Contacts of the helix formed by residues 362 - 379 (chain C) in PDB entry 5Q1B
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 SER 362 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C GLY 3.8 1.4 + - - -
361C ILE* 1.4 82.0 - - - +
363C ASP* 1.3 64.4 + - - +
364C GLU* 3.8 27.1 + - - -
365C TYR* 3.1 15.9 + - - -
366C ILE* 3.2 11.0 + - - +
457C SER* 3.2 37.3 + - - -
459C ARG* 5.9 4.5 - - - +
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Residues in contact with ASP 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ARG* 5.7 0.7 - - - +
361C ILE 5.3 0.7 - - - -
362C SER* 1.3 72.1 - - - +
364C GLU* 1.3 62.7 + - - +
365C TYR 3.2 1.2 + - - -
366C ILE* 3.2 32.9 + - + +
367C THR* 3.4 18.8 + - - +
459C ARG* 5.9 1.6 + - - -
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Residues in contact with GLU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C SER* 3.8 14.9 + - - -
363C ASP* 1.3 77.1 - - - +
365C TYR* 1.3 100.1 + - + +
367C THR* 5.4 0.2 - - - -
368C PRO* 3.3 20.3 - - - +
457C SER* 4.8 3.5 - - - -
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Residues in contact with TYR 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C ILE* 3.9 9.4 - - + -
362C SER* 3.1 12.2 + - - +
363C ASP 3.1 0.4 - - - -
364C GLU* 1.3 111.6 + - + +
366C ILE* 1.3 63.5 + - - +
367C THR 3.6 0.7 - - - -
368C PRO* 3.5 8.8 - - + +
369C MET* 3.3 28.4 + - - +
447C PHE* 4.9 1.7 - - - -
450C HIS* 4.0 28.3 - + + -
453C GLU* 3.2 34.1 + - + +
454C MET* 3.3 39.2 - - + +
457C SER* 3.5 25.6 - - - -
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Residues in contact with ILE 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ARG* 3.4 63.0 - - + +
361C ILE* 3.4 35.2 - - + +
362C SER 3.2 10.7 + - - +
363C ASP* 3.2 30.9 + - - +
365C TYR* 1.3 74.2 - - - +
367C THR* 1.4 62.8 + - - +
369C MET* 3.3 10.0 + - + +
370C PHE* 3.0 46.9 + - + -
459C ARG* 5.9 0.4 - - - +
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Residues in contact with THR 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ARG* 4.6 14.3 + - - +
363C ASP* 3.4 12.7 + - - +
364C GLU 5.3 0.2 - - - -
366C ILE* 1.4 74.8 - - - +
368C PRO* 1.4 67.0 - - - +
369C MET 3.1 0.5 + - - -
370C PHE* 3.2 2.6 + - - +
371C SER* 2.8 32.2 + - - -
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Residues in contact with PRO 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C GLU 3.3 25.8 - - - +
365C TYR* 3.5 15.3 - - + +
367C THR* 1.4 91.3 - - - +
369C MET* 1.4 53.3 + - - +
371C SER* 3.6 8.7 - - - -
372C PHE* 3.1 21.7 + - - +
443C GLU* 4.0 5.7 - - - +
446C THR* 6.3 2.9 - - + -
447C PHE* 3.3 21.9 - - + -
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Residues in contact with MET 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C PHE* 3.7 21.3 - - + -
356C ILE* 4.3 15.7 - - + -
361C ILE* 5.2 9.6 - - + -
365C TYR 3.3 17.2 + - - +
366C ILE* 3.3 8.5 + - + +
367C THR 3.1 0.6 + - - -
368C PRO* 1.4 74.6 - - - +
370C PHE* 1.3 64.5 + - + +
372C PHE* 3.3 3.1 + - - +
373C TYR* 3.0 63.3 + - + +
447C PHE* 3.7 15.0 - - + -
454C MET* 3.4 32.1 - - - -
501C 9N7 3.6 22.9 - - + +
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Residues in contact with PHE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C PHE* 3.5 39.5 - + - -
353C GLU* 3.5 29.2 - - + -
356C ILE* 3.7 24.7 - - + -
357C ARG* 3.6 37.7 - - + +
366C ILE* 3.0 42.2 + - + +
367C THR* 4.0 2.9 - - + +
369C MET* 1.3 76.9 - - + +
371C SER* 1.4 59.8 + - - +
373C TYR* 3.8 15.3 - + - +
374C LYS* 3.0 51.1 + - - +
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Residues in contact with SER 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C THR* 2.8 19.5 + - - -
368C PRO* 3.6 10.3 - - - -
