Contacts of the helix formed by residues 370 - 386 (chain A) in PDB entry 1GM5
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 THR 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A LEU* 1.3 76.8 - - - +
371A ASN* 1.3 57.0 + - - +
372A ALA* 2.4 41.3 + - + +
373A GLN* 2.4 50.8 + - + +
374A LYS* 2.9 33.5 + - - +
400A SER 4.7 4.0 - - - +
545A ASP* 5.4 0.2 - - - +
546A GLU 4.5 9.2 - - - +
547A MET 5.4 2.2 - - - -
548A PRO* 5.3 8.5 - - + -
549A PRO* 5.8 2.5 - - + -
1756A ADP 4.4 2.7 - - - +
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Residues in contact with ASN 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A THR* 1.3 74.4 + - - +
372A ALA* 1.3 61.6 + - - +
374A LYS* 3.3 24.4 - - - +
375A ARG* 3.1 20.8 + - - +
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A THR* 2.4 27.2 + - + +
371A ASN* 1.3 66.0 - - - +
373A GLN* 1.3 66.3 + - + +
374A LYS 2.9 1.6 - - - -
375A ARG* 2.8 31.7 + - - +
376A ALA* 2.9 12.2 + - - +
543A VAL* 5.1 0.3 - - - +
544A ILE 5.6 0.6 - - - +
545A ASP* 4.8 7.7 - - - +
546A GLU* 3.7 40.2 - - + +
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Residues in contact with GLN 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A LEU* 3.0 33.2 - - + +
370A THR* 2.4 59.6 + - + +
372A ALA* 1.3 71.9 - - - +
374A LYS* 1.3 67.4 + - - +
376A ALA* 3.1 12.6 - - - +
377A HIS* 3.0 19.1 + - - +
400A SER 3.1 15.9 - - - +
401A GLY* 3.6 6.4 - - - +
404A VAL* 5.6 1.3 - - - -
405A VAL* 4.0 19.7 - - + +
545A ASP* 3.8 18.4 - - - +
548A PRO* 4.8 0.7 - - - +
1756A ADP 3.4 23.0 + - - -
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Residues in contact with LYS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A ILE* 5.8 1.4 - - - +
369A LEU* 4.2 28.5 - - + +
370A THR 2.9 21.6 + - - +
371A ASN* 3.3 31.9 - - - +
373A GLN* 1.3 76.4 - - - +
375A ARG* 1.3 54.6 + - - +
377A HIS* 2.6 39.8 + - + +
378A GLN* 3.1 16.2 + - + +
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Residues in contact with ARG 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A ASN 3.1 8.9 + - - +
372A ALA* 2.8 24.6 + - - +
374A LYS* 1.3 74.3 - - - +
376A ALA* 1.3 70.0 + - - +
377A HIS 2.5 3.5 + - - -
378A GLN* 3.0 10.2 + - + +
379A GLU* 3.0 31.7 + - + +
542A THR 5.5 1.0 + - - -
543A VAL* 3.7 20.8 - - + +
544A ILE* 3.3 31.6 + - - +
546A GLU* 5.1 9.1 - - - +
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Residues in contact with ALA 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A ALA 2.9 10.0 + - - +
373A GLN* 3.1 19.7 - - - +
375A ARG* 1.3 75.5 - - - +
377A HIS* 1.3 56.1 + - - +
379A GLU* 3.5 2.9 + - - +
380A ILE* 3.1 32.5 + - + +
394A LEU* 4.3 13.7 - - + -
405A VAL* 3.4 24.7 - - + -
543A VAL* 3.4 21.2 - - + +
545A ASP* 4.7 4.7 - - - +
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Residues in contact with HIS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A ALA* 3.9 9.3 - - - +
362A ILE* 4.7 6.5 - - + -
369A LEU* 6.2 2.9 - - + -
373A GLN 3.0 9.3 + - - +
374A LYS* 2.6 21.9 + - + +
375A ARG 2.5 7.1 + - - -
376A ALA* 1.3 67.4 - - - +
378A GLN* 1.3 61.1 + - - +
379A GLU 2.8 14.4 + - - -
380A ILE* 3.3 8.3 + - + +
381A ARG* 2.8 66.0 + - - +
405A VAL* 4.9 6.3 - - + +
408A LEU* 3.4 42.1 - - + +
409A ALA 5.5 0.2 + - - -
412A ASP* 3.5 0.7 - - - -
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Residues in contact with GLN 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LYS* 3.1 20.4 + - + +
375A ARG* 3.0 10.8 + - + +
377A HIS* 1.3 89.3 + - - +
