Contacts of the helix formed by residues 375 - 392 (chain B) in PDB entry 5M7S
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 375 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B VAL* 6.0 3.4 - - - -
373B LEU 4.3 0.6 + - - -
374B TYR* 1.3 75.6 - - - +
376B PRO* 1.3 68.9 - - - +
377B GLN* 3.6 6.2 + - - +
378B MET* 3.2 42.4 + - - +
379B ALA* 3.0 22.5 + - - +
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Residues in contact with PRO 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PRO* 3.4 28.7 - - + +
296B TYR 4.0 4.9 - - - +
297B LYS* 3.9 28.7 - - + +
298B GLY 5.5 0.4 - - - +
374B TYR* 3.8 33.2 - - + +
375B SER* 1.3 84.3 - - - +
377B GLN* 1.3 57.0 + - - +
379B ALA* 3.3 0.7 + - - +
380B LEU 2.9 25.3 + - - -
566B TYR* 5.7 0.4 - - - +
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Residues in contact with GLN 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PRO* 5.2 1.3 - - - -
375B SER* 3.3 5.9 + - - +
376B PRO* 1.3 79.8 - - - +
378B MET* 1.3 68.1 + - + +
380B LEU* 3.4 11.1 + - + +
381B LYS* 3.2 21.7 + - - +
566B TYR* 5.4 5.2 - - - +
573B PRO* 5.5 7.1 - - - +
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Residues in contact with MET 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B SER* 3.2 29.9 + - - +
377B GLN* 1.3 80.4 - - + +
379B ALA* 1.3 56.8 + - - +
381B LYS* 3.5 7.3 + - - +
382B LEU* 3.1 26.9 + - - +
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B HIS* 4.7 1.2 + - - -
327B THR* 3.6 11.8 - - + +
330B THR* 4.2 16.6 - - + -
374B TYR* 3.7 29.6 - - + +
375B SER 3.0 16.9 + - - +
376B PRO 3.6 4.3 - - - +
377B GLN 3.2 0.2 - - - -
378B MET* 1.3 75.7 - - - +
380B LEU* 1.3 66.4 + - - +
382B LEU* 3.1 8.0 + - - +
383B ALA* 2.9 25.6 + - - +
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LEU 3.7 23.6 - - - +
295B PRO* 4.0 10.1 - - + -
323B VAL* 3.8 9.6 - - + -
327B THR* 4.0 8.6 - - - +
376B PRO 2.9 13.9 + - - +
377B GLN* 3.6 12.1 - - - +
379B ALA* 1.3 75.2 - - - +
381B LYS* 1.3 64.2 + - - +
383B ALA* 3.1 2.4 + - - +
384B LEU* 2.8 55.8 + - + +
559B GLN* 5.8 2.0 - - + +
562B ALA* 4.3 5.2 - - + -
563B ASP* 4.4 9.6 - - - +
566B TYR* 3.9 31.2 - - + +
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Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLN 3.2 9.9 + - - +
378B MET* 3.7 10.3 - - - +
379B ALA 3.3 0.2 - - - -
380B LEU* 1.3 81.6 - - - +
382B LEU* 1.3 61.2 + - - +
384B LEU* 3.9 5.9 - - - +
385B THR* 2.8 36.8 + - - +
555B LEU* 4.3 19.1 - - + -
559B GLN* 4.0 26.7 - - - +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B HIS* 4.2 11.5 - - + -
330B THR* 4.2 28.0 - - + +
378B MET 3.1 19.2 + - - +
379B ALA* 3.1 7.1 + - - +
381B LYS* 1.3 76.8 - - - +
383B ALA* 1.3 61.6 + - - +
385B THR* 3.6 7.2 + - - -
386B GLU* 3.4 21.5 + - - +
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B TYR* 3.9 3.8 - - + -
323B VAL* 4.1 15.5 - - + -
326B HIS* 3.4 39.9 - - + +
327B THR* 4.0 10.8 - - + -
379B ALA 2.9 15.3 + - - +
380B LEU 3.6 3.6 - - - +
382B LEU* 1.3 75.0 - - - +
384B LEU* 1.3 61.1 + - - +
386B GLU* 3.2 3.6 + - - +
387B TRP* 2.8 29.2 + - - +
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LEU* 5.9 0.2 - - + -
323B VAL* 3.5 25.1 - - + -
380B LEU* 2.8 46.7 + - + +
381B LYS* 4.0 4.7 - - - +
383B ALA* 1.3 69.4 - - - +
385B THR* 1.3 65.6 + - - +
387B TRP* 3.8 21.7 - - + +
388B LEU* 3.0 24.4 + - - +
555B LEU* 4.0 12.0 - - + +
558B LEU* 3.8 22.7 - - + +
559B GLN* 3.8 38.6 - - + +
562B ALA* 4.2 5.8 - - + -
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Residues in contact with THR 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LYS* 2.8 27.6 + - - +
