Contacts of the helix formed by residues 373 - 388 (chain C) in PDB entry 6XAV
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 373 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372C THR* 1.3 80.1 - - - +
374C GLN* 1.3 60.4 + - - +
375C GLU* 3.8 7.4 + - - +
376C GLU* 3.2 27.9 + - - +
377C LEU* 2.8 27.8 + - - +
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Residues in contact with GLN 374 (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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373C THR* 1.3 75.3 - - - +
375C GLU* 1.3 70.7 + - + +
377C LEU* 3.5 8.6 + - + +
378C GLN* 3.1 26.7 + - + +
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Residues in contact with GLU 375 (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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373C THR* 3.3 6.6 + - - +
374C GLN* 1.3 87.3 - - + +
376C GLU* 1.3 61.7 + - - +
378C GLN* 3.3 17.4 + - - +
379C LYS* 3.0 47.0 + - - +
417C LYS* 5.8 1.6 + - - -
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Residues in contact with GLU 376 (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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144C ARG* 3.5 25.8 + - - -
146C ARG* 5.6 4.1 + - - -
164C LEU* 5.5 2.3 - - - +
372C THR* 3.5 23.4 - - - -
373C THR* 3.2 23.3 + - - +
375C GLU* 1.3 79.8 - - - +
377C LEU* 1.3 63.2 + - - +
379C LYS* 3.3 10.6 + - - +
380C MET* 3.0 50.0 + - + +
413C PHE* 5.3 10.0 - - + -
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Residues in contact with LEU 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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368C GLU* 3.3 40.4 - - + +
369C GLU* 3.9 26.7 - - + +
372C THR* 4.0 11.8 + - - +
373C THR 2.8 18.3 + - - +
374C GLN* 3.8 9.2 - - + +
376C GLU* 1.3 77.4 - - - +
378C GLN* 1.3 62.1 + - - +
380C MET* 3.4 6.9 + - + +
381C TRP* 3.1 59.9 + - + +
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Residues in contact with GLN 378 (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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374C GLN* 3.1 20.6 + - + +
375C GLU* 3.8 18.6 - - - +
376C GLU 3.3 0.4 - - - -
377C LEU* 1.3 77.6 - - - +
379C LYS* 1.3 58.3 + - + +
381C TRP* 3.2 12.9 + - + +
382C ILE* 3.0 53.9 + - + +
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Residues in contact with LYS 379 (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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375C GLU* 3.0 40.3 + - - +
376C GLU* 3.8 7.0 - - - +
377C LEU 3.3 0.2 - - - -
378C GLN* 1.3 78.6 - - + +
380C MET* 1.3 58.3 + - - +
382C ILE* 3.6 9.2 + - + +
383C LEU* 3.0 28.8 + - - +
410C ASP* 4.2 13.9 + - - -
413C PHE* 3.6 58.4 - - + +
414C GLU* 5.3 3.6 + - - -
417C LYS* 4.6 27.9 - - + +
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Residues in contact with MET 380 (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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163C ASP 3.5 24.9 - - - +
164C LEU* 4.0 33.7 - - + +
167C PRO* 3.9 15.3 - - + -
360C TYR* 4.5 2.2 + - - +
368C GLU* 4.4 17.5 - - - +
372C THR* 4.1 8.7 - - + -
376C GLU* 3.0 51.1 + - + +
377C LEU* 3.8 8.1 - - + +
378C GLN 3.3 0.4 - - - -
379C LYS* 1.3 75.3 - - - +
381C TRP* 1.3 64.5 + - + +
383C LEU* 3.4 8.0 + - + +
384C ARG* 3.0 38.8 + - - +
413C PHE* 5.2 3.8 - - + -
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Residues in contact with TRP 381 (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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368C GLU* 3.4 21.7 + - - -
