Contacts of the helix formed by residues 370 - 388 (chain A) in PDB entry 1G3I
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A PHE* 1.3 76.0 - - - +
371A THR* 1.3 66.9 + - - +
372A ASP* 3.4 10.0 + - - +
373A ALA* 2.8 33.1 + - - +
374A VAL* 3.0 7.1 + - - +
420A ASN* 4.1 18.4 - - - +
421A ILE 3.0 20.4 + - - +
422A ASP* 3.4 23.0 - - + +
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Residues in contact with THR 371 (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 PHE 3.9 0.6 + - - -
370A THR* 1.3 70.5 - - - +
372A ASP* 1.3 62.0 + - - +
374A VAL* 2.7 30.5 + - + +
375A LYS* 2.8 21.8 + - + +
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Residues in contact with ASP 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A THR* 3.3 8.2 + - - +
371A THR* 1.3 81.9 - - - +
373A ALA* 1.3 56.7 + - - +
375A LYS* 3.6 17.5 - - - +
376A LYS* 2.9 29.1 + - - +
423A ALA* 4.1 19.6 - - + +
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A PHE* 4.4 6.5 - - + -
370A THR* 2.8 24.1 + - - +
372A ASP* 1.3 77.2 - - - +
374A VAL* 1.3 55.8 + - - +
376A LYS* 3.1 3.9 + - - +
377A ILE* 2.8 33.9 + - - +
421A ILE* 3.0 30.1 - - + +
422A ASP* 3.7 9.2 - - - +
423A ALA* 3.9 10.1 - - - +
426A VAL* 4.0 7.9 - - + +
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Residues in contact with VAL 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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342A GLU* 3.5 31.0 - - + +
345A LEU* 3.8 19.7 - - + -
346A THR* 3.8 20.9 - - + -
353A THR* 4.7 5.8 - - + -
369A PHE* 4.3 18.4 - - + +
370A THR 3.0 14.5 + - - +
371A THR* 2.7 15.3 + - + +
373A ALA* 1.3 68.7 - - - +
375A LYS* 1.3 66.8 + - - +
376A LYS 3.0 0.2 + - - -
377A ILE* 4.3 8.5 - - + -
378A ALA* 2.9 25.3 + - - +
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Residues in contact with LYS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A GLU* 3.6 37.9 + - - +
371A THR* 2.8 19.1 + - + +
372A ASP* 3.6 21.3 - - - +
374A VAL* 1.3 76.5 - - - +
376A LYS* 1.3 57.0 + - - +
378A ALA* 4.0 1.0 - - - +
379A GLU* 3.0 54.1 + - - +
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Residues in contact with LYS 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 ASP 2.9 17.8 + - - +
373A ALA* 3.3 7.2 - - - +
375A LYS* 1.3 73.4 - - - +
377A ILE* 1.3 66.8 + - - +
378A ALA 3.2 1.8 - - - -
379A GLU* 3.2 8.9 + - + +
380A ALA* 2.8 30.2 + - + +
423A ALA* 4.3 17.7 - - + +
426A VAL* 3.9 20.2 - - + -
427A ALA* 4.0 24.8 - - + +
430A LEU* 6.1 1.8 - - - -
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Residues in contact with ILE 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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345A LEU* 3.5 21.1 - - + -
353A THR* 5.3 2.0 - - + -
369A PHE* 4.1 19.1 - - + -
373A ALA 2.8 24.0 + - - +
374A VAL* 3.6 9.2 - - - +
376A LYS* 1.3 70.8 - - - +
378A ALA* 1.3 57.3 + - - +
380A ALA* 2.8 24.8 - - - +
381A ALA* 2.9 9.9 + - - +
396A LEU* 4.8 5.4 - - + -
399A VAL* 4.3 16.0 - - + +
400A MET* 3.7 29.2 - - + -
403A LEU* 3.4 32.5 - - + -
426A VAL* 3.7 13.9 - - + -
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Residues in contact with ALA 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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338A ALA 3.9 2.5 - - - +
341A PHE* 3.6 28.8 - - + -
342A GLU* 3.7 24.7 - - + +
345A LEU* 3.9 10.5 - - + -
374A VAL 2.9 15.5 + - - +
377A ILE* 1.3 73.8 - - - +
379A GLU* 1.3 64.9 + - - +
380A ALA 2.7 6.4 + - - -
381A ALA* 2.9 12.3 + - - +
382A PHE* 2.9 15.2 + - - +
396A LEU* 4.4 2.9 - - - -
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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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338A ALA* 4.1 19.0 - - + +
342A GLU* 3.8 15.9 - - - +
375A LYS* 3.0 41.7 + - - +
376A LYS* 3.7 10.0 - - + +
378A ALA* 1.3 77.9 - - - +
380A ALA* 1.3 55.8 + - - +
382A PHE* 3.9 5.8 - - - +
383A ARG* 2.9 29.2 + - - +
