Contacts of the helix formed by residues 383 - 396 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376I PHE* 4.0 1.6 - - - -
381I SER 3.9 2.0 + - - +
382I ALA* 1.3 70.9 - - - +
384I ILE* 1.3 67.0 + - - +
385I GLU* 2.9 43.7 + - - +
386I GLU* 3.2 34.1 + - - +
387I TRP* 3.1 19.0 - - - -
566I LYS* 4.6 4.6 - - - +
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Residues in contact with ILE 384 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376I PHE* 3.4 41.1 - - + -
382I ALA 3.7 2.0 + - - -
383I ASP* 1.3 74.3 + - - +
385I GLU* 1.3 66.6 + - + +
387I TRP* 3.4 1.2 + - - -
388I MET* 3.0 38.8 + - + +
577I LEU* 4.3 21.1 - - + -
599I TRP* 5.1 4.0 - - + -
602I ARG* 4.6 15.9 - - + +
603I LEU* 4.9 11.2 - - + -
606I GLU* 4.6 19.5 - - + +
607I PHE* 4.1 16.6 - - + -
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Residues in contact with GLU 385 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383I ASP* 2.9 20.3 + - - +
384I ILE* 1.3 82.3 - - + +
386I GLU* 1.3 61.1 + - - +
388I MET* 3.4 3.8 + - - +
389I ALA* 3.1 21.3 + - - +
607I PHE* 3.4 31.5 - - + -
611I VAL* 5.9 1.4 - - - +
615I MET* 4.4 0.7 - - - +
626I LEU* 3.5 34.6 - - + +
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Residues in contact with GLU 386 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383I ASP* 3.2 26.6 + - + +
385I GLU* 1.3 75.1 - - + +
387I TRP* 1.3 60.5 + - + +
389I ALA* 3.0 6.3 + - - +
390I GLY 3.0 22.3 + - - -
562I PHE* 3.1 38.4 - - + +
563I LEU* 3.6 8.0 - - - +
566I LYS* 2.7 39.6 + - - +
568I ILE* 3.8 15.4 - - + +
626I LEU* 4.1 17.0 - - + -
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Residues in contact with TRP 387 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375I MET* 3.5 25.0 - - + +
376I PHE* 3.8 18.4 - + + -
382I ALA* 4.1 10.0 - - + +
383I ASP 3.1 25.6 - - - +
384I ILE 3.4 4.4 + - - +
385I GLU 3.4 0.4 - - - -
386I GLU* 1.3 81.1 + - + +
388I MET* 1.3 58.4 + - - +
390I GLY* 3.4 1.9 + - - -
391I VAL* 3.1 26.7 + - - +
566I LYS* 4.3 14.2 - - + +
567I ARG 3.9 9.6 - - - -
568I ILE* 3.7 40.1 - - + +
571I SER* 3.2 33.9 - - - -
573I ILE* 3.6 23.3 - - + -
574I ALA* 3.9 14.6 - - - +
577I LEU* 3.6 18.9 - - + +
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Residues in contact with MET 388 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384I ILE* 3.0 36.4 + - + +
385I GLU* 3.6 6.5 - - - +
387I TRP* 1.3 75.7 - - - +
389I ALA* 1.3 62.7 + - - +
391I VAL* 3.4 23.8 + - + +
392I ALA* 3.5 4.3 + - - +
577I LEU* 3.5 49.1 - - + +
581I TRP* 3.5 34.8 - - + -
603I LEU* 3.7 15.7 - - + -
607I PHE* 4.2 15.3 - - + -
612I TYR* 4.0 6.1 - - + -
615I MET* 3.8 24.0 - - + +
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Residues in contact with ALA 389 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385I GLU 3.1 13.0 + - - +
386I GLU* 3.0 14.0 + - - +
388I MET* 1.3 76.7 - - - +
390I GLY* 1.3 61.7 + - - +
392I ALA* 3.0 16.0 + - - +
393I TRP* 3.1 13.0 + - - +
562I PHE* 4.2 2.5 - - + -
563I LEU* 4.4 1.8 - - - -
615I MET* 3.7 9.6 - - - -
625I VAL* 3.4 33.5 - - + +
626I LEU* 3.6 17.0 - - + -
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Residues in contact with GLY 390 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386I GLU 3.0 10.0 + - - -
387I TRP 3.4 4.6 + - - -
388I MET 3.3 0.4 - - - -
389I ALA* 1.3 74.1 - - - +
