Contacts of the helix formed by residues 358 - 367 (chain B) in PDB entry 4OSI
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 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356B GLY 4.4 0.2 - - - -
357B LEU* 1.3 77.8 - - - +
359B PRO* 1.3 70.8 - - - +
360B GLU* 2.6 35.5 + - + +
361B GLN* 2.8 41.4 + - + +
362B VAL* 3.5 17.2 + - - +
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Residues in contact with PRO 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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321B HIS 4.9 7.9 - - - +
322B GLY 6.0 0.9 - - - +
323B LEU* 4.0 23.3 - - + -
348B LEU* 4.7 8.2 - - + +
352B CYS* 4.6 12.1 - - - -
357B LEU 3.8 1.3 - - - +
358B THR* 1.3 92.3 - - - +
360B GLU* 1.3 65.1 + - - +
362B VAL* 2.9 11.1 + - + +
363B VAL* 2.9 36.3 + - - +
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Residues in contact with GLU 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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324B THR* 6.0 0.3 - - - +
327B GLN* 4.3 18.4 + - - +
358B THR* 2.6 20.5 + - + +
359B PRO* 1.3 86.1 - - - +
361B GLN* 1.3 57.7 + - + +
363B VAL* 3.7 10.4 - - - +
364B ALA* 2.9 29.8 + - - +
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Residues in contact with GLN 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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356B GLY 5.0 0.3 - - - +
357B LEU* 2.1 43.0 - - + +
358B THR* 2.8 29.1 + - + +
359B PRO 3.2 0.8 - - - -
360B GLU* 1.3 75.3 - - + +
362B VAL* 1.3 60.7 + - - +
364B ALA* 3.2 7.5 + - - +
365B ILE* 2.9 35.1 + - - +
393B PRO* 5.3 1.2 - - - +
394B GLU* 3.6 38.6 + - - +
397B VAL* 3.6 30.1 - - + +
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Residues in contact with VAL 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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344B VAL* 4.5 13.7 - - + -
348B LEU* 3.5 26.0 - - + -
351B LEU* 4.3 16.8 - - + -
352B CYS* 4.1 17.7 - - - -
357B LEU* 4.3 19.0 - - + +
358B THR 3.5 12.7 + - - +
359B PRO 2.9 8.3 + - - +
361B GLN* 1.3 76.7 - - - +
363B VAL* 1.3 56.3 + - + +
365B ILE* 3.3 11.0 + - + +
366B ALA* 2.9 26.3 + - - +
375B LEU* 4.2 16.9 - - + +
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Residues in contact with VAL 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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323B LEU* 4.1 15.9 - - + -
327B GLN* 3.1 59.5 - - + +
330B ALA* 5.1 2.5 - - + -
331B ILE* 4.2 9.4 - - + -
344B VAL* 6.1 0.2 - - - -
348B LEU* 5.7 1.8 - - + -
359B PRO 2.9 25.5 + - - +
360B GLU 3.7 4.9 - - - +
362B VAL* 1.3 72.5 - - + +
364B ALA* 1.3 65.2 + - - +
366B ALA* 2.8 17.8 + - - +
367B SER* 3.0 27.4 + - - +
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Residues in contact with ALA 364 (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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360B GLU 2.9 19.6 + - - +
361B GLN* 3.2 7.2 + - - +
363B VAL* 1.3 76.4 - - - +
365B ILE* 1.3 50.4 + - - +
367B SER* 3.9 6.1 + - - -
368B HIS* 2.5 35.5 + - - -
397B VAL* 5.5 1.1 - - + -
401B SER* 3.7 15.1 + - - +
5H A 5.4 7.6 - - - +
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Residues in contact with ILE 365 (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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351B LEU* 6.3 1.3 - - + -
357B LEU* 4.9 7.0 - - + -
361B GLN 2.9 19.8 + - - +
362B VAL* 3.4 12.1 - - + +
363B VAL 3.0 0.2 - - - -
364B ALA* 1.3 76.1 - - - +
366B ALA* 1.3 62.1 + - - +
367B SER 3.3 0.4 - - - -
368B HIS* 3.5 13.5 - - - +
371B GLY* 4.4 3.5 - - - -
374B ALA* 3.9 23.6 - - + +
375B LEU* 3.7 20.0 - - + -
378B VAL* 3.9 16.2 - - + -
397B VAL* 3.6 30.3 - - + -
400B ALA* 3.6 32.3 - - + +
401B SER* 3.8 9.6 - - - +
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Residues in contact with ALA 366 (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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331B ILE* 4.2 20.1 - - + +
340B ALA* 4.1 12.5 - - + +
344B VAL* 3.6 31.0 - - + -
362B VAL 2.9 11.9 + - - +
363B VAL* 2.8 5.1 + - - +
365B ILE* 1.3 74.6 - - - +
367B SER* 1.3 58.1 + - - +
368B HIS 2.8 20.4 + - - +
371B GLY* 4.0 11.0 - - - -
375B LEU* 4.2 11.2 - - + -
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Residues in contact with SER 367 (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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330B ALA* 3.4 36.9 + - - +
331B ILE* 3.6 7.3 + - - +
334B HIS* 2.9 24.2 + - - -
363B VAL* 3.0 19.7 + - - +
364B ALA* 4.4 7.0 - - - -
365B ILE 3.3 1.8 - - - -
366B ALA* 1.3 74.6 - - - +
368B HIS* 1.3 76.6 + - - +
6H T 4.8 10.1 + - - -
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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