Contacts of the helix formed by residues 383 - 396 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376B PHE* 4.0 2.0 - - - -
381B SER 3.9 2.4 + - - +
382B ALA* 1.3 70.7 - - - +
384B ILE* 1.3 67.3 + - - +
385B GLU* 2.9 42.7 + - - +
386B GLU* 3.2 33.3 + - - +
387B TRP* 3.1 19.3 - - - +
566B LYS* 4.6 5.1 - - - +
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Residues in contact with ILE 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B PHE* 3.4 41.4 - - + -
382B ALA 3.7 1.8 + - - -
383B ASP* 1.3 74.1 + - - +
385B GLU* 1.3 64.1 + - + +
387B TRP* 3.4 0.8 + - - -
388B MET* 3.0 40.6 + - + +
577B LEU* 4.3 21.3 - - + -
599B TRP* 5.0 3.8 - - + -
602B ARG* 4.6 15.0 - - + +
603B LEU* 4.9 11.2 - - + -
606B GLU* 4.6 20.9 - - + +
607B PHE* 4.1 16.4 - - + -
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Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B ASP* 2.9 21.0 + - - +
384B ILE* 1.3 82.4 - - + +
386B GLU* 1.3 60.5 + - - +
388B MET* 3.4 3.8 + - - +
389B ALA* 3.1 21.0 + - - +
607B PHE* 3.4 31.5 - - + -
611B VAL* 5.9 0.9 - - - +
615B MET* 4.4 0.9 - - - +
626B LEU* 3.5 34.4 - - + +
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B ASP* 3.2 27.2 + - + +
385B GLU* 1.3 74.5 - - - +
387B TRP* 1.3 60.0 - - - +
389B ALA* 3.0 6.5 + - - +
390B GLY 3.0 22.0 + - - -
562B PHE* 3.1 38.3 - - + +
563B LEU* 3.6 8.3 - - - +
566B LYS* 2.7 40.4 + - - +
568B ILE* 3.8 15.4 - - + +
626B LEU* 4.1 16.8 - - + -
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Residues in contact with TRP 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B MET* 3.5 26.9 - - + +
376B PHE* 3.8 14.4 - + + -
382B ALA* 4.1 10.0 - - + +
383B ASP 3.1 26.4 + - - +
384B ILE 3.4 5.1 + - - +
385B GLU 3.4 0.2 - - - -
386B GLU* 1.3 81.2 + - + +
388B MET* 1.3 59.9 + - - +
390B GLY* 3.4 1.6 + - - -
391B VAL* 3.1 26.4 + - - +
566B LYS* 4.3 14.3 - - + +
567B ARG 3.9 10.1 - - - -
568B ILE* 3.7 40.5 - - + +
571B SER* 3.2 33.7 - - - -
573B ILE* 3.5 22.7 - - + -
574B ALA* 3.9 14.5 - - - +
577B LEU* 3.6 19.4 - - + +
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Residues in contact with MET 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B ILE* 3.0 36.1 + - + +
385B GLU* 3.6 7.0 - - - +
387B TRP* 1.3 77.2 - - - +
389B ALA* 1.3 60.7 + - - +
391B VAL* 3.4 23.4 + - + +
392B ALA* 3.5 4.9 + - - +
577B LEU* 3.5 48.9 - - + +
581B TRP* 3.5 35.9 - - + -
603B LEU* 3.7 14.8 - - + -
607B PHE* 4.2 15.0 - - + -
612B TYR* 4.0 6.2 - - - -
615B MET* 3.8 23.6 - - + +
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B GLU 3.1 13.0 + - - +
386B GLU* 3.0 14.1 + - - +
388B MET* 1.3 77.2 - - - +
390B GLY* 1.3 62.4 + - - +
392B ALA* 3.0 15.1 + - - +
393B TRP* 3.1 13.0 + - - +
562B PHE* 4.2 2.2 - - + -
563B LEU* 4.4 1.6 - - - -
615B MET* 3.7 9.2 - - - -
625B VAL* 3.4 34.3 - - + +
626B LEU* 3.6 15.9 - - + -
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Residues in contact with GLY 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B GLU 3.0 10.1 + - - -
387B TRP 3.4 5.1 + - - -
388B MET 3.3 0.4 - - - -
389B ALA* 1.3 74.2 - - - +
391B VAL* 1.3 58.8 + - - +
392B ALA 3.0 2.0 - - - -
393B TRP* 3.2 5.5 + - - +
394B LEU* 2.8 41.9 + - - +
563B LEU* 3.6 19.7 - - - +
