Contacts of the helix formed by residues 383 - 396 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376D PHE* 4.0 2.0 - - - -
381D SER 3.9 2.2 + - - +
382D ALA* 1.3 70.1 - - - +
384D ILE* 1.3 66.6 + - - +
385D GLU* 2.9 43.9 + - - +
386D GLU* 3.2 34.2 + - - +
387D TRP* 3.1 18.7 - - - -
566D LYS* 4.6 5.0 - - - +
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Residues in contact with ILE 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D PHE* 3.4 42.3 - - + -
382D ALA 3.7 2.0 + - - -
383D ASP* 1.3 74.0 + - - +
385D GLU* 1.3 65.8 + - + +
387D TRP* 3.4 0.6 + - - -
388D MET* 3.0 40.2 + - + +
577D LEU* 4.3 21.5 - - + -
599D TRP* 5.0 3.6 - - + -
602D ARG* 4.6 14.8 - - + +
603D LEU* 4.9 10.1 - - + -
606D GLU* 4.6 20.4 - - + +
607D PHE* 4.1 16.8 - - + -
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Residues in contact with GLU 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ASP* 2.9 21.3 + - - +
384D ILE* 1.3 81.7 - - + +
386D GLU* 1.3 60.5 - - + +
388D MET* 3.4 3.8 + - - +
389D ALA* 3.1 21.7 + - - +
607D PHE* 3.4 31.3 - - + -
611D VAL* 5.9 1.2 - - - +
615D MET* 4.4 0.5 - - - +
626D LEU* 3.5 34.5 - - + +
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Residues in contact with GLU 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ASP* 3.2 26.8 + - + +
385D GLU* 1.3 75.9 - - + +
387D TRP* 1.3 59.5 + - + +
389D ALA* 3.0 6.0 + - - +
390D GLY 3.0 22.2 + - - -
562D PHE* 3.1 38.2 - - + +
563D LEU* 3.6 8.3 - - - +
566D LYS* 2.7 39.9 + - - +
568D ILE* 3.8 15.6 - - + +
626D LEU* 4.1 16.8 - - + -
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Residues in contact with TRP 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D MET* 3.5 24.6 - - + +
376D PHE* 3.8 16.8 - + + -
382D ALA* 4.1 10.4 - - + +
383D ASP 3.1 26.3 - - - +
384D ILE 3.4 4.9 + - - +
385D GLU 3.4 0.4 - - - -
386D GLU* 1.3 82.4 + - + +
388D MET* 1.3 58.8 + - - +
390D GLY* 3.4 2.1 + - - -
391D VAL* 3.1 26.4 + - - +
566D LYS* 4.3 14.3 - - + +
567D ARG 3.9 10.3 - - - -
568D ILE* 3.7 38.1 - - + +
571D SER* 3.2 34.1 - - - -
573D ILE* 3.6 22.4 - - + -
574D ALA* 3.9 14.7 - - - +
577D LEU* 3.6 18.6 - - + +
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Residues in contact with MET 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D ILE* 3.0 35.1 + - + +
385D GLU* 3.6 7.2 - - - +
386D GLU 3.2 0.2 - - - -
387D TRP* 1.3 76.5 - - - +
389D ALA* 1.3 62.4 + - - +
391D VAL* 3.4 23.2 + - + +
392D ALA 3.5 3.6 + - - -
577D LEU* 3.5 49.1 - - + +
581D TRP* 3.5 34.3 - - + -
603D LEU* 3.7 15.0 - - + -
607D PHE* 4.2 15.5 - - + -
612D TYR* 4.0 6.5 - - - -
615D MET* 3.8 24.0 - - + +
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Residues in contact with ALA 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D GLU 3.1 12.6 + - - +
386D GLU* 3.0 13.0 + - - +
388D MET* 1.3 77.5 - - - +
390D GLY* 1.3 62.2 + - - +
392D ALA* 3.0 15.6 + - - +
393D TRP* 3.1 13.0 + - - +
562D PHE* 4.2 2.5 - - + -
563D LEU* 4.4 1.6 - - - -
615D MET* 3.7 10.3 - - - -
625D VAL* 3.4 33.4 - - + +
626D LEU* 3.6 17.0 - - + -
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Residues in contact with GLY 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D GLU 3.0 10.5 + - - -
387D TRP 3.4 4.2 + - - -
388D MET 3.3 0.4 - - - -
389D ALA* 1.3 72.7 - - - +
