Contacts of the helix formed by residues 383 - 396 (chain A) in PDB entry 4E2I
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 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A PHE* 4.0 1.6 - - - -
381A SER 3.9 2.4 + - - +
382A ALA* 1.3 71.5 - - - +
384A ILE* 1.3 66.5 + - - +
385A GLU* 2.9 43.6 + - - +
386A GLU* 3.2 33.8 + - - +
387A TRP* 3.1 19.4 - - - +
566A LYS* 4.6 4.8 - - - +
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Residues in contact with ILE 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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376A PHE* 3.4 42.1 - - + -
382A ALA 3.7 2.0 + - - -
383A ASP* 1.3 73.8 + - - +
385A GLU* 1.3 65.7 + - + +
387A TRP* 3.4 0.8 + - - -
388A MET* 3.0 40.3 + - + +
577A LEU* 4.3 21.3 - - + -
599A TRP* 5.0 4.3 - - + -
602A ARG* 4.6 20.0 - - + +
603A LEU* 4.9 11.0 - - + -
606A GLU* 4.6 15.9 - - + +
607A PHE* 4.1 15.0 - - + -
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Residues in contact with GLU 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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383A ASP* 2.9 20.5 + - - +
384A ILE* 1.3 81.2 - - + +
386A GLU* 1.3 61.5 + - + +
388A MET* 3.4 3.8 + - - +
389A ALA* 3.1 20.8 + - - +
607A PHE* 3.4 31.1 - - + -
615A MET* 4.4 0.5 - - - +
626A LEU* 3.5 35.8 - - + +
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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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383A ASP* 3.2 26.1 + - + +
385A GLU* 1.3 74.3 - - - +
387A TRP* 1.3 61.0 + - + +
389A ALA* 3.0 6.4 + - - +
390A GLY 3.0 22.2 + - - -
562A PHE* 3.1 38.7 - - + +
563A LEU* 3.6 8.0 - - - +
566A LYS* 2.7 40.8 + - - +
568A ILE* 3.8 15.3 - - + -
626A LEU* 4.1 17.3 - - + -
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Residues in contact with TRP 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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375A MET* 3.5 26.4 - - + +
376A PHE* 3.8 16.6 - + + -
382A ALA* 4.1 10.4 - - + +
383A ASP 3.1 25.6 - - - +
384A ILE 3.4 5.6 + - - +
385A GLU 3.4 0.4 - - - -
386A GLU* 1.3 81.1 + - + +
388A MET* 1.3 58.6 + - - +
390A GLY* 3.4 1.9 + - - -
391A VAL* 3.1 26.6 + - - +
566A LYS* 4.3 14.6 - - + +
567A ARG 3.9 10.8 - - - -
568A ILE* 3.7 40.1 - - + +
571A SER* 3.2 33.9 - - - -
573A ILE* 3.6 23.8 - - + -
574A ALA* 3.9 15.2 - - - +
577A LEU* 3.6 18.9 - - + +
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Residues in contact with MET 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 ILE* 3.0 36.3 + - + +
385A GLU* 3.6 6.7 - - - +
386A GLU 3.2 0.2 - - - -
387A TRP* 1.3 76.1 - - - +
389A ALA* 1.3 62.0 + - - +
390A GLY 3.3 0.2 - - - -
391A VAL* 3.4 23.2 + - + +
392A ALA* 3.5 4.2 + - - +
577A LEU* 3.5 49.4 - - + +
581A TRP* 3.5 35.0 - - + -
603A LEU* 3.7 15.3 - - + -
607A PHE* 4.1 15.0 - - + -
612A TYR* 4.0 7.2 - - + -
615A MET* 3.8 23.2 - - + +
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Residues in contact with ALA 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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385A GLU 3.1 13.0 + - - +
386A GLU* 3.0 13.2 + - - +
388A MET* 1.3 77.0 - - - +
390A GLY* 1.3 63.1 + - - +
392A ALA* 3.0 15.5 + - - +
393A TRP* 3.1 12.3 + - - +
562A PHE* 4.2 2.2 - - + -
563A LEU* 4.4 2.0 - - - -
615A MET* 3.7 9.2 - - - -
625A VAL* 3.4 33.4 - - + +
626A LEU* 3.6 15.9 - - + -
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Residues in contact with GLY 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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386A GLU 3.0 10.3 + - - -
