Contacts of the helix formed by residues 318 - 332 (chain A) in PDB entry 2BAP
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 GLU 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A ALA* 3.4 1.6 - - - +
317A GLU* 1.3 78.1 - - + +
319A LEU* 1.3 67.3 + - - +
320A ASP* 4.5 14.4 - - + +
321A PHE* 3.0 33.9 + - + +
322A ARG* 3.5 9.6 + - - +
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Residues in contact with LEU 319 (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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317A GLU 3.7 4.6 + - - -
318A GLU* 1.3 70.1 - - - +
320A ASP* 1.3 63.2 + - - +
321A PHE 3.1 1.0 + - - -
322A ARG* 3.2 29.1 + - - +
323A VAL* 3.1 20.6 + - + +
362A GLU 5.4 0.2 - - - +
363A ASP* 3.7 34.8 - - + +
366A ASP* 3.4 38.1 - - + +
367A LEU* 3.8 29.6 - - + -
370A ARG* 4.2 14.6 - - - +
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Residues in contact with ASP 320 (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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318A GLU* 3.2 13.2 - - + +
319A LEU* 1.3 75.3 - - - +
321A PHE* 1.3 57.0 + - - +
323A VAL* 3.4 9.8 - - - +
324A HIS* 3.1 27.4 + - - +
367A LEU* 5.3 1.3 - - - +
370A ARG* 2.7 43.3 + - - -
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Residues in contact with PHE 321 (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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267A ASN* 4.8 7.9 - - + -
268A GLU* 5.0 22.0 - - + -
271A LEU* 3.6 30.5 - - + -
312A LEU 4.7 8.1 - - - -
313A ILE* 6.1 0.2 - - - -
316A ALA* 3.8 25.4 - - + -
318A GLU* 3.0 25.5 + - + +
320A ASP* 1.3 77.9 - - - +
322A ARG* 1.3 64.6 + - - +
324A HIS* 3.0 34.0 + + - +
325A ILE* 3.1 31.4 + - + +
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Residues in contact with ARG 322 (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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313A ILE* 3.9 28.0 + - + +
314A THR 5.1 2.9 + - - -
316A ALA* 2.8 30.9 + - + +
317A GLU* 3.6 17.2 + - - +
318A GLU 3.7 9.5 + - - +
319A LEU* 3.2 25.3 + - - +
321A PHE* 1.3 76.2 - - - +
323A VAL* 1.3 57.7 + - - +
325A ILE* 3.2 13.5 - - - +
326A ARG* 3.0 36.7 + - - +
359A GLN* 4.5 14.6 + - - +
363A ASP* 2.6 49.3 + - - +
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Residues in contact with VAL 323 (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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319A LEU* 3.1 28.3 - - + +
320A ASP* 3.4 16.6 - - - +
322A ARG* 1.3 73.9 - - - +
324A HIS* 1.3 66.6 + - - +
326A ARG* 3.8 15.8 - - - +
327A SER* 2.8 26.3 + - - -
363A ASP* 5.8 3.6 - - + +
367A LEU* 4.5 17.3 - - + -
432A ILE 5.1 0.4 - - - +
433A VAL* 3.4 33.0 - - + +
434A LEU 5.6 1.6 - - - +
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Residues in contact with HIS 324 (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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285A ARG* 4.4 16.3 + - - -
320A ASP 3.1 17.8 + - - +
321A PHE* 3.0 26.6 + + - +
323A VAL* 1.3 80.5 - - - +
325A ILE* 1.3 62.1 + - + +
327A SER* 3.1 5.5 + - - -
328A GLU* 2.9 31.9 + - + +
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Residues in contact with ILE 325 (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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271A LEU* 4.3 12.6 - - + -
285A ARG* 3.4 29.4 - - - +
286A PHE* 4.1 15.0 - - + -
312A LEU 3.9 8.5 - - - +
313A ILE* 3.5 31.0 - - + -
