.0 13.2 + - - +
308A GLN* 1.3 73.4 - - - +
310A TYR* 1.3 67.1 + - - +
312A LEU* 3.2 8.8 + - + +
313A TYR* 3.0 37.8 + - + -
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Residues in contact with TYR 310 (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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30A TYR* 4.0 14.6 - + + -
31A VAL* 3.9 34.3 - - + -
34A GLU* 3.4 38.8 + - + +
35A GLY 2.6 32.0 + - - -
36A PRO 4.0 2.3 + - - -
37A ILE* 3.7 25.9 - - + +
60A THR* 3.7 13.1 + - + +
306A ILE 2.9 19.1 + - - +
307A GLU 3.9 2.9 - - - +
309A VAL* 1.3 79.5 - - - +
311A SER* 1.3 62.8 + - - +
313A TYR* 3.3 2.4 + - - +
314A LYS* 2.9 57.7 + - + +
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLU* 4.5 8.5 + - - -
307A GLU 3.2 12.7 + - - -
308A GLN* 3.0 23.7 + - - -
310A TYR* 1.3 82.8 - - - +
312A LEU* 1.3 59.7 + - - +
314A LYS* 4.4 4.5 - - - +
315A ASP* 2.8 51.7 + - - +
332A ALA* 5.1 1.6 - - - +
334A TYR* 5.6 1.5 + - - -
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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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223A PHE* 3.9 30.1 - - + -
269A SER* 3.8 29.2 - - - +
271A LEU* 4.0 9.6 - - + -
308A GLN* 3.0 16.1 + - - +
309A VAL* 3.5 14.4 - - + +
311A SER* 1.3 75.7 + - - +
313A TYR* 1.3 58.1 + - + +
315A ASP* 5.3 0.2 - - - -
316A SER* 3.0 25.0 + - - +
317A LEU* 2.9 41.5 + - + -
330A LEU* 4.4 7.9 - - + +
332A ALA* 4.1 25.8 - - + +
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Residues in contact with TYR 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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37A ILE* 3.8 6.5 - - + -
41A PRO* 4.5 3.1 - - + -
44A VAL* 4.5 0.5 - - - +
57A ALA* 3.7 24.7 + - + +
60A THR* 3.5 22.0 - - + -
61A ALA* 3.9 16.3 - - + +
65A CYS* 3.8 21.8 - - - -
134A GLN* 2.7 38.5 + - - -
136A ILE* 3.4 16.4 - - + +
223A PHE* 5.8 0.7 - + - -
309A VAL* 3.0 40.0 + - + -
310A TYR 3.7 2.2 - - - +
312A LEU* 1.3 76.8 - - + +
314A LYS* 1.3 61.3 + - - +
315A ASP 3.5 0.2 + - - -
317A LEU* 3.8 20.0 - - + -
318A CYS* 2.8 44.9 + - - +
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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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34A GLU 5.6 3.2 + - - -
36A PRO 4.9 7.6 - - - -
37A ILE* 3.9 24.3 - - + +
310A TYR* 2.9 49.5 + - + +
311A SER* 4.1 2.7 - - - +
313A TYR* 1.3 77.0 - - - +
315A ASP* 1.3 67.9 + - - +
318A CYS 4.2 0.5 - - - -
319A GLY* 3.1 21.7 + - - -
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Residues in contact with ASP 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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311A SER* 2.8 38.8 + - - +
314A LYS* 1.3 86.8 - - - +
316A SER* 1.3 64.9 + - - +
319A GLY* 3.6 10.2 - - - -
321A SER 3.5 10.6 - - - +
322A PRO* 3.1 23.4 - - - +
323A HIS* 5.7 3.4 - - + +
334A TYR* 4.3 14.2 + - - +
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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
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312A LEU* 3.0 27.1 + - - +
313A TYR 3.8 0.2 + - - -
314A LYS 3.6 0.6 - - - -
315A ASP* 1.3 81.9 - - - +
317A LEU* 1.3 68.9 + - - +
318A CYS 3.3 1.1 - - - -
319A GLY 4.2 4.1 + - - +
322A PRO* 3.8 18.3 - - - +
323A HIS* 3.2 31.8 + - - +
330A LEU* 4.4 19.2 - - - +
331A ARG 4.6 4.5 + - - -
332A ALA* 6.0 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