Contacts of the helix formed by residues 306 - 315 (chain A) in PDB entry 2JB3
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 PRO 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A ASN 3.7 5.4 - - - +
305A LEU* 1.3 89.1 - - + +
307A GLY* 1.3 66.7 + - - +
308A ASP* 3.2 16.4 - - - +
309A VAL* 3.0 21.0 + - + +
310A LEU* 3.2 10.2 + - - +
451A VAL* 3.5 26.7 - - + -
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Residues in contact with GLY 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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305A LEU 3.7 2.1 + - - -
306A PRO* 1.3 72.6 - - - +
308A ASP* 1.3 56.4 + - - +
310A LEU* 3.4 11.8 + - - +
311A THR* 2.9 31.9 + - - -
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Residues in contact with ASP 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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306A PRO* 3.5 18.5 - - - +
307A GLY* 1.3 72.3 - - - +
309A VAL* 1.3 68.7 + - - +
311A THR* 3.5 7.7 + - - -
312A ALA* 3.0 29.0 + - - +
446A LYS* 3.5 32.0 + - + +
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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
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305A LEU* 4.3 10.5 - - + -
306A PRO* 3.0 27.7 + - + +
308A ASP* 1.3 90.1 + - - +
310A LEU* 1.3 64.6 + - - +
312A ALA* 3.1 8.4 + - - +
313A LEU* 3.0 27.3 + - + +
446A LYS* 4.2 18.2 - - + +
447A LEU* 4.0 9.0 - - + -
451A VAL* 4.1 16.2 - - + -
456A PHE* 3.9 32.5 - - + -
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Residues in contact with LEU 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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299A GLY* 4.7 13.9 - - - +
303A ASN* 3.6 31.9 - - - +
305A LEU* 3.7 34.3 - - + +
306A PRO 3.2 10.8 + - - +
307A GLY* 3.4 11.9 + - - +
309A VAL* 1.3 77.9 - - - +
311A THR* 1.3 62.3 + - - +
313A LEU* 3.4 18.3 + - + +
314A LYS* 3.5 24.4 + - - +
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Residues in contact with THR 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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307A GLY 2.9 20.5 + - - -
308A ASP* 3.7 8.5 - - - -
309A VAL 3.2 0.4 - - - -
310A LEU* 1.3 75.1 - - - +
312A ALA* 1.3 62.9 + - - +
314A LYS* 3.2 26.3 + - + +
315A ALA* 3.7 6.4 + - - +
443A GLU* 4.9 3.7 - - + +
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Residues in contact with ALA 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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308A ASP 3.0 15.8 + - - +
309A VAL 3.1 9.2 + - - +
311A THR* 1.3 78.3 - - - +
313A LEU* 1.3 60.7 + - - +
315A ALA* 3.2 16.8 + - - +
429A TRP* 3.7 3.8 - - - -
443A GLU* 3.6 44.2 - - + +
446A LYS* 4.3 10.3 - - + -
447A LEU* 3.7 16.9 - - + +
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Residues in contact with LEU 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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295A PRO* 3.8 50.1 - - + +
296A HIS* 4.5 1.4 + - - -
298A VAL* 3.8 28.5 - - + -
299A GLY* 4.9 3.1 - - - +
305A LEU* 4.1 17.7 - - + -
309A VAL* 3.0 21.4 + - + +
310A LEU* 3.6 17.3 - - + +
311A THR 3.3 0.2 - - - -
312A ALA* 1.3 75.3 - - - +
314A LYS* 1.3 61.6 + - + +
315A ALA 3.4 0.5 + - - -
316A ALA* 3.5 12.4 + - - +
447A LEU* 3.7 28.7 - - + +
456A PHE* 4.5 15.7 - - + -
460A HIS* 5.7 2.2 - - - +
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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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296A HIS* 6.0 2.5 - - - +
299A GLY* 6.5 0.9 - - - -
310A LEU* 3.5 19.4 - - - +
311A THR* 3.2 16.8 + - + +
312A ALA 3.1 0.6 - - - -
313A LEU* 1.3 77.0 - - + +
315A ALA* 1.3 60.9 + - - +
316A ALA 3.2 3.3 + - - +
317A LYS* 2.8 32.9 + - - +
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Residues in contact with ALA 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 THR 3.7 3.6 + - - +
312A ALA 3.2 7.3 + - - +
314A LYS* 1.3 77.2 - - - +
316A ALA* 1.3 57.2 + - - +
317A LYS* 3.2 15.2 + - - +
429A TRP* 3.3 6.6 - - + -
430A ALA* 3.0 38.8 + - + +
443A GLU* 3.5 42.2 - - + +
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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