Contacts of the helix formed by residues 389 - 401 (chain B) in PDB entry 4OMC
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 389 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B ARG* 4.0 2.6 + - - -
284B GLY 5.7 0.4 - - - +
285B LEU* 3.3 26.5 - - + +
288B ILE* 4.6 0.2 - - - +
387B ASN 4.2 5.4 - - - +
388B LEU* 1.3 76.7 - - - +
390B TRP* 1.3 68.4 + - - +
391B ARG* 3.3 10.9 + - - +
392B ASP* 2.8 40.9 + - - +
393B MET* 3.0 21.8 + - - +
443B THR* 3.9 17.5 - - + -
444B VAL* 4.5 3.2 - - + +
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Residues in contact with TRP 390 (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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278B VAL* 3.4 44.6 + - + +
282B ARG* 4.0 1.2 - - - +
284B GLY 5.7 0.2 - - - -
285B LEU 2.9 19.2 + - - +
286B GLY* 4.0 2.0 - - - +
287B SER 3.8 21.3 - - - +
288B ILE* 3.7 14.9 - - + +
312B ILE* 3.5 26.5 - - + -
313B TYR* 4.1 18.6 - + - +
315B LEU* 5.6 0.9 - - - +
389B THR* 1.3 75.6 - - - +
391B ARG* 1.3 91.5 + - + +
393B MET* 3.7 3.6 + - - +
394B GLN* 3.5 42.6 + - - +
447B GLN* 3.8 22.9 - - - -
486B HIS* 4.4 5.6 - + - -
601B FMT 3.9 21.8 + - - -
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Residues in contact with ARG 391 (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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389B THR* 3.1 9.5 + - - +
390B TRP* 1.3 120.3 - - + +
392B ASP* 1.3 65.6 + - - +
393B MET 3.1 1.3 - - - -
394B GLN* 3.1 8.0 + - - +
395B HIS* 3.0 30.0 + - + -
444B VAL* 3.7 18.9 + - + +
445B ALA 2.7 29.9 + - - -
446B PRO* 3.8 1.8 - - - +
447B GLN* 3.2 36.8 - - - +
485B GLU* 2.9 39.7 + - - +
486B HIS* 5.3 4.0 - - + -
539B TRP* 4.7 1.7 - - + -
573B THR* 3.4 13.9 - - - +
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Residues in contact with ASP 392 (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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388B LEU* 3.6 16.1 - - + -
389B THR* 2.8 47.0 + - - +
391B ARG* 1.3 75.0 - - - +
393B MET* 1.3 64.4 + - - +
395B HIS* 3.0 9.0 + - - +
396B LEU* 3.0 27.0 + - - +
441B TRP* 2.8 33.6 + - - +
443B THR* 3.5 13.3 + - - +
444B VAL* 3.0 24.5 + - - +
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Residues in contact with MET 393 (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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288B ILE* 4.1 15.5 - - + -
315B LEU* 4.3 15.9 - - + -
378B ILE* 3.6 36.3 - - + +
381B THR* 3.9 22.2 - - + -
382B LEU* 3.8 31.2 - - + -
388B LEU* 3.8 18.3 - - + +
389B THR 3.0 10.1 + - - +
390B TRP 3.7 10.5 - - - +
391B ARG 3.1 0.2 - - - -
392B ASP* 1.3 76.9 - - - +
394B GLN* 1.3 61.9 + - - +
396B LEU* 3.3 7.7 + - - +
397B VAL* 3.2 26.3 + - + +
434B MET* 3.9 12.8 - - - -
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Residues in contact with GLN 394 (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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312B ILE 3.0 22.5 + - - +
313B TYR 4.3 5.1 + - - -
314B THR 4.3 10.6 + - - +
315B LEU* 3.9 28.1 - - + +
337B LEU* 4.1 19.5 - - + +
390B TRP* 3.5 28.2 + - - +
391B ARG* 3.1 9.2 + - - +
393B MET* 1.3 76.1 - - - +
395B HIS* 1.3 63.4 + - - +
397B VAL* 3.3 3.3 + - - +
398B VAL* 3.0 27.0 + - - +
486B HIS* 2.8 28.2 + - - -
536B THR* 5.9 0.2 - - - +
539B TRP* 3.8 18.3 - - + -
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Residues in contact with HIS 395 (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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391B ARG* 3.0 28.4 + - + -
