Contacts of the helix formed by residues 360 - 371 (chain B) in PDB entry 6S1M
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 ASP 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358B MET* 5.0 1.0 - - - +
359B GLU* 1.3 75.3 - - - +
361B HIS* 1.3 58.2 + - - +
362B LEU* 3.0 16.4 + - - +
363B GLU* 2.5 43.7 + - + +
364B ILE* 3.0 29.3 + - - +
413B LYS* 5.1 1.9 + - - -
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Residues in contact with HIS 361 (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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349B VAL* 3.4 29.5 - - + +
350B SER* 5.1 9.0 - - - -
353B PHE* 3.9 29.9 - + + -
359B GLU 3.2 14.3 + - - -
360B ASP* 1.3 70.2 + - - +
362B LEU* 1.3 60.3 + - - +
364B ILE* 3.4 8.4 + - + +
365B LEU* 3.0 28.1 + - - +
407B THR* 4.3 22.1 - - + +
408B PRO* 4.1 31.6 - - + +
427B THR* 4.6 7.0 - - + +
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Residues in contact with LEU 362 (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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360B ASP* 3.0 12.2 + - - +
361B HIS* 1.3 77.0 - - - +
363B GLU* 1.3 59.3 + - - +
365B LEU* 3.4 7.2 + - + +
366B GLU* 3.0 26.9 + - - +
411B GLY* 4.0 6.7 - - - -
412B SER 3.7 31.2 - - - +
413B LYS* 3.8 31.1 + - + +
425B LEU* 3.7 37.0 - - + +
427B THR* 3.8 24.2 - - + +
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Residues in contact with GLU 363 (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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152B LYS* 5.1 7.5 + - - -
358B MET* 4.7 19.3 - - + +
360B ASP* 2.5 33.8 + - + +
362B LEU* 1.3 72.1 - - - +
364B ILE* 1.3 58.6 + - - +
366B GLU* 3.2 18.7 + - - +
367B TRP* 2.8 37.9 + - - +
413B LYS* 4.6 8.7 + - - +
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Residues in contact with ILE 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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349B VAL* 4.0 24.0 - - + +
352B ILE* 3.8 29.4 - - + -
353B PHE* 3.9 30.7 - - + +
356B SER* 6.0 0.4 - - - +
358B MET* 3.7 45.5 - - + +
360B ASP 3.0 17.3 + - - +
361B HIS* 3.8 8.3 - - - +
363B GLU* 1.3 75.9 - - - +
365B LEU* 1.3 58.8 + - - +
367B TRP* 3.4 6.9 + - - +
368B THR* 3.0 32.6 + - - -
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ASN* 5.8 1.3 - - - +
349B VAL* 3.9 16.1 - - + +
361B HIS 3.0 17.4 + - - +
362B LEU* 3.6 11.4 - - + +
364B ILE* 1.3 77.9 - - - +
366B GLU* 1.3 56.2 + - - +
368B THR* 3.5 6.2 - - - -
369B LEU* 3.1 24.4 + - - +
402B TYR* 3.5 54.9 - - + +
403B PHE 4.4 4.3 - - - +
404B CYS* 3.8 25.1 - - + -
425B LEU* 4.2 16.8 - - + -
426B VAL 3.9 16.8 - - - +
427B THR* 4.6 2.2 - - + -
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Residues in contact with GLU 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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362B LEU 3.0 16.0 + - - +
363B GLU* 3.2 16.7 + - - +
365B LEU* 1.3 73.4 - - - +
367B TRP* 1.3 60.6 + - - +
369B LEU* 3.1 8.5 + - - +
370B ARG* 2.9 60.7 + - + +
413B LYS* 3.7 21.0 + - - +
415B ILE* 3.4 37.8 - - + +
425B LEU* 3.7 13.1 - - + +
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Residues in contact with TRP 367 (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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152B LYS* 3.6 37.8 - - - +
153B LEU* 5.1 6.7 - - + -
154B VAL* 3.9 20.6 - - + -
157B THR* 3.8 24.0 - - + -
178B PHE* 4.0 18.9 - + - -
352B ILE* 4.2 23.8 - - + -
358B MET* 4.2 22.2 - - + -
363B GLU* 2.8 26.2 + - - +
364B ILE* 3.7 7.6 - - - +
366B GLU* 1.3 74.1 - - - +
368B THR* 1.3 64.9 + - - +
370B ARG* 2.8 30.7 + - + +
371B VAL* 3.2 37.1 + - + +
376B PRO* 4.3 9.9 - - + -
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Residues in contact with THR 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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348B ASN* 4.8 2.8 + - - +
349B VAL* 5.2 4.2 - - + +
352B ILE* 3.3 26.3 - - - +
364B ILE* 3.0 18.3 + - - +
365B LEU* 3.5 7.4 - - + -
367B TRP* 1.3 79.7 - - - +
369B LEU* 1.3 62.0 + - - +
371B VAL* 3.8 6.0 - - - +
373B HIS 3.1 35.5 + - - +
374B ILE* 3.3 26.1 + - - +
376B PRO* 4.9 0.8 - - - +
395B PHE* 4.1 1.8 - - + -
402B TYR* 3.3 23.6 - - + +
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Residues in contact with LEU 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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180B ASP 4.6 2.3 - - - +
181B LEU* 3.6 26.1 - - + +
365B LEU 3.1 13.5 + - - +
366B GLU* 3.1 12.5 + - + +
368B THR* 1.3 76.1 - - - +
370B ARG* 1.3 61.4 + - + +
371B VAL 3.5 0.3 + - - -
372B ARG* 3.6 10.6 + - - -
395B PHE* 3.8 32.5 - - + -
398B CYS* 5.4 3.1 - - - -
399B PRO* 5.0 9.9 - - + -
402B TYR* 4.3 11.4 - - + -
415B ILE* 3.9 15.3 - - + -
423B VAL* 3.9 19.3 - - + -
425B LEU* 3.8 28.7 - - + -
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Residues in contact with ARG 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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178B PHE* 4.2 11.6 - - + +
180B ASP* 3.1 57.1 + - - +
181B LEU* 4.0 17.5 - - - +
366B GLU* 2.9 44.9 + - + +
367B TRP* 2.8 26.6 + - + +
369B LEU* 1.3 74.0 - - - +
371B VAL* 1.3 58.3 + - + +
372B ARG 3.3 0.9 - - - -
415B ILE* 4.4 12.4 - - - +
416B ARG 3.7 24.4 + - - +
418B PRO* 4.8 4.0 - - - +
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Residues in contact with VAL 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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61B MET* 4.1 11.8 - - - +
157B THR* 4.0 22.7 - - + -
158B VAL* 5.4 4.9 - - - +
178B PHE* 4.1 19.7 - - + -
179B ALA* 4.2 4.2 - - - +
180B ASP 4.8 0.4 - - - +
367B TRP* 3.7 49.8 - - + +
368B THR* 3.8 15.5 - - - +
370B ARG* 1.3 78.1 - - - +
372B ARG* 1.3 67.7 + - - +
373B HIS* 4.1 18.5 - - + +
376B PRO* 4.8 6.5 - - + -
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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