382B LEU* 3.8 8.4 - - - -
384B LEU* 1.3 77.6 - - - +
386B GLU* 1.3 59.9 + - - +
388B LEU* 3.7 6.3 - - + +
389B GLN* 2.9 35.4 + - - +
555B LEU* 3.9 25.9 - - + +
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 3.7 16.6 + - - +
88B TRP* 3.0 25.1 + - - -
322B TYR* 2.6 28.2 + - + +
326B HIS* 3.5 18.8 + - - +
382B LEU 3.4 10.2 + - - +
383B ALA 3.2 7.7 + - - +
384B LEU 3.2 0.2 - - - -
385B THR* 1.3 78.6 - - - +
387B TRP* 1.3 65.2 + - - +
388B LEU 3.2 0.2 - - - -
389B GLN* 3.2 23.0 + - + +
390B GLU* 4.2 5.0 + - - +
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Residues in contact with TRP 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 5.7 0.4 - - - +
293B LEU* 4.3 24.0 - - + -
319B GLU* 3.5 22.5 + - - -
320B ALA* 4.6 1.3 - - - -
322B TYR* 3.3 46.5 - + + +
323B VAL* 4.3 11.4 - - + -
383B ALA 2.8 17.4 + - - +
384B LEU* 3.4 29.6 + - + +
386B GLU* 1.3 76.5 - - - +
388B LEU* 1.3 63.3 - - - +
390B GLU* 2.8 29.9 + - + +
391B PHE* 3.4 37.2 - + - -
558B LEU* 4.3 7.9 - - + -
561B LEU* 4.9 6.5 - - + -
562B ALA* 6.3 0.2 - - + -
636B ILE* 3.9 16.1 - - + +
640B MET* 3.9 25.1 - - - -
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Residues in contact with LEU 388 (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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384B LEU 3.0 17.2 + - - +
385B THR* 3.7 8.7 - - + +
386B GLU 3.2 0.2 - - - -
387B TRP* 1.3 74.8 - - - +
389B GLN* 1.3 75.9 + - - +
390B GLU 3.1 1.6 + - - -
391B PHE* 3.1 17.5 + - + +
392B GLY 4.3 1.7 + - - -
553B VAL* 3.4 32.8 - - + +
554B THR* 3.8 14.8 - - - +
555B LEU* 3.6 29.2 - - + +
558B LEU* 3.7 16.7 - - + +
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Residues in contact with GLN 389 (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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385B THR* 2.9 29.0 + - - +
386B GLU* 3.7 15.3 - - + +
387B TRP 3.0 1.0 + - - -
388B LEU* 1.3 91.8 - - - +
390B GLU* 1.3 65.8 + - - +
391B PHE 3.6 0.2 + - - -
392B GLY* 4.0 5.2 + - - -
393B VAL* 4.0 15.8 - - - +
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Residues in contact with GLU 390 (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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83B ARG* 5.5 7.1 + - - -
84B ARG* 5.5 6.4 + - - +
87B LYS* 5.9 2.4 - - - -
322B TYR* 4.1 30.9 + - + -
386B GLU 4.4 4.7 - - - +
387B TRP* 2.8 17.9 + - + +
389B GLN* 1.3 80.4 - - - +
391B PHE* 1.3 62.4 + - - +
392B GLY 3.4 0.6 + - - -
393B VAL* 3.6 18.4 + - - +
633B ASN* 3.0 27.2 + - - +
636B ILE* 3.8 17.5 - - + -
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Residues in contact with PHE 391 (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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387B TRP* 3.4 53.2 - + - -
388B LEU* 3.1 16.6 + - + +
390B GLU* 1.3 79.5 - - - +
392B GLY* 1.3 57.1 + - - +
393B VAL 3.4 0.7 - - - -
553B VAL* 4.3 23.6 - - + -
558B LEU* 3.7 22.9 - - + -
561B LEU* 5.8 0.7 - - + -
628B LEU* 3.4 32.1 - - + -
631B CYS* 3.7 18.7 - - + +
632B ALA 3.3 7.6 + - - -
633B ASN* 3.1 28.2 + - - +
636B ILE* 3.6 31.0 - - + -
640B MET* 5.7 1.6 - - + -
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Residues in contact with GLY 392 (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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388B LEU 4.3 2.4 + - - -
389B GLN 4.0 5.6 + - - -
390B GLU 3.4 0.8 - - - -
391B PHE* 1.3 76.2 - - - +
393B VAL* 1.3 59.6 + - - +
394B PRO* 4.1 3.5 - - - +
632B ALA* 3.7 17.1 - - - +
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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