Contacts of the helix formed by residues 315 - 322 (chain A) in PDB entry 2JBO
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 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A MET* 3.9 3.4 - - - -
313A ARG 4.9 4.0 - - - +
314A MET* 1.3 77.1 - - - +
316A ILE* 1.3 61.1 + - - +
317A THR* 3.1 10.8 + - - -
318A GLU* 2.8 45.3 + - - +
319A PHE* 2.8 28.4 + - - +
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Residues in contact with ILE 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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171A GLY* 3.8 13.0 - - - +
174A ILE* 3.6 16.2 - - + -
175A GLN* 3.4 44.9 - - + +
178A HIS* 4.1 25.2 + - + +
246A MET* 3.6 30.2 - - + +
249A LEU* 4.0 6.1 - - + -
315A THR* 1.3 72.2 - - - +
317A THR* 1.3 72.6 + - - +
319A PHE* 3.2 19.1 - - + +
320A MET* 3.0 23.6 + - + +
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Residues in contact with THR 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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175A GLN* 4.6 16.6 + - - +
315A THR* 3.0 9.9 + - - -
316A ILE* 1.3 84.4 - - - +
318A GLU* 1.3 67.1 + - + +
320A MET* 3.1 12.5 + - - +
321A ASN* 3.1 31.3 + - - +
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Residues in contact with GLU 318 (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 ARG 4.7 0.9 - - - +
314A MET* 3.5 25.2 - - + +
315A THR* 2.8 42.5 + - - +
317A THR* 1.3 80.0 - - - +
319A PHE* 1.3 65.3 + - - +
321A ASN* 3.2 13.0 + - - +
322A HIS* 3.2 12.0 + - - +
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Residues in contact with PHE 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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167A MET* 4.0 28.0 - - + -
171A GLY* 4.2 1.3 - - - -
246A MET* 4.0 7.9 - - + -
249A LEU* 4.1 18.2 - - + -
253A MET* 4.9 2.0 - - - -
301A LEU* 4.6 8.1 - - + -
305A LEU* 3.9 38.8 - - + -
314A MET* 3.8 13.0 - - - -
315A THR 2.8 13.0 + - - +
316A ILE* 3.2 21.1 - - + +
318A GLU* 1.3 74.7 - - - +
320A MET* 1.3 84.8 + - - +
322A HIS* 2.9 21.6 + - - +
325A ILE* 3.3 43.4 - - + +
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Residues in contact with MET 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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168A LYS* 3.7 15.9 - - + +
171A GLY* 3.8 14.1 - - - -
172A GLU* 3.4 46.2 - - - +
175A GLN* 3.5 30.3 - - + +
316A ILE* 3.0 17.5 + - + +
317A THR* 3.1 4.0 + - - +
319A PHE* 1.3 93.7 - - - +
321A ASN* 1.3 65.0 + - - +
322A HIS 3.5 0.3 + - - -
325A ILE* 3.7 15.2 - - + +
326A MET* 3.6 20.8 - - - +
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Residues in contact with ASN 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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317A THR* 3.1 34.8 + - - +
318A GLU* 3.2 6.3 + - - +
319A PHE 2.9 1.8 + - - -
320A MET* 1.3 80.9 - - - +
322A HIS* 1.3 64.4 + - - +
323A PRO* 3.4 5.9 - - - +
326A MET* 3.7 33.3 - - - +
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Residues in contact with HIS 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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297A GLU* 4.0 23.4 + - + +
300A MET* 6.2 0.2 - - - +
301A LEU* 3.6 41.1 - - + +
314A MET* 4.6 8.3 - - + -
318A GLU 3.2 10.1 + - - +
319A PHE* 2.9 17.0 + - - +
321A ASN* 1.3 77.0 - - - +
323A PRO* 1.3 64.2 - - + +
324A TRP* 3.0 29.9 + - + +
325A ILE* 2.8 11.1 + - + +
326A MET 2.7 31.6 + - - -
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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
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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