379A GLU* 1.3 58.0 + - - +
381A ARG* 4.2 15.1 - - - +
382A ASN* 2.1 40.4 + - - +
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Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A ARG* 3.0 20.9 + - + +
376A ALA 3.6 0.9 - - - +
377A HIS 2.8 1.4 + - - -
378A GLN* 1.3 77.5 - - - +
380A ILE* 1.3 67.8 + - - +
382A ASN* 3.1 7.7 + - - +
383A ASP* 3.1 20.1 + - - +
392A ARG* 2.3 57.7 + - - +
541A VAL* 3.4 1.9 - - - +
543A VAL* 1.2 85.5 + - + +
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Residues in contact with ILE 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ALA* 3.1 20.6 + - + +
377A HIS* 3.9 7.9 - - - +
379A GLU* 1.3 76.0 - - - +
381A ARG* 1.3 72.5 + - - +
383A ASP 3.0 2.6 + - - -
384A MET* 2.6 61.7 + - + +
390A MET* 2.9 27.4 - - + +
392A ARG* 4.7 7.9 - - - -
394A LEU* 5.3 7.4 - - + -
405A VAL* 4.6 16.6 - - + +
409A ALA* 4.4 13.9 - - + +
412A ASP* 6.0 1.1 - - - +
520A LEU* 4.2 27.6 - - + -
543A VAL* 5.7 1.8 - - + -
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Residues in contact with ARG 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A ILE* 3.0 31.2 - - + +
354A GLU 5.3 5.5 + - - -
355A GLY* 5.5 3.0 - - - +
358A ALA* 4.1 12.5 - - - +
377A HIS* 2.8 43.4 + - - +
378A GLN* 4.2 17.9 - - - +
380A ILE* 1.3 85.7 - - - +
382A ASN* 1.3 55.7 + - - +
384A MET* 2.7 26.0 + - - +
385A ILE* 2.8 36.5 + - + +
412A ASP* 1.5 59.7 + - - -
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Residues in contact with ASN 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLN* 2.1 33.6 + - - +
379A GLU* 3.1 5.6 + - - +
381A ARG* 1.3 82.9 - - - +
383A ASP* 1.3 58.1 + - - +
385A ILE* 3.1 22.5 - - - +
386A SER* 2.9 27.7 + - - -
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Residues in contact with ASP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A GLU 3.1 10.4 + - - +
380A ILE 3.0 7.0 + - - +
382A ASN* 1.3 73.9 - - - +
384A MET* 1.3 66.2 + - - +
386A SER* 3.6 13.7 + - - -
388A LYS 3.8 3.1 - - - +
389A PRO 3.6 18.4 - - - +
390A MET* 3.1 41.4 - - + +
391A ASN 4.1 1.7 + - - -
392A ARG* 4.2 23.3 + - - +
540A ASP* 3.9 20.4 - - - +
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Residues in contact with MET 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ILE 3.4 15.1 - - - +
350A PRO* 3.6 3.4 - - - +
351A LYS 5.0 0.9 - - - -
353A ILE* 5.6 6.1 - - + -
380A ILE* 2.6 53.1 + - + +
381A ARG* 2.7 11.8 + - - +
383A ASP* 1.3 79.1 - - - +
385A ILE* 1.3 62.8 + - + +
386A SER 3.2 9.2 + - - +
390A MET* 3.7 14.8 - - + +
409A ALA* 3.9 25.1 - - + +
412A ASP* 4.5 10.8 - - + -
413A ASN* 4.6 19.1 - - - -
492A GLY 5.2 0.4 - - - +
493A LEU* 5.0 6.1 - - - -
518A ASP* 2.9 32.9 - - - +
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Residues in contact with ILE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A PRO* 2.5 26.1 - - - +
351A LYS 3.6 26.7 - - - +
353A ILE* 4.0 16.8 - - + +
381A ARG* 2.8 38.7 + - + +
382A ASN* 3.1 27.1 - - - +
384A MET* 1.3 73.3 - - - +
386A SER* 1.3 58.0 + - - +
387A GLU* 3.7 5.6 + - - +
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Residues in contact with SER 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ILE 3.8 1.4 - - - +
350A PRO* 3.6 3.6 - - - +
382A ASN 2.9 15.9 + - - -
383A ASP* 3.8 15.0 - - - -
384A MET 3.2 5.9 - - - +
385A ILE* 1.3 80.9 - - - +
387A GLU* 1.3 58.8 + - - +
388A LYS* 2.5 38.0 + - - +
389A PRO 5.5 0.2 - - - -
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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