391I VAL* 1.3 58.3 + - - +
392I ALA 3.0 2.0 - - - -
393I TRP* 3.7 4.8 - - - +
394I LEU* 2.8 41.8 + - - +
563I LEU* 3.6 20.4 - - - +
568I ILE* 4.2 8.5 - - - -
569I ILE* 4.8 4.7 - - - -
574I ALA* 5.6 0.2 - - - -
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Residues in contact with VAL 391 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387I TRP 3.1 17.9 - - - +
388I MET* 3.5 28.9 - - + +
389I ALA 3.2 0.2 - - - -
390I GLY* 1.3 76.7 - - - +
392I ALA* 1.3 56.0 + - - +
394I LEU* 4.0 8.7 - - - +
395I HIS* 3.2 26.3 + - - +
574I ALA 3.8 20.6 - - - +
577I LEU* 3.9 5.6 - - + +
578I MET* 3.5 34.5 - - + +
581I TRP* 5.2 2.2 - - + -
582I TYR* 4.5 2.0 - - + -
612I TYR* 3.3 23.0 + - + +
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Residues in contact with ALA 392 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388I MET 3.5 5.2 + - - +
389I ALA 3.0 13.2 + - - +
390I GLY 3.0 0.8 - - - -
391I VAL* 1.3 78.7 - - - +
393I TRP* 1.3 64.9 + - - +
395I HIS* 3.2 3.4 + - - +
396I CYS* 3.1 30.0 + - - -
612I TYR* 4.4 6.3 + - + -
615I MET* 4.1 12.8 - - + -
616I LYS* 3.5 39.0 - - + +
619I VAL* 4.6 3.1 - - + -
625I VAL* 4.9 0.4 - - + -
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Residues in contact with TRP 393 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389I ALA 3.1 8.4 + - - +
390I GLY* 3.8 5.8 - - - +
392I ALA* 1.3 79.0 - - - +
394I LEU* 1.3 74.1 + - + +
396I CYS* 3.1 17.7 + - - +
397I LEU* 3.3 26.1 + - + +
430I SER 5.3 0.9 - - - -
431I GLY* 5.2 2.9 - - - -
434I THR* 3.9 17.7 - - + -
553I LEU* 3.2 55.6 + - + +
556I CYS* 3.4 26.0 - - - -
557I LEU* 3.7 27.2 - - + +
563I LEU* 4.4 10.8 - - + -
569I ILE* 3.5 45.3 - - + -
619I VAL* 4.3 5.6 - - + +
625I VAL* 4.7 3.6 - - + -
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Residues in contact with LEU 394 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390I GLY 2.8 21.8 + - - +
391I VAL* 4.1 6.3 - - - +
393I TRP* 1.3 92.8 - - + +
395I HIS* 1.3 60.2 + - - +
397I LEU* 3.2 27.0 - - + +
401I MET* 3.2 22.2 - - + +
434I THR* 4.8 2.9 - - + +
435I LEU* 5.5 5.8 - - + -
438I ALA* 5.8 0.9 - - + -
569I ILE* 3.1 32.8 - - - +
571I SER 5.3 0.2 - - - +
574I ALA* 3.9 29.8 - - + -
575I LEU* 4.0 23.8 - - + -
578I MET* 4.4 9.4 - - - -
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Residues in contact with HIS 395 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139 GLN 6.0 0.2 - - - -
149 ILE* 3.9 21.3 - - + +
391I VAL 3.2 19.7 + - - +
392I ALA 3.2 6.9 + - - +
394I LEU* 1.3 74.8 - - - +
396I CYS* 1.3 57.0 + - - +
397I LEU 3.2 2.9 - - - -
398I LEU 3.4 17.0 - - - +
400I LYS* 4.6 15.2 - - - -
401I MET* 3.8 6.9 + - - -
402I ASP* 2.9 38.0 + - + -
578I MET* 4.5 4.5 - - - -
582I TYR* 3.4 30.9 - + - +
616I LYS* 2.9 29.9 + - - +
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Residues in contact with CYS 396 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149 ILE* 4.1 9.9 - - + -
159 PHE* 3.8 25.8 - - - -
392I ALA 3.1 21.2 + - - +
393I TRP 3.1 8.6 + - - +
395I HIS* 1.3 76.6 - - - +
397I LEU* 1.3 59.2 + - - +
398I LEU 3.6 0.9 - - - -
550I LYS* 3.6 2.3 + - - -
552I TYR* 2.7 29.3 + - + +
553I LEU* 3.4 8.0 - - + +
616I LYS* 4.1 20.2 - - - -
619I VAL* 3.6 34.1 - - + -
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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