Contacts of the helix formed by residues 298 - 312 (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 SER 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A PRO* 4.1 19.0 - - - +
245A ASN* 5.5 1.0 + - - -
248A ILE* 4.2 4.2 - - - +
296A GLY 3.7 1.8 + - - -
297A THR* 1.3 75.9 + - - +
299A ILE* 1.3 55.4 + - - +
300A ALA* 2.9 9.9 - - - -
301A LEU* 2.7 49.0 + - - +
302A LYS* 3.4 1.9 + - - +
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A THR 3.9 2.7 - - - +
298A SER* 1.3 70.2 - - - +
300A ALA* 1.3 56.8 + - - +
301A LEU 3.5 0.2 - - - -
302A LYS* 3.6 31.4 + - + +
303A VAL* 3.3 24.3 + - - +
344A ILE* 3.9 38.6 - - + -
346A ASN* 3.8 22.2 - - + +
349A MET* 5.1 0.9 - - + -
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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
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248A ILE* 3.9 15.1 - - + +
252A LYS* 4.5 8.9 + - - +
298A SER* 2.8 7.5 + - - +
299A ILE* 1.3 78.4 - - - +
301A LEU* 1.3 64.0 + - - +
302A LYS 3.4 0.2 - - - -
303A VAL* 3.5 9.8 + - - +
304A GLY* 3.4 14.0 + - - -
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Residues in contact with LEU 301 (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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241A PRO* 5.2 10.5 - - + +
244A PRO* 3.9 25.4 - - + +
247A MET* 4.1 27.4 - - + -
248A ILE* 3.2 30.6 - - + +
292A GLY* 4.0 19.1 - - - +
297A THR* 3.4 27.1 - - - +
298A SER* 2.7 29.3 + - - +
300A ALA* 1.3 71.2 - - - +
302A LYS* 1.3 55.0 + - - +
304A GLY* 2.8 24.3 + - - -
305A CYS* 3.1 17.1 + - - -
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Residues in contact with LYS 302 (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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292A GLY 3.6 14.6 - - - +
293A LEU* 3.7 15.8 - - + +
294A LYS 3.3 30.1 + - - +
296A GLY 4.9 1.0 - - - +
297A THR* 2.6 48.6 + - - +
298A SER 3.4 3.3 + - - +
299A ILE* 3.6 26.8 - - + +
300A ALA 3.4 0.2 - - - -
301A LEU* 1.3 75.0 - - - +
303A VAL* 1.3 60.7 + - - +
305A CYS* 3.2 11.7 + - - +
306A LEU* 3.4 13.2 + - - +
341A LEU* 3.8 17.9 - - + -
344A ILE* 4.9 4.7 - - + -
349A MET* 3.4 20.1 - - + +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LYS* 5.7 2.5 - - - +
299A ILE 3.3 18.2 - - - +
300A ALA* 3.5 10.7 + - - +
301A LEU 3.2 0.8 - - - -
302A LYS* 1.3 76.2 - - - +
304A GLY* 1.3 50.6 + - - +
306A LEU* 4.5 0.4 - - - -
307A GLN* 2.7 50.7 + - - +
346A ASN* 4.7 5.6 - - - +
348A ASP* 3.8 28.0 - - + +
349A MET* 3.6 36.3 - - + +
352A GLN* 4.2 8.5 - - + +
1190C GLN* 5.1 8.5 - - + +
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Residues in contact with GLY 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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248A ILE* 5.8 2.7 - - - -
251A ALA* 3.5 24.9 - - - +
252A LYS* 4.5 13.2 - - - +
300A ALA 3.4 6.9 + - - -
301A LEU* 2.8 9.9 + - - -
303A VAL* 1.3 76.2 - - - +
305A CYS* 1.3 66.0 + - - +
307A GLN* 3.7 16.8 + - - +
308A LEU* 3.3 12.0 + - - +
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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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247A MET* 4.7 8.7 - - - -
251A ALA* 5.6 0.2 - - - -
289A LEU* 3.5 41.0 - - + +
292A GLY* 3.2 33.4 - - - -
293A LEU* 3.9 9.4 - - + -
301A LEU* 3.1 17.1 + - - -
302A LYS 3.2 7.2 + - - +
304A GLY* 1.3 73.0 - - - +
306A LEU* 1.3 57.1 + - - +
307A GLN 2.9 3.4 - - - -
