Contacts of the helix formed by residues 376 - 388 (chain A) in PDB entry 4OGB
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 ILE 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A MET* 4.2 6.3 - - + -
276A HIS* 3.7 37.3 + - + +
277A MET* 5.1 7.0 - - + -
319A LEU* 4.0 18.8 - - + -
372A PHE* 3.0 30.1 + - + +
374A ASP 3.6 0.4 - - - -
375A TYR* 1.3 89.7 - - + +
377A VAL* 1.3 69.2 + - - +
379A PRO* 3.3 4.0 - - - +
380A LEU* 3.3 22.0 + - - +
501A 2SR 3.2 41.3 - - + -
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Residues in contact with VAL 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 3.8 20.6 - - + +
322A PRO* 4.2 10.3 - - + -
323A THR* 4.7 0.7 - - + -
372A PHE* 3.0 52.5 + - + +
373A ILE* 4.0 7.4 - - + -
376A ILE* 1.3 80.0 - - + +
378A HIS* 1.3 63.7 + - - +
380A LEU* 3.5 4.1 - - - +
381A TRP* 3.0 44.1 + - + -
399A LEU* 3.9 20.0 - - + -
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Residues in contact with HIS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ILE* 2.7 37.2 + - + +
374A ASP* 4.6 4.7 - - - +
377A VAL* 1.3 74.8 - - - +
379A PRO* 1.3 59.1 - - + +
382A GLU* 2.8 68.1 + - + +
396A LEU* 3.8 7.6 - - + +
399A LEU* 3.7 22.2 - - + +
400A GLU* 2.9 43.2 + - + +
403A ARG* 6.3 0.4 - - + -
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Residues in contact with PRO 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 4.0 18.4 - - + -
284A LYS* 5.5 5.6 - - - +
373A ILE 3.5 0.2 - - - +
374A ASP 3.4 26.2 - - - +
375A TYR* 3.7 14.4 - - - +
376A ILE 3.3 14.4 - - - +
378A HIS* 1.3 91.3 - - + +
380A LEU* 1.3 56.6 + - - +
382A GLU* 3.7 12.2 - - + +
383A THR* 2.7 35.0 + - - -
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A HIS* 4.2 8.3 - - + -
280A LEU* 3.8 20.2 - - + +
283A LEU* 4.3 4.9 - - + -
312A ASN* 4.2 18.8 - - - +
315A HIS* 3.6 27.6 - - + +
316A CYS* 3.6 36.1 - - - -
319A LEU* 3.6 24.2 - - + -
376A ILE 3.3 11.5 + - - +
377A VAL* 3.5 7.6 - - - +
379A PRO* 1.3 79.5 - - - +
381A TRP* 1.3 61.4 + - + +
383A THR* 3.1 5.0 + - - -
384A TRP* 2.8 25.8 + - - +
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Residues in contact with TRP 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TRP* 3.7 24.2 - + - -
175A LEU* 3.8 15.3 - - + -
316A CYS* 3.2 41.5 + - + +
319A LEU* 3.2 19.2 + - - +
320A SER* 3.9 12.1 - - - -
323A THR* 3.6 15.0 - - + +
377A VAL* 3.0 41.0 + - + +
380A LEU* 1.3 79.8 - - + +
382A GLU* 1.3 57.2 + - - +
384A TRP* 3.7 30.0 - + + +
385A ALA* 2.7 37.3 + - + +
392A ALA* 5.0 4.7 - - + -
395A ILE* 3.8 24.7 - - + -
396A LEU* 4.1 7.4 - - + -
399A LEU* 4.0 14.1 - - + -
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Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A HIS* 2.8 46.7 + - + +
379A PRO* 3.7 9.4 - - - +
381A TRP* 1.3 76.6 - - - +
383A THR* 1.3 59.6 + - - +
385A ALA* 3.3 4.5 + - - +
386A ASP* 3.0 36.0 + - - +
396A LEU* 3.9 16.4 - - + +
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Residues in contact with THR 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 3.5 13.6 - - + +
283A LEU* 3.6 24.9 - - + +
284A LYS* 3.8 40.6 - - + +
287A VAL* 3.6 11.1 - - + +
379A PRO 2.7 22.6 + - - -
380A LEU 3.5 4.3 - - - -
382A GLU* 1.3 77.5 + - - +
384A TRP* 1.3 64.7 + - - +
386A ASP* 3.3 9.6 + - - +
387A LEU* 3.1 16.6 + - - +
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Residues in contact with TRP 384 (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 LEU* 4.0 21.5 - - + +
178A THR* 5.2 1.8 + - + +
181A LEU* 4.1 12.6 - - + -
283A LEU* 4.1 15.0 - - + +
309A VAL* 3.8 15.9 - - + -
312A ASN* 4.2 4.0 - - + -
313A MET* 3.6 52.9 - - + -
316A CYS* 3.9 26.9 - - - -
380A LEU 2.8 16.0 + - - +
381A TRP* 3.7 24.9 - + + +
383A THR* 1.3 76.0 - - - +
385A ALA* 1.3 61.7 + - - +
387A LEU* 2.9 42.2 + - + +
388A VAL* 3.1 41.0 + - + +
392A ALA* 4.3 4.7 - - + +
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Residues in contact with ALA 385 (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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381A TRP 2.7 22.3 + - - +
382A GLU 3.6 4.5 - - - +
384A TRP* 1.3 74.8 - - - +
386A ASP* 1.3 58.3 + - - +
388A VAL* 3.4 1.2 + - - +
389A HIS* 2.9 35.3 + - + +
390A PRO* 4.9 0.9 - - - +
392A ALA* 3.7 32.9 - - + +
393A GLN* 5.6 1.3 - - - +
396A LEU* 4.0 22.9 - - + -
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Residues in contact with ASP 386 (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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287A VAL* 3.9 24.3 - - + +
290A LYS* 3.0 17.7 + - - +
382A GLU* 3.0 21.6 + - - +
383A THR* 3.4 12.7 - - - +
384A TRP 3.1 0.2 - - - -
385A ALA* 1.3 76.4 - - - +
387A LEU* 1.3 66.3 + - - +
388A VAL 3.4 0.2 + - - -
389A HIS* 3.5 23.1 + - - +
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Residues in contact with LEU 387 (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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180A ALA* 4.8 0.5 - - - +
181A LEU* 5.7 0.7 - - + -
283A LEU* 3.9 15.9 - - + -
286A MET* 4.4 23.3 - - + -
287A VAL* 4.0 20.4 - - + +
290A LYS* 3.2 23.5 + - + +
298A LEU* 3.6 36.4 - - + +
309A VAL* 4.4 15.7 - - + -
383A THR 3.1 11.4 + - - +
384A TRP* 2.9 43.4 + - + +
386A ASP* 1.3 75.4 - - - +
388A VAL* 1.3 64.3 + - + +
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 4.1 16.2 - - + +
180A ALA* 3.7 23.7 - - + +
181A LEU* 4.5 2.5 - - + -
298A LEU* 4.4 5.4 - - + -
384A TRP* 3.1 46.8 + - + +
385A ALA 4.1 0.7 - - - +
387A LEU* 1.3 88.5 - - + +
389A HIS* 1.3 66.4 + - - +
391A ASP* 2.8 31.7 + - + +
392A ALA* 3.9 24.5 - - + +
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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