321A PHE* 3.1 27.1 - - + +
322A ARG* 3.2 24.0 - - - +
324A HIS* 1.3 82.2 - - - +
326A ARG* 1.3 64.0 + - - +
328A GLU* 3.1 12.2 + - - +
329A LEU* 2.8 37.5 + - + +
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Residues in contact with ARG 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 4.3 13.5 - - + +
322A ARG* 3.0 30.3 + - - +
323A VAL* 3.8 11.3 - - - +
325A ILE* 1.3 78.9 - - - +
327A SER* 1.3 57.8 + - - +
329A LEU* 3.4 10.4 - - - +
330A MET* 3.1 55.3 + - - +
334A LEU* 5.1 2.0 - - + -
356A PHE* 3.5 36.6 + - + -
359A GLN* 4.2 5.7 - - - +
360A GLY* 3.5 31.1 + - - +
363A ASP* 2.6 39.4 + - - +
434A LEU 5.8 2.2 - - - -
435A HIS 4.8 7.0 - - - -
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Residues in contact with SER 327 (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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323A VAL* 2.8 22.6 + - - -
324A HIS* 3.4 5.2 - - - -
326A ARG* 1.3 75.8 - - - +
328A GLU* 1.3 64.5 + - - +
330A MET* 3.4 7.8 + - - +
331A ARG* 3.0 24.8 + - - +
432A ILE* 2.6 47.0 + - - +
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Residues in contact with GLU 328 (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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284A GLU* 3.4 20.9 - - - +
285A ARG* 2.6 48.3 + - - +
286A PHE* 3.4 21.9 - - + -
324A HIS* 2.9 15.4 + - + +
325A ILE* 3.1 18.1 - - - +
327A SER* 1.3 77.8 - - - +
329A LEU* 1.3 64.8 + - - +
331A ARG* 3.2 35.7 + - - +
332A LEU* 3.5 10.0 + - + +
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Residues in contact with LEU 329 (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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286A PHE* 3.8 41.3 - - + +
289A LEU* 5.0 8.3 - - + -
290A LEU* 4.0 10.1 - - + +
309A ILE* 4.1 38.6 - - + -
313A ILE* 5.5 0.2 - - + -
325A ILE* 2.8 34.5 + - + +
326A ARG* 3.4 12.3 - - - +
328A GLU* 1.3 72.1 - - - +
330A MET* 1.3 53.5 + - - +
332A LEU* 2.8 31.4 + - + +
333A GLY 3.3 6.6 + - - -
334A LEU* 3.6 32.9 + - + +
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Residues in contact with MET 330 (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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326A ARG* 3.1 41.8 + - - +
327A SER* 3.4 7.6 + - - +
329A LEU* 1.3 77.7 - - - +
331A ARG* 1.3 60.6 + - - +
332A LEU 3.3 0.2 - - - -
333A GLY* 3.4 11.6 + - - -
334A LEU* 3.7 22.6 + - + +
335A HIS* 3.7 45.2 + - + +
338A LEU* 5.7 6.1 - - + -
356A PHE* 5.5 2.5 - - + -
435A HIS* 3.1 37.5 - - + +
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Residues in contact with ARG 331 (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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284A GLU* 3.2 35.8 + - - +
327A SER 3.0 13.1 + - - +
328A GLU* 3.2 32.5 + - - +
329A LEU 3.1 0.2 - - - -
330A MET* 1.3 77.5 - - - +
332A LEU* 1.3 65.8 + - - +
333A GLY* 3.3 0.6 - - - -
432A ILE* 6.5 0.4 - - + -
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Residues in contact with LEU 332 (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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284A GLU* 4.0 28.9 - - + -
286A PHE* 3.7 31.9 - - + +
287A GLN* 4.0 30.1 - - + +
290A LEU* 3.7 24.3 - - + +
328A GLU* 3.5 10.3 + - + +
329A LEU* 2.8 10.0 + - - +
331A ARG* 1.3 87.3 - - - +
333A GLY* 1.3 56.5 + - - +
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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