377C LEU* 3.1 43.9 + - + +
378C GLN* 3.2 15.7 + - + +
380C MET* 1.3 78.2 - - + +
382C ILE* 1.3 65.6 + - + +
384C ARG* 3.2 14.4 + - - +
385C LYS* 3.1 35.2 + - + +
353D ARG* 4.4 42.2 - - + +
355D PHE* 6.3 1.3 - + - -
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Residues in contact with ILE 382 (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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378C GLN* 3.0 40.8 + - + +
379C LYS* 4.0 8.1 - - + +
381C TRP* 1.3 76.4 - - + +
383C LEU* 1.3 63.2 + - - +
385C LYS* 3.3 15.9 + - + +
386C ILE* 3.4 27.9 - - + +
416C MET* 6.1 5.2 - - + -
417C LYS* 6.0 6.7 - - + -
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Residues in contact with LEU 383 (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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164C LEU* 4.1 26.7 - - + -
360C TYR* 3.5 19.7 - - + +
379C LYS 3.0 18.8 + - - +
380C MET* 3.7 7.2 - - + +
382C ILE* 1.3 78.3 - - - +
384C ARG* 1.3 57.1 + - - +
386C ILE* 3.3 8.4 + - + -
387C ILE* 3.0 53.5 + - + +
398C PHE* 4.8 9.9 - - + -
399C LEU* 5.0 6.7 - - + -
412C PHE* 4.0 27.1 - - + -
413C PHE* 4.3 13.9 - - + -
416C MET* 5.8 4.5 - - + -
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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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164C LEU 4.5 2.4 + - - -
165C ALA* 2.9 34.2 + - - +
360C TYR* 3.2 50.3 + - + +
361C ASN* 4.4 5.5 + - - +
363C SER 3.7 21.5 + - - -
364C GLY* 3.9 7.5 - - - -
368C GLU* 5.5 9.3 + - - -
380C MET* 3.0 27.3 + - - +
381C TRP* 3.2 12.1 + - - +
383C LEU* 1.3 77.2 - - - +
385C LYS* 1.3 63.8 + - + +
387C ILE* 4.4 1.3 - - - +
388C HIS* 2.9 34.9 + - + +
181D LYS* 5.9 0.2 - - - +
353D ARG* 4.3 21.6 - - - +
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Residues in contact with LYS 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 TRP* 3.1 22.4 + - + +
382C ILE* 3.8 9.0 - - + +
383C LEU 3.3 0.2 - - - -
384C ARG* 1.3 81.0 - - + +
386C ILE* 1.3 60.5 + - + +
388C HIS* 4.9 2.9 - - + -
389C PRO* 3.1 22.3 - - - +
351D GLU 2.6 30.1 + - - -
352D LYS* 3.3 25.3 - - + +
353D ARG* 3.7 19.2 - - - +
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Residues in contact with ILE 386 (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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382C ILE* 3.4 26.0 - - + +
383C LEU* 3.3 10.2 + - + +
384C ARG 3.2 0.6 - - - -
385C LYS* 1.3 82.4 - - + +
387C ILE* 1.3 64.4 + - + +
388C HIS 3.5 0.4 - - - -
389C PRO* 3.3 9.9 - - - +
390C MET* 3.5 20.4 - - + +
398C PHE* 4.6 22.7 - - + -
416C MET* 3.9 27.1 - - + -
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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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360C TYR* 3.6 50.0 - - + -
361C ASN* 3.8 10.5 - - - +
383C LEU* 3.0 37.9 + - + +
384C ARG 4.2 2.2 - - - +
386C ILE* 1.3 77.9 - - - +
388C HIS* 1.3 65.8 + - - +
390C MET* 3.1 36.4 + - + +
395C ALA* 3.6 23.5 - - + +
398C PHE* 4.6 9.4 - - + -
399C LEU* 5.0 15.0 - - + -
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Residues in contact with HIS 388 (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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361C ASN* 3.7 30.4 + - + +
384C ARG* 2.9 20.3 + - + +
385C LYS* 4.9 3.6 - - + -
387C ILE* 1.3 76.7 - - - +
389C PRO* 1.3 71.7 - - + +
390C MET 3.2 9.2 - - - +
351D GLU* 3.1 35.4 + - + -
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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