Contacts of the helix formed by residues 363 - 381 (chain C) in PDB entry 5DO7
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 GLY 363 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ARG* 3.4 34.2 + - - +
362C PRO* 1.3 77.0 - - - +
364C VAL* 1.3 65.6 + - - -
365C PHE* 3.2 8.4 + - - -
366C SER* 3.9 1.6 + - - -
367C LYS* 3.0 24.0 + - - +
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Residues in contact with VAL 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C PRO 4.2 1.3 + - - +
363C GLY* 1.3 69.9 - - - -
365C PHE* 1.3 83.6 + - + +
367C LYS* 2.7 47.6 + - - +
368C LEU* 2.8 12.4 + - + +
461C TRP* 4.8 9.2 - - + -
462C GLN* 4.2 26.0 - - - +
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Residues in contact with PHE 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ARG* 4.5 13.9 - - - +
363C GLY* 4.3 6.5 - - - -
364C VAL* 1.3 109.8 - - + +
366C SER* 1.3 58.9 + - - +
368C LEU* 3.8 9.7 + - - +
369C GLY* 4.1 4.3 + - - -
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Residues in contact with SER 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ARG* 3.9 22.7 - - - +
363C GLY 3.9 2.1 + - - -
365C PHE* 1.3 73.9 - - - +
367C LYS* 1.3 65.5 + - - +
368C LEU 3.1 2.0 - - - -
369C GLY* 2.8 17.4 + - - +
370C VAL* 2.8 14.9 + - - +
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Residues in contact with LYS 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C LEU* 4.1 23.6 - - + +
362C PRO* 4.4 25.0 + - - +
363C GLY 3.0 22.1 + - - +
364C VAL* 2.7 43.9 + - + +
366C SER* 1.3 68.8 - - - +
368C LEU* 1.3 62.3 + - - +
370C VAL* 2.8 29.2 - - - +
371C LEU* 3.3 5.9 + - + +
457C LEU 3.8 23.7 + - - +
458C TYR* 4.2 14.3 - - + +
462C GLN* 4.7 13.8 - - - +
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Residues in contact with LEU 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C VAL* 2.8 10.1 + - + +
365C PHE* 4.1 9.2 - - - +
366C SER 3.1 0.2 - - - -
367C LYS* 1.3 75.9 - - - +
369C GLY* 1.3 62.5 + - - +
371C LEU* 3.1 10.3 + - + +
372C LEU* 3.0 21.6 + - + +
461C TRP* 4.6 5.4 - - + -
462C GLN* 3.0 47.7 + - + +
465C LEU* 3.7 29.2 - - + -
466C ALA* 3.9 17.0 - - + +
469C LEU* 4.2 10.3 - - + -
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Residues in contact with GLY 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C PHE 4.1 3.0 + - - -
366C SER* 2.8 20.3 + - - -
368C LEU* 1.3 74.3 - - - +
370C VAL* 1.3 59.7 + - - -
372C LEU* 3.3 12.5 - - - +
373C ARG* 3.1 19.9 + - - +
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Residues in contact with VAL 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C TYR* 3.8 31.9 - - + +
153C LEU* 3.5 31.0 - - + +
154C LEU* 4.1 27.4 - - + -
366C SER* 2.8 12.9 + - - +
367C LYS* 2.8 31.2 + - - +
369C GLY* 1.3 70.2 - - - +
371C LEU* 1.3 74.0 + - + +
373C ARG* 2.8 19.8 + - + +
374C ARG* 2.8 13.4 + - + +
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Residues in contact with LEU 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C LEU* 3.9 20.6 - - + -
367C LYS* 3.9 6.3 - - + +
368C LEU* 3.1 11.6 + - + +
370C VAL* 1.3 80.9 - - + +
372C LEU* 1.3 57.6 + - - +
374C ARG* 3.4 36.9 - - - +
375C VAL* 2.8 36.1 + - - +
458C TYR* 3.2 42.0 - - + -
462C GLN* 3.8 19.7 - - + -
463C MET* 3.9 22.7 - - + +
466C ALA* 4.3 6.1 - - + -
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Residues in contact with LEU 372 (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 LEU* 3.0 11.6 + - + +
369C GLY* 3.3 15.0 - - - +
371C LEU* 1.3 75.6 - - - +
373C ARG* 1.3 64.9 + - - +
375C VAL* 2.9 3.4 + - - +
376C THR* 2.8 32.1 + - + -
466C ALA* 3.6 34.0 - - + +
469C LEU* 4.1 14.8 - - + -
470C HIS* 3.8 28.0 - - + +
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Residues in contact with ARG 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C GLU* 6.3 0.2 - - - +
149C HIS* 3.9 19.8 + - - -
150C TYR* 3.0 41.6 + - + +
153C LEU* 5.3 4.9 - - - +
369C GLY 3.1 8.0 + - - +
370C VAL* 2.8 18.6 + - - +