387A TRP 3.4 4.4 + - - -
388A MET 3.3 0.6 - - - -
389A ALA* 1.3 73.8 - - - +
391A VAL* 1.3 59.4 + - - +
392A ALA 3.0 1.8 - - - -
393A TRP* 3.2 5.1 + - - +
394A LEU* 2.8 42.0 + - - +
563A LEU* 3.6 20.2 - - - +
568A ILE* 4.2 8.5 - - - -
569A ILE* 4.8 3.8 - - - -
574A ALA* 5.5 0.4 - - - -
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Residues in contact with VAL 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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387A TRP 3.1 17.9 + - - +
388A MET* 3.5 28.5 - - + +
389A ALA 3.2 0.4 - - - -
390A GLY* 1.3 76.4 - - - +
392A ALA* 1.3 56.9 + - - +
394A LEU* 4.0 9.1 - - - +
395A HIS* 3.2 26.0 + - - +
574A ALA 3.8 20.0 - - - +
577A LEU* 3.9 5.4 - - + +
578A MET* 3.5 34.8 - - + +
581A TRP* 5.2 2.2 - - + -
582A TYR* 4.5 1.8 - - + -
612A TYR* 3.3 23.0 + - + +
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Residues in contact with ALA 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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388A MET 3.5 4.6 + - - +
389A ALA 3.0 13.4 + - - +
391A VAL* 1.3 79.4 - - - +
393A TRP* 1.3 65.7 + - - +
395A HIS* 3.2 3.9 + - - +
396A CYS* 3.0 29.6 + - - -
612A TYR* 4.5 6.7 - - + -
615A MET* 4.1 12.8 - - + -
616A LYS* 3.5 39.4 - - + +
619A VAL* 4.6 2.9 - - + -
625A VAL* 4.9 0.4 - - + -
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Residues in contact with TRP 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 ALA 3.1 8.6 + - - +
390A GLY* 3.2 5.4 + - - +
392A ALA* 1.3 79.0 - - - +
394A LEU* 1.3 74.7 + - + +
396A CYS* 3.1 16.6 + - - +
397A LEU* 3.3 27.4 + - + +
430A SER 5.4 1.1 - - - -
431A GLY* 5.2 2.7 - - - -
434A THR* 3.9 18.6 - - + -
553A LEU* 3.2 55.0 + - + +
556A CYS* 3.4 26.2 - - - -
557A LEU* 3.7 26.8 - - + +
563A LEU* 4.4 11.2 - - + -
569A ILE* 3.5 45.1 - - + -
619A VAL* 4.3 5.5 - - + +
625A VAL* 4.7 3.1 - - + -
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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 GLY 2.8 26.3 + - - +
391A VAL* 4.1 6.7 - - - +
393A TRP* 1.3 93.3 - - + +
395A HIS* 1.3 60.3 + - - +
397A LEU* 3.2 27.4 - - + +
401A MET* 3.2 22.5 - - + +
434A THR* 4.8 2.9 - - + +
435A LEU* 5.5 6.3 - - + -
438A ALA* 5.9 0.4 - - + -
569A ILE* 3.1 33.2 - - - +
571A SER 5.3 0.4 - - - +
574A ALA* 3.9 29.6 - - + +
575A LEU* 4.0 23.6 - - + -
578A MET* 4.4 9.2 - - - -
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Residues in contact with HIS 395 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131 GLN 4.8 4.0 - - - -
141 ILE* 3.5 22.5 + - - +
391A VAL 3.2 19.2 + - - +
392A ALA 3.2 5.9 + - - +
394A LEU* 1.3 74.6 - - - +
396A CYS* 1.3 57.2 + - - +
397A LEU 3.2 3.4 - - - -
398A LEU 3.4 16.8 - - - +
400A LYS* 4.6 14.3 - - - -
401A MET* 3.8 7.8 + - + -
402A ASP* 2.9 38.7 + - + -
578A MET* 4.5 4.0 - - - -
582A TYR* 3.3 31.3 - + - +
616A LYS* 2.9 31.2 + - - +
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Residues in contact with CYS 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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141 ILE* 3.4 28.0 - - + -
151 PHE* 3.5 22.0 - - - -
392A ALA 3.0 22.2 + - - +
393A TRP 3.1 8.0 + - - +
395A HIS* 1.3 76.6 - - - +
397A LEU* 1.3 60.1 + - - +
398A LEU 3.6 0.4 - - - -
550A LYS* 3.6 1.6 + - - -
552A TYR* 2.7 30.3 + - + -
553A LEU* 3.4 7.8 - - + +
616A LYS* 4.1 10.8 - - - -
619A VAL* 3.6 29.6 - - + -
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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