Contacts of the helix formed by residues 376 - 390 (chain C) in PDB entry 5WWZ
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 MET 376 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324C PRO 5.3 2.0 - - - +
325C GLY* 3.7 26.5 - - - +
326C GLN* 3.9 19.7 - - + +
357C HIS 5.4 0.2 + - - -
375C GLY* 1.3 73.9 - - - -
377C PRO* 1.3 78.6 - - + +
378C GLU* 3.3 3.6 - - + +
379C ASN* 2.9 33.2 + - - +
380C VAL* 2.8 21.3 + - - +
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Residues in contact with PRO 377 (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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325C GLY 3.7 18.2 - - - +
327C THR* 4.2 15.5 - - + -
375C GLY 3.6 1.5 - - - +
376C MET* 1.3 94.1 - - + +
378C GLU* 1.3 60.8 + - - +
380C VAL* 3.1 22.5 - - + +
381C ASP* 2.9 21.5 - - - +
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Residues in contact with GLU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C MET* 3.3 3.2 - - + +
377C PRO* 1.3 80.5 - - - +
379C ASN* 1.3 65.2 + - - +
381C ASP* 3.5 10.0 + - - +
382C ARG* 3.2 29.5 + - - +
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Residues in contact with ASN 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C THR* 3.3 20.9 + - - +
357C HIS* 4.3 20.1 + - - +
358C THR* 3.3 16.5 - - + +
376C MET* 2.9 36.5 + - + +
378C GLU* 1.3 79.2 - - - +
380C VAL* 1.3 57.9 + - - +
382C ARG* 3.2 30.9 + - - +
383C ALA 2.9 22.3 + - - -
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Residues in contact with VAL 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C THR* 4.0 11.4 - - + +
329C VAL* 4.4 20.8 - - + +
358C THR* 4.0 1.1 - - + -
373C VAL* 3.8 28.6 - - + +
374C THR 3.8 5.8 - - - -
375C GLY* 3.4 32.1 - - - +
376C MET 2.8 18.6 + - - +
377C PRO* 3.1 24.2 - - + +
379C ASN* 1.3 71.7 - - - +
381C ASP* 1.3 60.2 + - - +
383C ALA* 3.1 2.3 + - - +
384C ARG* 2.7 35.8 + - - +
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Residues in contact with ASP 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C PRO* 2.9 20.1 + - - +
378C GLU* 3.7 10.1 - - - +
379C ASN 3.3 0.6 - - - -
380C VAL* 1.3 82.6 - - - +
382C ARG* 1.3 56.5 + - + +
384C ARG* 3.4 17.4 + - - +
385C GLU* 2.9 31.2 + - - +
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Residues in contact with ARG 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C GLN* 3.2 26.7 + - - +
356C THR* 3.7 18.0 + - + +
357C HIS* 6.0 0.6 - - - +
378C GLU* 3.2 19.7 + - - +
379C ASN* 3.2 28.8 + - - +
381C ASP* 1.3 77.5 - - + +
383C ALA* 1.3 61.1 + - - +
385C GLU* 3.3 6.8 + - - +
386C GLU* 3.1 31.6 + - - +
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Residues in contact with ALA 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C ILE* 4.1 3.8 - - + +
356C THR* 3.5 25.9 - - - +
358C THR* 3.6 13.5 - - - +
360C ILE* 4.0 10.3 - - + -
373C VAL* 3.7 16.4 - - + -
379C ASN 2.9 9.5 + - - +
380C VAL 3.1 7.1 + - - +
382C ARG* 1.3 73.6 - - - +
384C ARG* 1.3 61.1 + - - +
386C GLU* 3.4 1.6 + - - +
387C ILE* 3.0 36.4 + - - +
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Residues in contact with ARG 384 (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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329C VAL* 3.9 17.2 - - + +
330C GLN 2.7 32.5 + - - -
331C VAL* 3.8 32.9 - - + +
332C ARG 5.1 1.4 - - - +
373C VAL* 5.3 0.2 - - - +
380C VAL 2.7 20.9 + - - +
381C ASP* 3.7 16.7 + - - +
383C ALA* 1.3 74.1 - - - +
385C GLU* 1.3 62.4 + - - +
387C ILE* 3.4 1.2 + - - +
388C GLU* 3.0 54.1 + - - +
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Residues in contact with GLU 385 (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 ASP 2.9 17.2 + - - +
382C ARG* 3.6 8.3 - - - +
383C ALA 3.2 0.2 - - - -
384C ARG* 1.3 79.0 - - - +
386C GLU* 1.3 58.7 + - + +
388C GLU* 3.7 5.4 - - - +
389C MET* 2.8 31.9 + - + +
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Residues in contact with GLU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C ILE* 3.4 42.6 - - + +
355C GLN* 3.4 25.7 - - - +
356C THR* 3.5 21.4 - - - +
382C ARG* 3.1 20.1 + - + +
383C ALA 3.9 3.4 - - - +
385C GLU* 1.3 73.5 - - + +
387C ILE* 1.3 64.4 + - - +
389C MET* 3.2 7.7 + - - +
390C HIS* 2.9 34.2 + - + +
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Residues in contact with ILE 387 (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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331C VAL* 3.9 17.7 - - + -
333C VAL* 3.9 23.8 - - + -
341C VAL* 3.7 30.2 - - + +
349C ILE* 4.5 2.7 - - + -
352C ILE* 4.1 17.5 - - + -
360C ILE* 4.2 11.4 - - + -
371C PHE* 4.3 17.0 - - + -
373C VAL* 4.1 25.6 - - + -
383C ALA 3.0 22.1 + - - +
384C ARG 3.8 4.0 - - - +
386C GLU* 1.3 76.2 - - - +
388C GLU* 1.3 61.6 + - - +
390C HIS* 3.2 15.6 + - - +
391C ILE* 3.5 7.3 + - - +
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Residues in contact with GLU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C VAL* 4.1 11.1 - - + +
332C ARG 5.2 4.7 - - - +
333C VAL* 5.4 6.3 - - + -
384C ARG* 3.0 53.4 + - - +
385C GLU* 3.7 5.0 - - - +
387C ILE* 1.3 77.0 - - + +
389C MET* 1.3 60.3 + - - +
390C HIS 3.3 0.2 - - - -
391C ILE* 3.2 22.3 + - + +
392C ALA* 3.8 8.7 + - - +
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Residues in contact with MET 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C GLU* 2.8 21.3 + - + +
386C GLU* 3.5 11.4 - - - +
387C ILE 3.1 0.4 - - - -
388C GLU* 1.3 77.6 - - - +
390C HIS* 1.3 60.5 + - + +
391C ILE 3.2 2.0 - - - -
392C ALA* 3.2 26.0 + - - +
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Residues in contact with HIS 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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340C LEU* 4.2 30.1 - - + +
341C VAL* 4.6 10.8 - - + -
348C THR* 3.4 33.8 - - + +
351C ARG* 4.8 9.9 + - - -
352C ILE* 4.1 13.6 - - + +
386C GLU* 2.9 25.6 + - + +
387C ILE* 3.2 10.9 + - - +
389C MET* 1.3 78.1 - - + +
391C ILE* 1.3 55.9 + - - +
392C ALA 3.3 6.9 + - - +
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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