372C LEU* 1.3 76.5 - - - +
374C ARG* 1.3 51.7 + - - +
376C THR* 3.4 13.4 - - + +
377C ARG* 2.8 42.0 + - + +
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Residues in contact with ARG 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU* 6.1 0.4 - - - +
139C LEU* 3.1 36.9 - - + +
142C LEU* 4.1 8.1 - - + +
147C THR* 4.2 23.6 + - - +
150C TYR* 3.8 47.7 - - + +
151C THR* 4.4 8.3 - - - +
154C LEU* 5.7 1.0 - - - +
370C VAL 2.8 14.5 + - - +
371C LEU* 3.4 30.9 - - - +
373C ARG* 1.3 72.0 - - - +
375C VAL* 1.3 60.9 + - - +
377C ARG* 2.9 7.4 + - - +
378C ASN* 2.8 26.9 + - - +
448C VAL* 4.5 0.6 - - - +
452C GLU* 2.7 35.5 + - - -
458C TYR* 3.5 15.8 + - - -
463C MET* 4.5 5.7 - - - +
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Residues in contact with VAL 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 5.8 1.8 - - + -
371C LEU* 2.8 27.8 + - - +
372C LEU* 2.9 7.1 + - - +
374C ARG* 1.3 73.0 - - + +
376C THR* 1.3 54.9 + - - +
378C ASN* 3.2 7.9 + - + +
379C LEU* 2.8 35.7 + - + +
445C LEU* 3.4 39.7 - - + -
463C MET* 3.9 15.7 - - + -
466C ALA* 4.3 8.5 - - + -
467C TYR* 4.6 1.8 - - - -
470C HIS* 3.3 33.4 - - + +
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Residues in contact with THR 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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372C LEU* 2.8 20.1 + - + +
373C ARG* 3.4 20.0 - - + +
375C VAL* 1.3 74.6 - - - +
377C ARG* 1.3 60.7 + - - +
379C LEU* 3.7 5.5 - - - +
380C VAL* 2.8 35.7 + - + +
470C HIS* 3.8 23.2 - - - +
474C PHE* 4.3 14.8 - - - -
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Residues in contact with ARG 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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141C SER 5.4 0.4 + - - -
142C LEU* 3.8 13.1 - - + +
143C THR* 5.5 1.2 - - - +
146C GLU* 2.8 40.8 + - - -
150C TYR* 3.5 21.5 - - - +
373C ARG* 2.8 23.3 + - + +
374C ARG* 2.9 12.7 + - - +
376C THR* 1.3 74.1 - - - +
378C ASN* 1.3 70.1 + - - +
380C VAL* 3.0 23.4 - - + +
381C ARG* 3.0 60.0 + - + +
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Residues in contact with ASN 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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139C LEU* 3.7 39.8 - - + +
140C SER* 4.6 2.8 + - - +
141C SER* 3.1 31.5 + - - +
142C LEU* 3.7 13.7 - - + +
374C ARG 2.8 13.9 + - - +
375C VAL* 3.3 12.6 - - + +
377C ARG* 1.3 70.2 - - - +
379C LEU* 1.3 60.5 + - - +
381C ARG* 2.8 26.2 + - - -
382C ASN* 3.7 12.3 + - - +
444C VAL* 5.3 4.0 - - - +
445C LEU* 4.9 14.2 - - + +
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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
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375C VAL* 2.8 21.5 + - + +
376C THR* 4.0 4.5 - - - +
378C ASN* 1.3 77.5 + - - +
380C VAL* 1.3 55.7 + - - +
382C ASN* 2.7 22.3 - - - +
385C ALA* 5.0 0.7 - - + -
386C VAL* 2.8 31.0 - - + +
389C ARG* 3.0 27.1 - - + +
441C LEU* 3.3 22.9 - - + -
467C TYR* 4.9 0.4 - - + -
470C HIS* 2.8 42.0 - - + +
474C PHE* 3.9 22.4 - - + -
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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
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376C THR* 2.8 22.9 + - + +
377C ARG* 3.0 26.2 - - + +
378C ASN 3.0 0.2 + - - -
379C LEU* 1.3 72.6 - - - +
381C ARG* 1.3 74.1 + - + +
382C ASN 3.0 11.3 + - - -
383C LYS* 4.8 0.5 + - - -
386C VAL* 3.8 17.1 - - + +
474C PHE* 5.2 11.6 - - + -
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Residues in contact with ARG 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C SER* 3.9 28.3 - - - +
377C ARG* 3.0 66.4 + - - +
378C ASN 2.8 12.4 + - - +
380C VAL* 1.3 82.3 - - + +
382C ASN* 1.3 61.1 + - - +
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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
------------------------------------------------------------
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