Contacts of the helix formed by residues 389 - 401 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282C ARG* 4.1 1.8 - - - -
284C GLY 5.6 0.4 - - - +
285C LEU* 3.3 32.3 - - + +
288C ILE* 4.5 0.3 - - - +
387C ASN 4.2 1.6 - - - +
388C LEU* 1.3 77.7 - - - +
390C TRP* 1.3 68.9 + - - +
391C ARG* 3.3 10.7 + - - +
392C ASP* 2.9 35.6 + - - +
393C MET* 3.0 22.9 + - - +
443C THR* 3.9 16.8 - - + -
444C VAL* 4.5 3.5 - - + +
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Residues in contact with TRP 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C VAL* 3.4 44.0 + - + +
282C ARG* 4.0 1.0 - - - +
284C GLY 5.8 0.2 - - - -
285C LEU 2.9 19.6 + - - +
286C GLY* 4.0 3.1 - - - +
287C SER 3.9 21.1 - - - +
288C ILE* 3.6 14.8 - - + +
312C ILE* 3.4 28.5 - - + -
313C TYR* 4.0 22.2 - + - +
315C LEU* 5.6 1.0 - - - +
389C THR* 1.3 75.9 - - - +
391C ARG* 1.3 94.1 + - + +
393C MET* 3.7 4.7 + - - +
394C GLN* 3.5 37.5 + - - +
447C GLN* 3.9 15.5 - - - -
486C HIS* 4.5 4.0 - + - -
603C FMT 3.8 22.9 + - - -
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Residues in contact with ARG 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C THR* 3.1 8.8 + - - +
390C TRP* 1.3 119.8 - - + +
392C ASP* 1.3 65.7 + - - +
393C MET 3.1 1.6 - - - -
394C GLN* 3.1 8.1 + - - +
395C HIS* 3.0 30.1 + - + -
444C VAL* 3.7 18.5 + - + +
445C ALA 2.9 29.7 + - - -
446C PRO* 4.2 1.2 - - - +
447C GLN* 3.3 37.8 - - - +
485C GLU* 2.9 39.9 + - - +
486C HIS* 5.2 5.6 - - + -
539C TRP* 4.7 0.8 - - + -
573C THR* 3.3 14.5 - - - +
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Residues in contact with ASP 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388C LEU* 3.6 14.7 - - + -
389C THR* 2.9 39.3 + - - +
391C ARG* 1.3 75.3 - - - +
393C MET* 1.3 63.9 + - - +
395C HIS* 3.0 9.1 + - - +
396C LEU* 2.9 27.3 + - - +
441C TRP* 2.6 35.6 + - - +
443C THR* 3.5 22.9 + - - +
444C VAL* 3.0 23.5 + - - +
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Residues in contact with MET 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C ILE* 4.1 16.2 - - + -
315C LEU* 4.4 15.5 - - + -
378C ILE* 3.7 35.4 - - + -
381C THR* 4.0 13.2 - - + -
382C LEU* 3.8 23.1 - - + -
388C LEU* 3.7 27.1 - - + +
389C THR 3.0 10.4 + - - +
390C TRP 3.7 9.9 - - - +
391C ARG 3.1 0.2 - - - -
392C ASP* 1.3 78.0 - - - +
394C GLN* 1.3 60.7 + - - +
396C LEU* 3.3 8.0 + - - +
397C VAL* 3.2 26.0 + - - +
434C MET* 3.9 21.8 - - + -
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Residues in contact with GLN 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C ILE 2.9 24.5 + - - -
313C TYR 4.4 4.8 + - - -
314C THR 4.2 10.6 + - - +
315C LEU* 3.9 24.5 - - + +
337C LEU* 4.0 20.9 - - + +
390C TRP* 3.5 26.6 + - - +
391C ARG* 3.1 9.8 + - - +
393C MET* 1.3 72.9 - - - +
395C HIS* 1.3 66.9 + - - +
397C VAL* 3.2 4.4 + - - +
398C VAL* 3.0 26.7 + - - +
486C HIS* 2.8 27.6 + - - -
536C THR* 5.6 0.2 - - - +
539C TRP* 3.7 17.7 - - + -
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Residues in contact with HIS 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C ARG* 3.0 28.8 + - + -