308A LEU* 2.8 26.2 + - - +
309A ILE* 3.0 17.5 + - - +
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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
----------------------------------------------------------
293A LEU* 4.9 2.9 - - + +
302A LYS 3.4 10.1 + - - +
303A VAL 4.7 1.3 - - - +
305A CYS* 1.3 78.8 - - - +
307A GLN* 1.3 60.5 + - - +
309A ILE* 3.9 19.4 - - + +
310A ASN* 2.9 44.7 + - - +
334A LEU* 6.1 2.0 - - + -
338A LEU* 5.1 5.8 - - + -
341A LEU* 4.0 19.3 - - + -
349A MET* 4.4 3.4 - - - -
352A GLN* 3.7 26.7 - - + -
353A LEU* 3.7 34.5 - - + +
356A PHE* 3.7 29.2 - - + -
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Residues in contact with GLN 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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252A LYS* 3.5 36.5 + - - +
255A SER* 3.9 6.5 + - - -
303A VAL* 2.7 28.2 + - - +
304A GLY* 3.7 8.2 + - - -
305A CYS 2.9 0.6 - - - -
306A LEU* 1.3 77.3 - - - +
308A LEU* 1.3 64.0 - - - +
310A ASN* 3.7 4.7 + - - +
311A ALA* 3.5 14.2 + - - +
352A GLN* 3.1 22.8 + - - +
1186C LEU* 5.0 0.4 - - - +
1189C LEU* 3.4 41.3 - - + +
1190C GLN* 3.2 32.6 + - - +
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MET* 3.6 38.4 - - + -
251A ALA* 4.0 12.6 - - + +
254A LEU* 4.6 6.7 - - + -
255A SER* 3.2 32.0 + - - +
258A CYS* 4.7 3.8 - - - -
270A VAL* 4.7 4.0 - - + -
274A MET* 4.8 3.8 - - + -
289A LEU* 3.8 21.5 - - + -
304A GLY 3.3 8.0 + - - +
305A CYS 2.8 15.1 + - - +
307A GLN* 1.3 71.6 - - - +
309A ILE* 1.3 56.6 + - - +
311A ALA* 2.7 26.2 + - - +
312A LEU* 2.8 36.4 + - + -
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 4.1 28.3 - - + +
293A LEU* 5.0 2.7 - - + -
305A CYS 3.0 16.0 + - - +
306A LEU* 3.7 22.0 - - + +
308A LEU* 1.3 73.4 - - - +
310A ASN* 1.3 63.3 + - - +
312A LEU* 3.2 26.2 + - - +
313A ILE* 3.3 26.7 + - + +
329A LEU* 4.1 36.3 - - + -
334A LEU* 4.5 15.7 - - + -
356A PHE* 4.6 13.5 - - + -
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Residues in contact with ASN 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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306A LEU* 2.9 31.6 + - - +
307A GLN 3.7 9.0 - - - +
309A ILE* 1.3 75.4 - - - +
311A ALA* 1.3 57.6 + - - +
313A ILE* 4.5 5.4 - - - -
314A THR* 2.9 37.0 + - - +
352A GLN* 3.2 33.9 + - - +
355A VAL* 3.4 25.6 - - + +
356A PHE* 3.4 15.2 - - - +
1195C PHE* 4.3 16.2 - - + -
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A SER* 3.7 22.2 - - - +
258A CYS* 3.2 37.3 - - + +
259A ILE* 4.3 15.3 - - + -
267A ASN* 4.1 1.0 - - - +
307A GLN 3.5 7.3 + - - +
308A LEU* 2.7 12.8 + - - +
310A ASN* 1.3 76.8 - - - +
312A LEU* 1.3 56.5 + - - +
313A ILE 3.3 0.9 - - - -
315A PRO* 3.2 20.5 - - - +
1189C LEU* 4.9 4.9 - - + -
1195C PHE* 4.9 1.6 - - - -
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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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258A CYS* 3.6 20.2 - - - -
267A ASN* 3.5 33.9 - - + +
270A VAL* 4.0 6.5 - - + -
271A LEU* 3.9 23.5 - - + +
274A MET* 3.6 33.0 - - + -
286A PHE* 4.8 5.8 - - + -
289A LEU* 5.2 3.8 - - + -
308A LEU* 2.8 28.4 + - + +
309A ILE* 3.3 10.3 - - - +
310A ASN 3.2 0.2 - - - -
311A ALA* 1.3 76.4 - - - +
313A ILE* 1.3 62.7 + - - +
315A PRO* 4.8 0.9 - - - -
316A ALA* 5.7 0.9 - - - -
321A PHE* 4.7 9.5 - - - -
325A ILE* 3.9 10.9 - - - +
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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