Contacts of the helix formed by residues 383 - 396 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376J PHE* 4.0 1.8 - - - -
381J SER 3.9 2.6 + - - +
382J ALA* 1.3 71.2 - - - +
384J ILE* 1.3 66.2 + - - +
385J GLU* 2.9 43.4 + - - +
386J GLU* 3.2 34.9 + - - +
387J TRP* 3.1 19.3 - - - +
566J LYS* 4.6 4.2 - - - +
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Residues in contact with ILE 384 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376J PHE* 3.4 42.6 - - + -
382J ALA 3.7 2.0 + - - -
383J ASP* 1.3 74.4 + - - +
385J GLU* 1.3 65.4 + - + +
387J TRP* 3.4 1.2 + - - -
388J MET* 3.0 39.0 + - + +
577J LEU* 4.3 20.9 - - + -
599J TRP* 5.1 3.4 - - + -
602J ARG* 4.6 16.8 - - + +
603J LEU* 4.9 10.1 - - + -
606J GLU* 4.6 19.5 - - + +
607J PHE* 4.1 16.2 - - + -
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Residues in contact with GLU 385 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383J ASP* 2.9 20.9 + - - +
384J ILE* 1.3 81.6 - - + +
386J GLU* 1.3 60.6 + - - +
388J MET* 3.4 3.3 + - - +
389J ALA* 3.1 21.1 + - - +
607J PHE* 3.4 31.5 - - + -
611J VAL* 5.9 1.0 - - - +
615J MET* 4.4 0.7 - - - +
626J LEU* 3.5 36.0 - - + +
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Residues in contact with GLU 386 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383J ASP* 3.2 26.3 + - + +
385J GLU* 1.3 74.1 - - + +
387J TRP* 1.3 61.3 + - + +
389J ALA* 3.0 6.5 + - - +
390J GLY 3.0 22.3 + - - -
562J PHE* 3.1 39.3 - - + +
563J LEU* 3.6 8.1 - - - +
566J LYS* 2.7 40.5 + - - +
568J ILE* 3.8 15.2 - - + +
626J LEU* 4.1 16.2 - - + -
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Residues in contact with TRP 387 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375J MET* 3.5 25.4 - - + +
376J PHE* 3.8 16.2 - + + -
382J ALA* 4.1 9.6 - - + +
383J ASP 3.1 26.5 - - - +
384J ILE 3.4 6.0 + - - +
385J GLU 3.4 0.4 - - - -
386J GLU* 1.3 81.6 + - + +
388J MET* 1.3 60.5 + - - +
390J GLY* 3.4 1.9 + - - -
391J VAL* 3.1 26.6 + - - +
566J LYS* 4.3 14.2 - - + +
567J ARG 3.9 10.1 - - - -
568J ILE* 3.7 37.9 - - + +
571J SER* 3.2 34.1 - - - -
573J ILE* 3.6 22.7 - - + -
574J ALA* 3.9 14.8 - - - +
577J LEU* 3.6 18.7 - - + +
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Residues in contact with MET 388 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384J ILE* 3.0 35.7 + - + +
385J GLU* 3.6 7.0 - - - +
386J GLU 3.2 0.2 - - - -
387J TRP* 1.3 76.5 - - - +
389J ALA* 1.3 61.4 + - - +
391J VAL* 3.4 23.0 + - + +
392J ALA* 3.5 4.5 + - - +
577J LEU* 3.5 49.6 - - + +
581J TRP* 3.5 34.5 - - + -
603J LEU* 3.7 15.7 - - + -
607J PHE* 4.2 15.9 - - + -
612J TYR* 4.0 5.8 - - + -
615J MET* 3.8 23.3 - - + +
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Residues in contact with ALA 389 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385J GLU 3.1 13.6 + - - +
386J GLU* 3.0 14.3 + - - +
388J MET* 1.3 76.5 - - - +
390J GLY* 1.3 62.0 + - - +
392J ALA* 3.0 16.4 + - - +
393J TRP* 3.1 12.6 + - - +
562J PHE* 4.2 2.9 - - + -
563J LEU* 4.4 1.1 - - - -
615J MET* 3.7 9.4 - - - -
625J VAL* 3.4 33.8 - - + +
626J LEU* 3.6 16.2 - - + -
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Residues in contact with GLY 390 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386J GLU 3.0 10.7 + - - -
387J TRP 3.4 4.2 + - - -
388J MET 3.3 0.4 - - - -
389J ALA* 1.3 73.9 - - - +
