Contacts of the helix formed by residues 383 - 396 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376K PHE* 4.0 2.5 - - - -
381K SER 3.9 2.0 + - - +
382K ALA* 1.3 71.1 - - - +
384K ILE* 1.3 65.9 + - - +
385K GLU* 2.9 42.5 + - - +
386K GLU* 3.2 33.2 + - - +
387K TRP* 3.1 19.9 - - - +
566K LYS* 4.6 5.1 - - - +
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Residues in contact with ILE 384 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376K PHE* 3.4 42.0 - - + -
382K ALA 3.7 2.2 + - - -
383K ASP* 1.3 74.1 + - - +
385K GLU* 1.3 64.9 + - + +
387K TRP* 3.4 1.0 + - - -
388K MET* 3.0 40.4 + - + +
577K LEU* 4.3 20.4 - - + -
599K TRP* 5.0 4.0 - - + -
602K ARG* 4.6 19.3 - - + +
603K LEU* 4.9 11.2 - - + -
606K GLU* 4.6 15.7 - - + +
607K PHE* 4.1 16.4 - - + -
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Residues in contact with GLU 385 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383K ASP* 2.9 19.5 + - - +
384K ILE* 1.3 81.1 - - + +
386K GLU* 1.3 61.3 + - - +
388K MET* 3.4 4.2 + - - +
389K ALA* 3.1 20.8 + - - +
607K PHE* 3.4 32.3 - - + -
611K VAL* 5.9 1.0 - - - +
615K MET* 4.4 0.3 - - - +
626K LEU* 3.5 35.7 - - + +
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Residues in contact with GLU 386 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383K ASP* 3.2 27.0 + - + +
385K GLU* 1.3 74.8 - - - +
387K TRP* 1.3 60.8 + - + +
389K ALA* 3.0 7.0 + - - +
390K GLY 3.0 22.2 + - - -
562K PHE* 3.1 38.7 - - + +
563K LEU* 3.6 7.6 - - - +
566K LYS* 2.7 40.3 + - - +
568K ILE* 3.8 15.4 - - + +
626K LEU* 4.1 17.0 - - + -
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Residues in contact with TRP 387 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375K MET* 3.5 24.6 - - + +
376K PHE* 3.8 17.3 - + + -
382K ALA* 4.1 10.2 - - + +
383K ASP 3.1 25.8 - - - +
384K ILE 3.4 5.5 + - - +
385K GLU 3.4 0.2 - - - -
386K GLU* 1.3 82.2 + - + +
388K MET* 1.3 58.8 + - - +
390K GLY* 3.4 1.9 + - - -
391K VAL* 3.1 27.0 + - - +
566K LYS* 4.3 14.9 - - + +
567K ARG 3.9 10.1 - - - -
568K ILE* 3.7 39.0 - - + +
571K SER* 3.2 32.8 - - - -
573K ILE* 3.6 23.6 - - + -
574K ALA* 3.9 14.8 - - - +
577K LEU* 3.6 17.5 - - + +
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Residues in contact with MET 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K ILE* 3.0 34.8 + - + +
385K GLU* 3.6 7.2 - - - +
387K TRP* 1.3 76.9 - - - +
389K ALA* 1.3 63.0 + - - +
391K VAL* 3.4 23.1 + - + +
392K ALA* 3.5 4.3 + - - +
577K LEU* 3.5 49.4 - - + +
581K TRP* 3.5 34.8 - - + -
603K LEU* 3.7 15.3 - - + -
607K PHE* 4.2 14.8 - - + -
612K TYR* 4.0 6.7 - - + -
615K MET* 3.8 23.0 - - + +
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Residues in contact with ALA 389 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385K GLU 3.1 13.2 + - - +
386K GLU* 3.0 13.6 + - - +
388K MET* 1.3 77.6 - - - +
390K GLY* 1.3 63.1 + - - +
392K ALA* 3.0 15.7 + - - +
393K TRP* 3.1 12.3 + - - +
562K PHE* 4.2 2.2 - - + -
563K LEU* 4.4 1.6 - - - -
615K MET* 3.7 9.2 - - - -
625K VAL* 3.4 33.9 - - + +
626K LEU* 3.6 15.3 - - + -
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Residues in contact with GLY 390 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386K GLU 3.0 10.7 + - - -