370C PHE* 1.4 76.1 - - - +
372C PHE* 1.3 56.5 + - - +
374C LYS* 3.9 5.6 - - - +
375C SER* 3.0 31.7 + - - -
443C GLU* 4.0 9.7 + - - -
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Residues in contact with PHE 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C PHE* 4.1 16.2 - - + -
334C LEU* 4.6 4.5 - - + -
337C ALA* 4.1 4.5 - - + -
368C PRO 3.1 18.1 + - - +
369C MET 3.3 2.7 + - - +
371C SER* 1.3 73.6 + - - +
373C TYR* 1.3 72.8 + + - +
375C SER* 3.4 6.0 + - - -
376C ILE* 3.0 59.5 + - + +
440C ARG* 3.4 40.2 - - + -
443C GLU* 3.8 20.4 + - + +
444C LEU* 3.6 35.2 - - + -
447C PHE* 3.6 22.7 - + + -
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Residues in contact with TYR 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C PHE* 3.7 33.7 - + - -
336C SER* 3.5 8.2 - - - -
337C ALA* 3.6 25.4 - - + -
340C PHE* 3.8 29.8 - + + -
341C ASN* 2.9 25.1 + - - -
356C ILE* 5.5 0.2 - - + -
369C MET* 3.0 45.6 + - + +
370C PHE* 3.8 24.2 - + - +
371C SER 3.4 0.2 - - - -
372C PHE* 1.3 84.0 - + - +
374C LYS* 1.3 58.6 + - - +
376C ILE* 3.3 1.7 + - - +
377C GLY 3.0 11.3 + - - -
501C 9N7 2.7 40.7 + + - -
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Residues in contact with LYS 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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340C PHE* 4.6 13.2 - - + -
341C ASN* 4.9 4.0 - - - -
353C GLU* 3.4 34.7 + - - -
357C ARG* 4.5 5.7 - - - +
370C PHE* 3.0 34.7 + - - +
371C SER* 4.0 4.5 - - - +
373C TYR* 1.3 72.8 - - - +
375C SER* 1.4 64.1 + - - +
377C GLY* 3.4 1.7 + - - +
378C GLU* 3.1 37.4 + - - +
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Residues in contact with SER 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C SER* 3.0 19.5 + - - -
372C PHE 3.5 1.6 - - - -
374C LYS* 1.4 73.7 - - - +
376C ILE* 1.4 61.3 + - - +
378C GLU* 3.6 25.5 + - - +
379C LEU* 3.7 13.1 + - - +
440C ARG* 2.8 39.5 + - - -
443C GLU* 4.9 1.1 - - - -
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Residues in contact with ILE 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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334C LEU* 4.5 9.9 - - + -
337C ALA* 3.7 19.5 - - + -
341C ASN* 3.8 3.4 - - - +
372C PHE* 3.0 46.7 + - + +
373C TYR 3.5 7.6 - - - +
375C SER* 1.4 74.4 - - - +
377C GLY* 1.3 64.3 + - - +
379C LEU* 3.1 22.8 + - + +
380C LYS 3.9 2.8 + - - -
381C MET* 4.2 19.4 + - + +
386C TYR* 3.3 32.5 + - + +
389C LEU* 5.3 1.3 - - + -
440C ARG* 3.8 31.4 - - + -
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Residues in contact with GLY 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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341C ASN* 3.2 32.5 - - - +
373C TYR 3.0 10.3 + - - -
374C LYS 3.4 3.3 + - - -
376C ILE* 1.3 75.8 - - - +
378C GLU* 1.3 61.4 + - - +
380C LYS* 3.3 20.1 + - - +
386C TYR* 5.3 0.9 - - - -
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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
----------------------------------------------------------
374C LYS* 3.1 26.5 + - - +
375C SER* 3.6 19.1 + - - +
376C ILE 3.3 0.4 - - - -
377C GLY* 1.3 74.8 - - - +
379C LEU* 1.3 60.3 + - + +
380C LYS* 3.5 13.4 + - - +
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Residues in contact with LEU 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C SER 3.7 11.4 + - - +
376C ILE* 3.1 16.1 + - + +
378C GLU* 1.3 77.6 - - + +
380C LYS* 1.4 67.8 + - - +
381C MET* 4.1 9.2 - - + -
427C GLN* 3.9 3.8 + - - +
430C ASN* 5.1 2.5 - - - +
433C HIS* 2.9 51.2 + - + +
436C CYS* 3.6 31.0 - - + -
437C LEU* 3.9 12.3 - - + -
440C ARG* 3.7 37.0 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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