391J VAL* 1.3 58.7 + - - +
392J ALA 3.0 1.8 - - - -
393J TRP* 3.2 5.7 + - - +
394J LEU* 2.8 42.2 + - - +
563J LEU* 3.6 19.7 - - - +
568J ILE* 4.2 8.3 - - - -
569J ILE* 4.8 4.7 - - - -
574J ALA* 5.6 0.4 - - - -
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Residues in contact with VAL 391 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387J TRP 3.1 18.1 + - - +
388J MET* 3.5 28.7 - - + +
389J ALA 3.2 0.4 - - - -
390J GLY* 1.3 76.0 - - - +
392J ALA* 1.3 56.4 + - - +
394J LEU* 4.1 8.5 - - - +
395J HIS* 3.2 26.2 + - - +
574J ALA 3.8 20.4 - - - +
577J LEU* 3.9 6.1 - - + +
578J MET* 3.5 33.4 - - + +
581J TRP* 5.2 2.2 - - + -
582J TYR* 4.5 2.0 - - + -
612J TYR* 3.3 22.7 + - + +
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Residues in contact with ALA 392 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388J MET 3.5 4.8 + - - +
389J ALA 3.0 13.4 + - - +
390J GLY 3.0 0.4 - - - -
391J VAL* 1.3 78.1 - - - +
393J TRP* 1.3 66.2 + - - +
395J HIS* 3.2 3.5 + - - +
396J CYS* 3.1 29.7 + - - -
612J TYR* 4.4 6.5 + - + -
615J MET* 4.1 13.0 - - + -
616J LYS* 3.5 39.9 - - + +
619J VAL* 4.6 2.7 - - + -
625J VAL* 4.9 0.4 - - + -
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Residues in contact with TRP 393 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389J ALA 3.1 9.0 + - - +
390J GLY* 3.2 5.8 + - - +
392J ALA* 1.3 78.4 - - - +
394J LEU* 1.3 74.1 + - + +
396J CYS* 3.1 16.7 + - - +
397J LEU* 3.3 26.9 + - + +
430J SER 5.4 0.9 - - - -
431J GLY* 5.2 3.1 - - - -
434J THR* 3.9 17.7 - - + -
553J LEU* 3.2 56.4 + - + +
556J CYS* 3.4 26.5 - - - -
557J LEU* 3.7 26.3 - - + +
563J LEU* 4.4 11.2 - - + -
569J ILE* 3.5 45.1 - - + -
619J VAL* 4.3 6.0 - - + +
625J VAL* 4.7 3.4 - - + -
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Residues in contact with LEU 394 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390J GLY 2.8 22.3 + - - +
391J VAL* 4.1 5.6 - - - +
393J TRP* 1.3 92.7 - - + +
395J HIS* 1.3 61.2 + - - +
397J LEU* 3.2 26.4 - - + +
401J MET* 3.2 22.5 - - + +
434J THR* 4.8 2.9 - - + +
435J LEU* 5.5 6.5 - - + -
438J ALA* 5.9 0.2 - - + -
569J ILE* 3.1 33.2 - - - +
571J SER 5.3 0.2 - - - +
574J ALA* 3.9 30.7 - - + +
575J LEU* 4.0 23.3 - - + -
578J MET* 4.4 9.6 - - - -
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Residues in contact with HIS 395 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391J VAL 3.2 19.0 + - - +
392J ALA 3.2 6.3 + - - +
394J LEU* 1.3 74.1 - - - +
396J CYS* 1.3 58.2 + - - +
397J LEU 3.2 3.1 - - - -
398J LEU 3.4 16.3 - - - +
400J LYS* 4.6 15.4 - - - -
401J MET* 3.8 7.7 + - + -
402J ASP* 2.9 37.4 + - + -
578J MET* 4.5 4.2 - - - -
582J TYR* 3.3 30.4 - + - +
616J LYS* 2.9 31.0 + - - +
13U GLN 5.7 2.2 - - - -
14U ILE* 4.2 16.1 + - - +
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Residues in contact with CYS 396 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392J ALA 3.1 20.9 + - - +
393J TRP 3.1 9.4 + - - +
395J HIS* 1.3 76.6 - - - +
397J LEU* 1.3 58.6 + - - +
398J LEU 3.6 0.7 - - - -
550J LYS* 3.6 1.2 + - - -
552J TYR* 2.7 30.8 + - + +
553J LEU* 3.4 8.2 - - + +
616J LYS* 4.1 28.3 - - - -
619J VAL* 3.6 36.6 - - + -
14U ILE* 3.8 11.7 - - + -
15U PHE* 4.5 14.6 - - - -
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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