391D VAL* 1.3 57.9 + - - +
392D ALA 3.0 1.8 - - - -
393D TRP* 3.2 5.7 + - - +
394D LEU* 2.8 41.9 + - - +
563D LEU* 3.6 20.1 - - - +
568D ILE* 4.2 8.3 - - - -
569D ILE* 4.8 4.5 - - - -
574D ALA* 5.6 0.7 - - - -
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Residues in contact with VAL 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D TRP 3.1 18.8 + - - +
388D MET* 3.4 28.3 - - + +
389D ALA 3.2 0.6 - - - -
390D GLY* 1.3 76.2 - - - +
392D ALA* 1.3 57.1 + - - +
394D LEU* 4.0 8.1 - - - +
395D HIS* 3.2 26.2 + - - +
574D ALA* 3.8 20.4 - - - +
577D LEU* 3.9 5.4 - - + +
578D MET* 3.5 34.3 - - + +
581D TRP* 5.2 2.2 - - + -
582D TYR* 4.5 1.8 - - + -
612D TYR* 3.3 23.4 + - + +
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Residues in contact with ALA 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D MET 3.5 5.6 + - - +
389D ALA 3.0 13.4 + - - +
390D GLY 3.0 0.2 - - - -
391D VAL* 1.3 78.9 - - - +
393D TRP* 1.3 65.8 + - - +
395D HIS* 3.2 3.3 + - - +
396D CYS* 3.1 29.7 + - - -
612D TYR* 4.4 6.3 + - + -
615D MET* 4.1 13.0 - - + -
616D LYS* 3.5 39.9 - - + +
619D VAL* 4.6 2.9 - - + -
625D VAL* 4.9 0.2 - - + -
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Residues in contact with TRP 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D ALA 3.1 8.2 + - - +
390D GLY* 3.7 5.6 - - - +
392D ALA* 1.3 78.4 - - - +
394D LEU* 1.3 73.9 + - + +
396D CYS* 3.1 16.7 + - - +
397D LEU* 3.3 26.1 + - + +
430D SER 5.3 1.6 - - - -
431D GLY* 5.2 2.7 - - - -
434D THR* 3.9 18.4 - - + -
553D LEU* 3.2 53.7 + - + +
556D CYS* 3.4 26.5 - - - -
557D LEU* 3.7 27.2 - - + +
563D LEU* 4.4 11.2 - - + -
569D ILE* 3.5 43.7 - - + -
619D VAL* 4.3 6.0 - - + +
625D VAL* 4.7 3.1 - - + -
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Residues in contact with LEU 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D GLY 2.8 21.6 + - - +
391D VAL* 4.1 6.5 - - - +
393D TRP* 1.3 93.0 - - + +
395D HIS* 1.3 60.9 + - - +
397D LEU* 3.2 26.4 - - + +
401D MET* 3.2 22.2 - - + +
434D THR* 4.8 2.9 - - + +
435D LEU* 5.5 6.5 - - + -
438D ALA* 5.8 0.9 - - + -
569D ILE* 3.1 33.4 - - - +
571D SER 5.3 0.4 - - - +
574D ALA* 3.9 31.0 - - + -
575D LEU* 4.0 23.3 - - + -
578D MET* 4.4 9.0 - - - -
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Residues in contact with HIS 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134 GLN 5.3 3.8 - - - -
144 ILE* 4.3 13.0 + - - +
391D VAL 3.2 19.0 + - - +
392D ALA 3.2 6.8 + - - +
394D LEU* 1.3 75.2 - - - +
396D CYS* 1.3 57.4 + - - +
397D LEU 3.2 2.5 - - - -
398D LEU 3.4 17.0 - - - +
400D LYS* 4.6 15.6 - - - -
401D MET* 3.9 8.0 + - + -
402D ASP* 2.9 37.4 + - + -
578D MET* 4.5 4.0 - - - -
582D TYR* 3.3 31.8 - + - +
616D LYS* 2.9 30.3 + - - +
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Residues in contact with CYS 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144 ILE* 3.4 24.1 - - + +
154 PHE* 4.6 6.5 - - - -
392D ALA 3.1 21.8 + - - +
393D TRP 3.1 9.1 + - - +
395D HIS* 1.3 76.6 - - - +
397D LEU* 1.3 59.0 + - - +
398D LEU 3.6 0.4 - - - -
550D LYS* 3.6 0.7 + - - -
552D TYR* 2.7 26.7 + - + -
553D LEU* 3.4 8.1 - - + +
616D LYS* 4.1 28.5 - - - -
619D VAL* 3.6 35.4 - - + -
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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