Contacts of the helix formed by residues 379 - 396 (chain A) in PDB entry 1A8H
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 GLU 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A ALA* 3.4 10.1 - - + +
378A GLY* 1.3 79.3 - - - +
380A GLU* 1.3 82.9 + - + +
381A LEU 3.1 0.9 + - - -
382A ALA* 3.2 18.6 + - - +
383A GLU 4.5 1.0 + - - -
417A TYR* 5.2 1.1 - - - +
421A LYS* 5.7 3.7 + - - -
440A ARG* 2.9 37.4 + - - +
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Residues in contact with GLU 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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379A GLU* 1.3 107.8 - - + +
381A LEU* 1.3 63.3 + - + +
382A ALA 3.4 0.4 - - - -
383A GLU* 3.4 24.4 - - - +
417A TYR* 3.7 30.3 + - - -
420A GLU* 5.0 4.3 - - - +
421A LYS* 4.7 10.8 + - - -
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Residues in contact with LEU 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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378A GLY 3.0 11.0 + - - +
380A GLU* 1.3 82.3 - - + +
382A ALA* 1.3 64.3 + - - +
383A GLU 3.1 4.0 + - - -
384A GLY 3.3 5.5 + - - -
410A TYR* 2.8 33.8 + - + +
413A ALA* 4.6 12.6 - - + +
414A LEU* 3.7 33.0 - - + -
417A TYR* 3.9 42.2 - - + -
440A ARG* 3.9 28.9 - - + +
441A VAL* 4.8 0.4 - - - +
481A TRP* 3.5 13.9 - - + -
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Residues in contact with ALA 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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378A GLY* 3.7 9.8 + - - +
379A GLU 3.2 23.4 + - - +
381A LEU* 1.3 74.3 - - - +
383A GLU* 1.3 57.6 + - - +
384A GLY 3.0 6.6 + - - -
385A THR* 3.0 28.7 + - - +
481A TRP* 4.0 20.0 - - + -
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Residues in contact with GLU 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 4.5 1.0 + - - +
380A GLU 3.4 21.6 + - - +
381A LEU* 4.6 1.8 - - - -
382A ALA* 1.3 77.4 - - - +
384A GLY* 1.3 64.7 + - - +
385A THR* 3.2 1.3 - - - -
386A GLY* 3.2 14.1 + - - -
387A LEU* 3.7 12.3 - - - +
390A ARG* 5.2 4.9 + - - -
410A TYR* 5.1 8.6 - - + -
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Residues in contact with GLY 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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381A LEU 3.3 5.6 + - - -
382A ALA 3.0 2.8 - - - -
383A GLU* 1.3 78.3 - - - +
385A THR* 1.3 56.6 + - - +
386A GLY 2.9 5.8 - - - -
387A LEU* 3.0 41.1 + - - +
388A ALA 4.6 0.2 + - - -
410A TYR* 3.7 25.8 - - - -
447A ILE* 4.0 14.3 - - - +
478A ALA 4.3 0.9 - - - +
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Residues in contact with THR 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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382A ALA 3.0 19.3 + - - +
383A GLU* 4.4 0.5 - - - -
384A GLY* 1.3 75.3 - - - +
386A GLY* 1.3 58.0 + - - +
387A LEU 3.3 2.3 + - - -
388A ALA 4.5 0.4 + - - -
389A GLY 5.1 0.3 + - - -
447A ILE* 3.8 18.6 - - + +
478A ALA 3.5 11.2 - - - +
479A GLU* 3.6 40.9 + - - +
480A ARG 4.0 2.5 - - - -
481A TRP* 3.8 35.9 - - + +
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Residues in contact with GLY 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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383A GLU 3.2 9.3 + - - -
384A GLY 2.9 1.8 - - - -
385A THR* 1.3 82.1 + - - +
387A LEU* 1.3 62.1 + - - +
388A ALA 3.6 0.2 - - - -
389A GLY* 3.9 5.4 + - - -
390A ARG* 2.9 32.2 + - - +
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Residues in contact with LEU 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 GLU* 3.7 14.8 - - - +
384A GLY* 3.0 35.9 + - - +
386A GLY* 1.3 77.0 - - - +
388A ALA* 1.3 57.4 + - - +
389A GLY 3.1 1.6 - - - -
390A ARG* 2.9 22.4 + - - +
391A LEU* 2.7 44.3 + - + +
406A GLU* 4.2 17.5 - - + +
407A ALA* 4.4 4.0 - - - -
410A TYR* 3.8 33.9 - - + -
451A LEU* 3.7 27.4 - - + -
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Residues in contact with ALA 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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35A TRP* 4.6 1.1 - - - -
384A GLY 4.6 0.6 + - - -