387K TRP 3.4 3.7 + - - -
388K MET 3.3 0.2 - - - -
389K ALA* 1.3 73.9 - - - +
391K VAL* 1.3 58.9 + - - +
392K ALA 3.0 1.8 - - - -
393K TRP* 3.2 5.1 + - - +
394K LEU* 2.8 41.8 + - - +
563K LEU* 3.6 20.2 - - - +
568K ILE* 4.2 8.5 - - - -
569K ILE* 4.8 4.0 - - - -
574K ALA* 5.6 0.4 - - - -
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Residues in contact with VAL 391 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387K TRP 3.1 18.1 + - - +
388K MET* 3.5 28.7 - - + +
389K ALA 3.2 0.2 - - - -
390K GLY* 1.3 77.3 - - - +
392K ALA* 1.3 57.0 + - - +
394K LEU* 4.1 9.0 - - - +
395K HIS* 3.2 26.2 + - - +
574K ALA 3.8 19.7 - - - +
577K LEU* 3.9 5.4 - - + +
578K MET* 3.5 34.5 - - + +
581K TRP* 5.2 2.2 - - + -
582K TYR* 4.5 1.8 - - + -
612K TYR* 3.3 22.9 + - + +
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Residues in contact with ALA 392 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388K MET 3.5 5.4 + - - +
389K ALA 3.0 13.9 + - - +
390K GLY 3.0 0.6 - - - -
391K VAL* 1.3 77.4 - - - +
393K TRP* 1.3 64.5 + - - +
395K HIS* 3.2 3.1 + - - +
396K CYS* 3.1 30.3 + - - -
612K TYR* 4.4 6.5 + - + -
615K MET* 4.1 13.0 - - + -
616K LYS* 3.5 40.5 - - + +
619K VAL* 4.6 3.4 - - + -
625K VAL* 4.9 0.2 - - + -
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Residues in contact with TRP 393 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389K ALA 3.1 8.2 + - - +
390K GLY* 3.8 4.9 - - - +
392K ALA* 1.3 79.4 - - - +
394K LEU* 1.3 75.0 + - + +
396K CYS* 3.1 17.0 + - - +
397K LEU* 3.3 26.6 + - + +
430K SER 5.3 1.1 - - - -
431K GLY* 5.2 3.1 - - - -
434K THR* 3.9 17.5 - - + -
553K LEU* 3.2 56.0 + - + +
556K CYS* 3.4 26.5 - - - -
557K LEU* 3.7 28.5 - - + +
563K LEU* 4.4 10.8 - - + -
569K ILE* 3.5 44.6 - - + -
619K VAL* 4.3 5.5 - - + +
625K VAL* 4.7 3.6 - - + -
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Residues in contact with LEU 394 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390K GLY 2.8 21.6 + - - +
391K VAL* 4.1 7.0 - - - +
393K TRP* 1.3 93.4 - - + +
395K HIS* 1.3 59.5 + - - +
397K LEU* 3.2 26.8 - - + +
401K MET* 3.2 22.0 - - + +
434K THR* 4.8 2.7 - - + +
435K LEU* 5.5 6.1 - - + -
438K ALA* 5.9 0.4 - - + -
569K ILE* 3.1 32.8 - - - +
571K SER 5.3 0.2 - - - +
574K ALA* 3.9 30.5 - - + +
575K LEU* 4.0 23.3 - - + -
578K MET* 4.4 8.7 - - - -
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Residues in contact with HIS 395 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391K VAL 3.2 19.4 + - - +
392K ALA 3.2 6.0 + - - +
394K LEU* 1.3 75.0 - - - +
396K CYS* 1.3 58.7 + - - +
397K LEU 3.2 2.7 - - - -
398K LEU 3.4 16.3 - - - +
400K LYS* 4.6 15.2 - - - -
401K MET* 3.9 7.6 + - + -
402K ASP* 2.9 37.8 + - + -
578K MET* 4.5 4.5 - - - -
582K TYR* 3.3 30.9 - + - +
616K LYS* 2.9 30.1 + - - +
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Residues in contact with CYS 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392K ALA 3.1 22.0 + - - +
393K TRP 3.1 8.4 + - - +
395K HIS* 1.3 76.6 - - - +
397K LEU* 1.3 58.2 + - - +
398K LEU 5.3 0.2 - - - -
550K LYS* 3.6 2.6 + - - -
552K TYR* 2.7 33.0 + - + +
553K LEU* 3.4 8.3 - - + +
616K LYS* 4.1 27.4 - - - -
619K VAL* 3.6 36.8 - - + -
620K 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