568B ILE* 4.2 9.2 - - - -
569B ILE* 4.8 4.3 - - - -
574B ALA* 5.6 0.2 - - - -
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Residues in contact with VAL 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B TRP 3.1 17.7 - - - +
388B MET* 3.4 29.2 - - + +
389B ALA 3.2 0.2 - - - -
390B GLY* 1.3 76.2 - - - +
392B ALA* 1.3 57.3 + - - +
394B LEU* 4.0 8.7 - - - +
395B HIS* 3.2 26.0 + - - +
574B ALA* 3.8 19.9 - - - +
577B LEU* 3.9 5.2 - - + +
578B MET* 3.5 34.6 - - + +
581B TRP* 5.2 2.7 - - + -
582B TYR* 4.5 2.0 - - + -
612B TYR* 3.3 22.1 + - + +
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Residues in contact with ALA 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B MET 3.5 4.6 + - - +
389B ALA 3.0 13.6 + - - +
390B GLY 3.0 0.6 - - - -
391B VAL* 1.3 78.4 - - - +
393B TRP* 1.3 65.0 + - - +
395B HIS* 3.2 2.9 + - - +
396B CYS* 3.1 29.9 + - - -
612B TYR* 4.4 6.5 + - + -
615B MET* 4.1 13.0 - - + -
616B LYS* 3.5 39.9 - - + +
619B VAL* 4.6 2.7 - - + -
625B VAL* 4.9 0.2 - - + -
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Residues in contact with TRP 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B ALA 3.1 8.6 + - - +
390B GLY* 3.7 5.4 - - - +
392B ALA* 1.3 78.8 - - - +
394B LEU* 1.3 73.4 + - + +
396B CYS* 3.1 16.3 + - - +
397B LEU* 3.3 27.6 + - + +
430B SER 5.3 1.3 - - - -
431B GLY* 5.2 2.5 - - - -
434B THR* 3.9 17.9 - - + -
553B LEU* 3.2 56.3 + - + +
556B CYS* 3.4 26.0 - - - -
557B LEU* 3.7 26.5 - - + +
563B LEU* 4.4 11.2 - - + -
569B ILE* 3.5 45.1 - - + -
619B VAL* 4.3 5.1 - - + +
625B VAL* 4.7 3.4 - - + -
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B GLY 2.8 21.8 + - - +
391B VAL* 4.1 6.1 - - - +
393B TRP* 1.3 92.6 - - + +
395B HIS* 1.3 61.0 + - - +
397B LEU* 3.2 26.7 - - + +
401B MET* 3.2 22.9 - - + +
434B THR* 4.8 2.9 - - + +
435B LEU* 5.5 5.8 - - + -
438B ALA* 5.9 0.7 - - + -
569B ILE* 3.1 32.8 - - - +
571B SER 5.3 0.2 - - - +
574B ALA* 3.9 30.5 - - + -
575B LEU* 4.0 24.0 - - + -
578B MET* 4.4 9.0 - - - -
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Residues in contact with HIS 395 (chain B).
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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132 GLN 6.0 0.4 - - - -
142 ILE* 4.6 18.4 - - + +
391B VAL 3.2 19.0 + - - +
392B ALA 3.2 6.3 + - - +
394B LEU* 1.3 75.2 - - - +
396B CYS* 1.3 56.8 + - - +
397B LEU 3.2 2.9 - - - -
398B LEU 3.4 16.6 - - - +
400B LYS* 4.6 15.6 - - - -
401B MET* 3.9 8.0 + - + -
402B ASP* 2.9 37.8 + - + -
578B MET* 4.5 4.0 - - - -
582B TYR* 3.3 32.2 - + - +
616B LYS* 2.9 30.3 + - - +
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Residues in contact with CYS 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112 GLU* 6.2 0.2 - - - -
142 ILE* 4.7 18.2 - - + -
152 PHE* 5.6 1.6 - - - -
392B ALA 3.1 21.4 + - - +
393B TRP 3.1 8.7 + - - +
395B HIS* 1.3 77.2 - - - +
397B LEU* 1.3 59.0 + - - +
398B LEU 3.6 0.7 - - - -
550B LYS* 3.6 2.2 + - - -
552B TYR* 2.7 32.7 + - + +
553B LEU* 3.4 7.6 - - + +
616B LYS* 4.1 27.6 - - - -
619B VAL* 3.6 36.1 - - + -
620B ALA 5.6 0.4 - - - -
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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