392C ASP 3.3 7.2 - - - +
394C GLN* 1.3 76.5 - - - +
396C LEU* 1.3 62.8 + - - +
398C VAL* 3.2 3.3 + - - +
399C GLN* 3.0 33.2 + - - +
441C TRP* 3.6 24.6 - + + -
444C VAL* 3.6 27.3 - - + +
483C ARG* 5.0 8.5 + - + -
485C GLU* 2.8 33.8 + - + +
539C TRP* 3.2 36.1 + + - +
540C ASP* 4.3 14.9 + - - -
573C THR* 6.1 0.7 - - + -
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Residues in contact with LEU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381C THR* 3.6 18.8 - - + -
388C LEU* 3.5 34.1 - - + -
392C ASP 2.9 15.9 + - - +
393C MET* 3.6 9.9 - - - +
394C GLN 3.3 0.2 - - - -
395C HIS* 1.3 77.7 - - - +
397C VAL* 1.3 60.0 + - - +
399C GLN 3.8 0.2 - - - -
400C THR* 2.8 32.6 + - - +
434C MET* 3.6 15.7 - - + +
437C LEU* 3.5 37.5 - - + -
438C ALA* 3.9 10.8 - - + +
441C TRP* 3.6 26.2 - - + -
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Residues in contact with VAL 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C LEU* 4.0 19.7 - - + -
317C ILE* 5.8 1.8 - - + -
337C LEU* 4.0 19.3 - - + +
338C ALA* 3.5 31.4 - - + -
378C ILE* 5.3 3.4 - - + -
393C MET* 3.2 14.9 + - + +
394C GLN 3.2 7.4 + - - +
396C LEU* 1.3 76.9 - - - +
398C VAL* 1.3 64.3 + - - +
401C SER* 2.6 35.3 + - - +
426C TYR* 5.8 0.2 - - + -
429C LEU* 3.8 10.1 - - + -
434C MET* 3.7 25.1 - - + -
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Residues in contact with VAL 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C LEU* 3.8 25.1 - - + -
394C GLN 3.0 17.9 + - - +
395C HIS 3.5 7.4 - - - +
397C VAL* 1.3 77.7 - - - +
399C GLN* 1.3 65.2 + - + +
401C SER 4.1 4.2 + - - +
418C ARG* 3.7 30.5 - - - +
426C TYR* 3.9 43.6 - - + +
539C TRP* 3.8 38.8 - - + -
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Residues in contact with GLN 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 5.5 2.4 - - - +
395C HIS* 3.0 21.2 + - - +
396C LEU 4.0 2.7 - - - +
398C VAL* 1.3 80.2 - - + +
400C THR* 1.3 59.2 + - - +
401C SER 3.6 2.5 - - - +
418C ARG* 3.7 30.8 + - - +
437C LEU* 3.8 22.8 - - + +
441C TRP* 3.6 32.2 - - - -
483C ARG* 4.2 17.6 - - - +
539C TRP* 6.3 0.2 - - - +
540C ASP* 4.6 5.4 + - - +
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Residues in contact with THR 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C LEU* 2.8 20.5 + - - +
397C VAL* 3.9 0.7 + - - -
399C GLN* 1.3 77.2 - - - +
401C SER* 1.3 64.2 + - - +
402C LYS* 2.8 30.3 + - - +
430C ASP* 3.7 8.2 + - - +
433C ALA* 3.8 35.2 - - + +
434C MET* 3.1 24.5 - - - +
437C LEU* 3.6 26.9 - - + -
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Residues in contact with SER 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C ALA* 3.8 1.3 - - - +
397C VAL* 2.6 35.6 + - - +
398C VAL 4.1 3.0 + - - +
399C GLN 3.6 3.9 - - - +
400C THR* 1.3 78.9 + - - +
402C LYS* 1.3 63.5 + - - +
403C PRO* 3.7 5.5 - - - +
426C TYR* 3.5 30.2 - - - +
427C GLY 3.8 8.7 - - - -
428C LEU 3.3 11.4 - - - -
429C LEU* 3.6 16.0 - - - +
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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