392B ASP 3.0 7.6 + - - +
394B GLN* 1.3 76.7 - - - +
396B LEU* 1.3 63.1 + - - +
398B VAL* 3.1 3.2 + - - +
399B GLN* 2.9 31.8 + - - +
441B TRP* 3.6 23.4 - + + -
444B VAL* 3.6 25.6 - - + +
483B ARG* 4.3 20.5 + - - -
485B GLU* 2.9 34.0 + - + -
539B TRP* 3.1 39.4 + + - +
540B ASP* 4.5 5.3 + - - -
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Residues in contact with LEU 396 (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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381B THR* 3.6 30.3 - - + -
388B LEU* 3.7 21.8 - - + -
392B ASP 3.0 16.8 + - - +
393B MET* 3.3 10.1 + - - +
395B HIS* 1.3 76.2 - - - +
397B VAL* 1.3 58.1 + - - +
399B GLN 3.3 0.5 + - - -
400B THR* 2.8 36.2 + - + +
434B MET* 3.7 16.2 - - + +
437B LEU* 3.6 26.2 - - + -
438B ALA* 4.0 10.3 - - + +
441B TRP* 3.6 37.0 - - + -
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Residues in contact with VAL 397 (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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315B LEU* 4.1 19.3 - - + -
317B ILE* 5.9 2.0 - - + -
337B LEU* 3.8 20.4 - - + +
338B ALA* 3.5 31.4 - - + -
378B ILE* 5.3 4.0 - - + -
393B MET* 3.2 14.7 + - + +
394B GLN 3.5 7.4 - - - +
395B HIS 3.2 0.2 - - - -
396B LEU* 1.3 77.4 - - - +
398B VAL* 1.3 63.0 + - - +
400B THR* 4.1 0.4 - - - -
401B SER* 2.7 34.4 + - - +
429B LEU* 3.8 11.0 - - + -
434B MET* 3.8 22.7 - - + -
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Residues in contact with VAL 398 (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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337B LEU* 3.9 24.5 - - + -
394B GLN 3.0 14.8 + - - +
395B HIS 3.1 6.7 + - - +
397B VAL* 1.3 77.1 - - - +
399B GLN* 1.3 61.9 + - + +
401B SER 4.1 4.9 + - - +
418B ARG* 3.6 37.4 - - - +
426B TYR* 3.7 41.6 - - + +
539B TRP* 3.9 32.5 - - + -
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Residues in contact with GLN 399 (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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395B HIS* 2.9 23.1 + - - +
396B LEU 3.9 2.7 - - - +
398B VAL* 1.3 78.9 - - + +
400B THR* 1.3 60.0 + - - +
401B SER 3.9 2.3 + - - +
418B ARG* 3.6 31.0 + - - +
437B LEU* 3.8 22.6 - - + +
441B TRP* 3.7 29.9 - - - -
483B ARG* 4.9 13.5 - - - +
539B TRP* 6.2 0.2 - - - +
540B ASP* 4.5 8.8 + - - +
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Residues in contact with THR 400 (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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396B LEU 2.8 23.6 + - - +
397B VAL* 4.0 0.9 + - - -
399B GLN* 1.3 76.0 - - - +
401B SER* 1.3 65.0 + - - +
402B LYS* 2.7 30.8 + - - +
429B LEU* 5.8 0.3 - - - +
430B ASP* 3.7 7.7 + - - +
433B ALA* 3.7 36.3 - - + +
434B MET* 3.1 25.2 - - - +
437B LEU* 3.6 26.7 - - + -
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Residues in contact with SER 401 (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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338B ALA* 3.8 1.3 - - - +
397B VAL* 2.7 25.7 + - - +
398B VAL 4.1 3.9 + - - +
399B GLN 3.6 3.8 - - - +
400B THR* 1.3 78.8 + - - +
402B LYS* 1.3 62.6 + - - +
403B PRO* 3.7 5.2 - - - +
426B TYR* 3.5 29.7 - - - +
427B GLY 3.8 8.5 - - - -
428B LEU 3.3 11.4 - - - -
429B LEU* 3.5 26.5 - - - +
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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