Contacts of the helix formed by residues 352 - 363 (chain B) in PDB entry 1OJ7
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 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273B LEU* 5.5 0.2 - - - +
276B MET* 4.0 9.0 - - - -
277B HIS* 2.7 40.3 + - - -
343B LEU* 6.1 0.7 - - - +
348B LEU* 5.6 2.1 - - - +
350B GLY* 3.1 5.2 + - - +
351B SER* 1.3 78.2 + - - +
353B ILE* 1.3 66.0 + - - +
354B PRO* 3.4 2.0 - - - -
355B ALA* 3.0 12.6 + - - +
356B LEU* 2.9 27.2 + - - +
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Residues in contact with ILE 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B LEU* 4.7 4.5 - - + -
350B GLY* 3.2 31.6 + - - +
352B SER* 1.3 77.7 - - - +
354B PRO* 1.3 71.1 - - + +
356B LEU* 3.0 16.0 + - + +
357B LEU* 2.9 39.4 + - + +
380B ARG* 4.1 15.9 - - + +
383B TYR* 3.7 49.6 - - + +
384B GLU* 3.8 17.5 - - + +
387B ARG* 4.4 4.9 - - - +
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Residues in contact with PRO 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLY 4.4 1.3 - - - +
351B SER* 3.5 16.6 - - - +
352B SER 3.6 0.4 - - - -
353B ILE* 1.3 95.4 - - + +
355B ALA* 1.3 60.9 + - - +
357B LEU* 3.3 13.0 + - + +
358B LYS* 3.0 30.5 + - + +
380B ARG* 4.8 11.9 - - - +
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B MET* 3.7 27.1 - - + +
352B SER* 3.0 14.7 + - - +
354B PRO* 1.3 78.4 - - - +
356B LEU* 1.3 60.5 + - - +
358B LYS* 3.3 10.7 + - - +
359B LYS* 3.2 18.9 + - - +
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B GLU* 3.6 36.2 - - + +
273B LEU* 3.6 28.0 - - + -
276B MET* 3.6 25.6 - - + -
277B HIS* 4.7 1.1 - - - +
343B LEU* 5.9 1.6 - - + -
352B SER* 2.9 29.9 + - - +
353B ILE* 3.4 19.3 - - + +
355B ALA* 1.3 76.4 - - - +
357B LEU* 1.3 56.2 + - - +
359B LYS* 3.1 6.5 + - - +
360B LEU* 3.0 31.9 + - - +
383B TYR* 3.9 24.7 - - + +
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ILE* 2.9 22.4 + - + +
354B PRO* 3.6 9.4 - - + +
355B ALA 3.3 0.2 - - - -
356B LEU* 1.3 71.9 - - - +
358B LYS* 1.3 60.0 + - - +
360B LEU* 3.4 12.9 + - + +
361B GLU* 3.0 30.3 + - - +
376B LEU* 3.6 34.9 - - + +
379B SER* 4.0 12.8 - - - -
380B ARG* 3.5 66.4 - - + +
383B TYR* 4.3 6.5 - - + -
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Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B PRO* 3.0 19.3 + - + +
355B ALA* 3.3 13.7 - - - +
356B LEU 3.2 0.2 - - - -
357B LEU* 1.3 77.2 - - + +
359B LYS* 1.3 57.6 + - + +
361B GLU* 3.5 24.7 + - - +
362B GLU* 3.0 42.2 + - + +
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Residues in contact with LYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B THR* 2.8 29.1 + - - -
158B GLY* 3.8 17.9 - - - +
159B ASP* 3.1 14.1 + - - -
272B GLU* 3.4 18.8 - - + +
276B MET* 4.3 15.5 - - + -
355B ALA 3.2 13.2 + - - +
356B LEU* 3.1 11.2 + - - +
358B LYS* 1.3 76.1 - - + +
360B LEU* 1.3 63.8 + - - +
362B GLU* 3.2 25.3 + - - +
363B HIS* 3.2 43.0 + - + +
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B MET 4.1 8.5 - - - +
269B LEU* 3.6 33.9 - - + -
272B GLU* 3.5 25.8 - - + +
356B LEU 3.0 18.3 + - - +
357B LEU* 3.4 14.3 + - + +
359B LYS* 1.3 76.4 - - - +
361B GLU* 1.3 60.5 + - - +
363B HIS 3.2 5.5 + - - -
365B MET* 2.9 53.2 + - + +
368B LEU* 4.7 0.7 - - + -
376B LEU* 3.8 11.4 - - + -
379B SER* 3.8 19.5 - - - +
383B TYR* 4.2 11.4 - - + +
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Residues in contact with GLU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A THR* 4.5 6.8 - - - +
357B LEU 3.0 17.3 + - - +
358B LYS* 3.6 25.8 + - - +
360B LEU* 1.3 75.1 - - - +
362B GLU* 1.3 65.2 + - + +
364B GLY* 3.1 13.7 + - - -
366B THR* 4.2 15.9 - - + +
376B LEU* 3.9 24.3 - - + +
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Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A THR* 4.1 7.6 - - - +
157A THR* 3.7 17.8 - - - +
358B LYS* 3.0 33.7 + - + +
359B LYS* 3.2 31.7 + - - +
361B GLU* 1.3 77.5 - - + +
363B HIS* 1.3 70.3 + - + +
364B GLY 3.4 1.5 + - - -
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Residues in contact with HIS 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A THR* 3.1 20.5 - - + +
159B ASP* 2.8 39.6 + - + -
160B LYS 5.1 1.1 - - - -
161B GLN* 3.8 28.6 + - + +
272B GLU* 3.2 25.4 + - - -
359B LYS* 3.2 31.6 + - + +
360B LEU 4.0 2.5 - - - +
361B GLU 3.1 1.0 - - - -
362B GLU* 1.3 85.5 - - + +
364B GLY* 1.3 63.1 + - - +
365B MET* 3.2 29.3 + - + +
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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