Contacts of the helix formed by residues 362 - 377 (chain B) in PDB entry 6TOS
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299B MET* 3.6 19.7 - - - -
358B TYR 2.8 18.0 + - - +
359B ASN 3.6 1.6 - - - +
360B PHE 3.8 0.4 - - - -
361B LEU* 1.3 78.6 - - - +
363B GLY* 1.3 56.7 + - - +
364B LYS* 4.0 1.4 - - - +
365B PHE* 3.1 30.1 + - - -
366B ARG* 3.0 29.0 + - - +
403B SO4 2.7 24.2 + - - -
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Residues in contact with GLY 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU 4.3 0.2 - - - -
362B SER* 1.3 71.5 - - - +
364B LYS* 1.3 57.2 + - - +
366B ARG* 3.4 22.0 + - - +
367B GLU* 3.1 40.2 + - - +
403B SO4 2.8 15.7 + - - -
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Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASN* 4.8 7.6 - - - +
76B HIS* 4.8 17.4 + - + +
77B MET* 3.5 32.5 - - + +
79B THR* 6.2 1.4 - - - +
82B ASN* 6.0 1.8 - - - +
362B SER* 3.3 1.5 + - - +
363B GLY* 1.3 77.0 - - - +
365B PHE* 1.4 60.1 + - + +
367B GLU* 4.1 11.6 - - - +
368B GLN* 3.4 26.9 + - - +
403B SO4 3.6 29.4 + - - +
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Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 3.7 39.9 - - + -
70B ALA* 3.9 13.7 - - + -
71B VAL* 3.9 19.3 - - + -
77B MET* 4.5 4.9 - - - -
82B ASN* 3.5 29.4 - - + -
85B LEU* 4.1 17.3 - - + -
299B MET* 4.9 3.4 - - + -
358B TYR* 3.7 32.1 - + + +
362B SER* 3.1 30.1 + - - +
364B LYS* 1.4 78.4 - - + +
366B ARG* 1.4 61.7 + - - +
368B GLN* 3.5 3.3 + - - +
369B PHE* 3.1 50.6 + + + -
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Residues in contact with ARG 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B TYR 4.5 0.2 + - - -
359B ASN* 2.9 44.3 + - - +
360B PHE* 2.9 34.2 + - - +
361B LEU* 4.0 1.0 - - - +
362B SER 3.0 21.4 + - - +
363B GLY* 3.4 25.2 + - - +
365B PHE* 1.4 76.4 - - - +
367B GLU* 1.4 57.7 + - + +
369B PHE* 3.5 2.1 + - - +
370B LYS* 2.9 34.7 + - + +
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG* 5.9 0.2 - - - -
74B ASN* 5.6 2.9 + - - -
363B GLY* 3.1 20.7 + - - +
364B LYS* 4.1 13.3 - - - +
365B PHE 3.4 0.4 - - - -
366B ARG* 1.4 73.5 - - + +
368B GLN* 1.3 68.2 + - - +
370B LYS* 3.4 8.4 + - - +
371B ALA* 3.0 28.9 + - - +
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Residues in contact with GLN 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ALA* 3.6 23.1 - - + -
73B ARG* 3.1 46.6 + - - +
74B ASN* 3.4 31.9 - - - +
77B MET* 3.1 28.7 - - + -
364B LYS 3.4 5.6 + - - +
365B PHE 3.5 5.3 + - - +
366B ARG 3.4 0.2 - - - -
367B GLU* 1.3 81.9 + - - +
369B PHE* 1.4 58.4 + - + +
371B ALA* 3.4 6.3 + - - +
372B ALA* 3.0 26.3 + - - +
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Residues in contact with PHE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLY* 4.7 2.0 - - - -
66B LEU* 3.7 43.1 - - + -
67B VAL* 4.0 16.8 - - + -
70B ALA* 4.3 1.3 - - + -
355B PRO* 3.4 24.9 - - + -
358B TYR* 4.3 1.1 - - + -
359B ASN* 3.5 34.1 - - + +
365B PHE* 3.1 44.8 + + + +
366B ARG 3.8 4.3 - - - +
368B GLN* 1.4 77.1 - - + +
370B LYS* 1.4 63.7 + - - +
372B ALA* 3.1 6.5 + - - +
373B PHE* 3.0 43.1 + - + -
413B SOG 4.0 10.8 - - + -
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Residues in contact with LYS 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B ARG* 2.9 24.4 + - + +
367B GLU* 3.4 9.6 + - - +
369B PHE* 1.4 72.7 - - - +
371B ALA* 1.4 57.0 + - - +
373B PHE* 3.4 6.4 + - - +
374B SER* 2.9 33.3 + - - -
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ARG* 3.8 28.7 - - - +
367B GLU 3.0 16.6 + - - +
368B GLN 3.5 6.3 - - - +
370B LYS* 1.4 75.5 - - - +
372B ALA* 1.3 58.7 + - - +
374B SER* 2.9 21.8 + - - -
375B TRP* 3.2 14.4 + - - +
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 3.6 33.2 - - + -
368B GLN 3.0 13.6 + - - +
369B PHE* 3.1 11.6 + - - +
371B ALA* 1.3 75.8 - - - +
373B PHE* 1.4 57.7 + - - +
375B TRP* 3.2 8.9 + - - +
376B TRP* 2.9 29.8 + - - +
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Residues in contact with PHE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B VAL* 4.5 7.0 - - + -
66B LEU* 3.9 24.0 - - + -
369B PHE* 3.0 33.7 + - + +
370B LYS* 4.1 5.2 - - - +
372B ALA* 1.4 75.0 - - - +
374B SER* 1.4 58.3 + - - +
376B TRP* 4.4 13.7 - + + +
377B LEU* 3.0 49.3 + - + +
413B SOG 3.7 48.5 - - + -
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Residues in contact with SER 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LYS* 2.9 17.6 + - - -
371B ALA* 2.9 24.9 + - - -
373B PHE* 1.4 75.2 - - - +
375B TRP* 1.4 59.7 + - - +
377B LEU* 3.7 15.9 - - - -
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Residues in contact with TRP 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B ALA 3.2 17.7 + - - +
372B ALA* 3.6 5.6 - - - +
374B SER* 1.4 75.9 + - - +
376B TRP* 1.3 65.5 + + + +
377B LEU 3.2 4.3 + - - -
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Residues in contact with TRP 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B ALA 2.9 17.0 + - - +
373B PHE* 3.6 15.0 + + + +
375B TRP* 1.3 77.1 - - + +
377B LEU* 1.4 87.3 + - + +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B PHE* 3.0 33.7 + - + +
374B SER* 3.7 17.7 - - - -
375B TRP 4.5 2.9 - - - -
376B TRP* 1.4 107.1 - - + +
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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
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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