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Residues in contact with ALA 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 LYS* 2.8 17.0 + - + +
377A ILE 2.8 16.4 - - - +
378A ALA 2.7 1.2 + - - -
379A GLU* 1.3 76.2 - - - +
381A ALA* 1.3 64.5 + - - +
383A ARG* 3.0 22.0 - - - +
384A VAL* 3.2 10.7 + - - +
399A VAL* 4.6 4.5 - - + -
430A LEU* 3.8 26.9 - - + -
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Residues in contact with ALA 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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341A PHE* 4.0 7.9 - - + -
377A ILE 2.9 8.0 + - - +
378A ALA 2.9 8.0 + - - +
380A ALA* 1.3 70.0 - - - +
382A PHE* 1.3 69.5 + - - +
384A VAL* 3.0 19.2 - - - +
385A ASN* 3.0 6.4 + - - +
395A ARG* 3.5 29.1 - - + +
396A LEU* 3.2 35.9 - - + -
399A VAL* 4.0 6.7 - - + +
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Residues in contact with PHE 382 (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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336A LEU 4.5 5.6 - - - -
337A SER* 3.7 12.8 - - - -
338A ALA* 2.9 43.7 - - + -
341A PHE* 3.5 17.6 - + + -
378A ALA 2.9 14.6 + - - +
379A GLU* 3.9 2.9 - - - +
381A ALA* 1.3 77.2 - - - +
383A ARG* 1.3 73.6 + - - +
385A ASN* 2.8 16.9 + - + +
386A GLU* 2.9 39.5 + - + -
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Residues in contact with ARG 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 2.9 17.9 + - - +
380A ALA* 3.0 15.5 - - - +
382A PHE* 1.3 82.7 - - - +
384A VAL* 1.3 63.4 + - - +
386A GLU* 3.1 6.0 + - - +
387A LYS* 3.0 55.8 + - + +
433A VAL* 4.3 23.6 - - + +
435A GLU* 5.8 2.4 + - - -
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Residues in contact with VAL 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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380A ALA 3.2 10.8 - - - +
381A ALA* 3.0 22.0 - - - +
383A ARG* 1.3 74.6 - - + +
385A ASN* 1.3 58.9 + - - +
387A LYS* 2.7 9.3 + - - +
388A THR* 2.6 54.8 + - + +
395A ARG* 3.6 31.9 - - - +
399A VAL* 4.8 5.8 - - + -
402A ARG* 5.3 9.4 - - - +
433A VAL* 4.9 15.0 - - + -
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Residues in contact with ASN 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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341A PHE* 4.1 8.1 - - + -
381A ALA 3.0 8.1 + - - +
382A PHE* 2.8 17.1 + - + +
384A VAL* 1.3 76.0 - - - +
386A GLU* 1.3 60.9 + - - +
388A THR 3.1 17.5 - - - +
389A GLU 4.6 0.7 - - - -
390A ASN* 3.2 31.8 + - - +
391A ILE 3.4 12.5 + - - -
392A GLY* 2.8 42.4 + - - +
395A ARG* 2.6 41.6 + - - +
68G GLN* 3.4 1.0 - - - +
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Residues in contact with GLU 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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382A PHE* 2.9 34.5 + - + +
383A ARG* 3.4 8.8 + - - +
385A ASN* 1.3 79.2 - - - +
387A LYS* 1.3 86.1 + - + +
388A THR 3.2 0.3 + - - -
390A ASN* 4.9 1.3 - - - +
68G GLN* 4.2 9.9 - - - +
70G HIS* 2.8 43.8 + - + -
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Residues in contact with LYS 387 (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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383A ARG* 3.0 54.6 + - - +
384A VAL* 2.7 15.1 + - - +
386A GLU* 1.3 96.9 + - + +
388A THR* 1.3 68.2 + - + +
433A VAL* 4.6 13.5 - - + -
435A GLU* 3.4 43.8 + - + +
70G HIS* 4.8 5.6 + - - -
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Residues in contact with THR 388 (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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384A VAL* 2.6 40.3 + - + +
385A ASN 3.1 5.9 - - - +
386A GLU 4.0 1.9 - - - +
387A LYS* 1.3 87.2 - - + +
389A GLU* 1.3 63.6 + - - -
390A ASN 3.0 8.9 + - - -
395A ARG* 4.0 3.6 + - - -
433A VAL* 6.1 0.7 - - + -
434A VAL 4.5 12.3 - - - +
435A GLU* 5.4 3.8 - - - +
317B SER* 6.3 2.7 - - - -
68G GLN* 3.2 9.4 - - - +
70G HIS* 4.5 5.0 + - - -
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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