385A THR 4.5 1.0 + - - -
386A GLY 3.6 0.4 - - - -
387A LEU* 1.3 77.6 - - - +
389A GLY* 1.3 58.4 + - - +
391A LEU* 3.2 3.3 + - - +
392A ARG* 3.0 38.4 + - - +
451A LEU* 4.0 23.0 - - + +
475A LEU* 4.2 18.4 - - + +
478A ALA* 4.7 4.7 + - + +
479A GLU* 3.5 33.0 - - + +
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Residues in contact with GLY 389 (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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386A GLY* 3.9 7.0 + - - -
387A LEU 3.1 0.4 - - - -
388A ALA* 1.3 80.8 - - - +
390A ARG* 1.3 57.2 + - - +
392A ARG* 3.8 17.3 - - - +
393A PRO* 3.0 24.1 - - - +
479A GLU* 3.8 6.0 + - - -
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Residues in contact with ARG 390 (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 GLU* 5.2 5.1 + - - -
386A GLY 2.9 25.5 + - - +
387A LEU* 2.9 24.7 + - - +
389A GLY* 1.3 77.0 - - - +
391A LEU* 1.3 64.5 + - + +
393A PRO* 3.5 10.8 - - - +
394A LEU* 3.5 21.0 + - - +
406A GLU* 3.3 38.8 + - - +
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Residues in contact with LEU 391 (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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35A TRP* 3.7 30.5 - - + -
387A LEU* 2.7 24.1 + - + +
388A ALA* 3.2 2.7 + - - +
390A ARG* 1.3 80.7 - - + +
392A ARG* 1.3 66.6 + - - +
393A PRO* 3.3 0.7 - - - -
394A LEU* 2.9 15.9 + - + +
395A VAL* 2.8 25.1 + - - +
403A ALA* 3.5 48.0 - - + +
404A LEU* 5.7 1.6 - - + -
406A GLU* 4.0 13.7 - - + -
407A ALA* 4.7 6.3 - - + +
451A LEU* 4.5 22.7 - - + +
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Residues in contact with ARG 392 (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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35A TRP* 3.9 21.2 + - + +
39A ASP* 2.9 41.9 + - - +
388A ALA* 3.0 14.7 + - - +
389A GLY* 3.8 17.3 - - - +
391A LEU* 1.3 75.4 - - - +
393A PRO* 1.3 67.2 - - + +
395A VAL* 3.5 1.9 + - - +
396A ARG* 2.9 33.2 + - + +
475A LEU* 3.7 20.7 + - - +
476A GLU* 4.6 2.8 - - - +
479A GLU* 2.6 43.8 + - - -
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Residues in contact with PRO 393 (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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389A GLY 3.0 22.7 - - - +
390A ARG* 3.5 7.9 - - - +
391A LEU 3.3 4.5 - - - -
392A ARG* 1.3 91.5 - - + +
394A LEU* 1.3 64.3 + - + +
396A ARG* 4.1 5.9 - - + +
397A GLU* 3.2 44.0 + - - +
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Residues in contact with LEU 394 (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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390A ARG* 3.5 18.8 - - - +
391A LEU* 2.9 27.3 + - + +
393A PRO* 1.3 82.5 - - + +
395A VAL* 1.3 60.0 + - - +
397A GLU* 3.5 11.6 + - - +
399A LYS* 2.9 51.0 + - + +
402A VAL* 3.8 36.3 - - + -
403A ALA* 4.1 7.0 - - + +
406A GLU* 4.1 12.1 - - - +
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Residues in contact with VAL 395 (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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31A PHE* 4.0 26.9 - - + -
32A LEU* 4.1 19.4 - - + +
35A TRP* 3.8 49.1 - - + +
36A HIS* 4.8 2.2 - - + -
391A LEU 2.8 19.0 + - - +
392A ARG 3.8 4.5 - - - +
394A LEU* 1.3 72.1 - - - +
396A ARG* 1.3 61.2 + - + +
397A GLU 3.1 1.6 - - - -
398A LEU* 2.9 22.2 + - - +
399A LYS 5.0 0.9 - - - -
400A PHE* 3.7 13.6 - - + -
403A ALA* 4.2 15.5 - - + -
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Residues in contact with ARG 396 (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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4A VAL 5.4 1.0 + - - -
5A PHE* 3.8 12.7 - - - -
32A LEU* 5.3 0.2 - - - -
35A TRP* 5.7 2.0 - - - +
36A HIS* 2.6 53.0 + - - -
41A TYR* 3.9 22.7 + - - -
182A ARG* 2.4 36.5 + - - +
254A TRP* 3.2 33.4 - - + +
282A ARG* 5.8 4.2 - - - +
283A HIS* 6.2 0.6 - - - -
392A ARG* 2.9 28.2 + - + +
393A PRO* 4.1 6.1 - - + +
395A VAL* 1.3 78.0 - - + +
397A GLU* 1.3 55.4 + - + +
398A LEU 3.4 2.4 + - - -
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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