Contacts of the helix formed by residues 431 - 444 (chain L) 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 GLY 431 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393L TRP* 5.2 3.1 - - - -
397L LEU* 3.9 11.5 - - - +
430L SER* 1.3 79.5 - - - +
432L LYS* 1.3 62.7 + - - +
433L THR 3.6 1.6 - - - -
434L THR* 3.3 20.3 + - - -
435L LEU* 2.9 25.6 + - - +
547L PHE* 3.3 17.0 - - - -
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Residues in contact with LYS 432 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418K LYS* 4.5 5.4 - - - +
540K ARG* 5.8 1.1 - - - +
424L PHE* 3.9 16.8 - - + +
426L GLY 3.1 28.3 - - - +
427L PRO 2.9 21.4 + - - -
428L ILE* 4.2 0.6 - - - +
429L ASP* 3.6 16.1 - - - +
430L SER* 3.0 22.6 + - - +
431L GLY* 1.3 73.4 - - - +
433L THR* 1.3 65.8 + - - +
434L THR 2.9 6.4 + - - -
435L LEU* 3.0 1.9 + - - +
436L ALA* 2.7 37.5 + - - +
474L ASP* 4.7 3.4 - - - -
527L THR* 4.9 7.4 - - + -
528L MET 3.9 3.8 - - - +
529L ASN* 3.3 21.5 - - - +
547L PHE* 3.4 26.9 - - + -
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Residues in contact with THR 433 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418K LYS* 5.3 6.2 + - - -
499K ASP* 5.7 0.7 - - - -
502K ASP* 4.0 25.0 + - + +
504K SER* 3.5 27.4 - - - +
505K VAL* 5.2 2.2 - - + -
540K ARG* 4.5 5.4 + - - -
431L GLY 3.6 0.2 - - - -
432L LYS* 1.3 86.2 + - - +
434L THR* 1.3 57.6 + - - +
436L ALA* 4.6 0.4 - - - -
437L ALA* 3.1 23.9 - - - +
473L GLU* 3.1 33.6 + - - +
474L ASP* 4.4 7.3 + - - -
527L THR* 5.8 1.2 - - - -
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Residues in contact with THR 434 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504K SER* 5.3 1.3 - - - -
393L TRP* 3.9 14.9 - - + -
394L LEU* 4.8 2.0 - - + -
397L LEU* 5.3 0.9 - - - -
431L GLY* 3.4 21.0 - - - -
432L LYS 2.9 0.6 - - - -
433L THR* 1.3 81.5 - - - +
435L LEU* 1.3 60.9 + - - +
438L ALA* 3.5 8.0 + - - +
569L ILE* 3.2 50.7 - - + +
570L GLN* 3.5 24.9 - - + +
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Residues in contact with LEU 435 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394L LEU* 5.5 4.9 - - + -
397L LEU* 4.4 6.7 - - + -
398L LEU* 4.1 3.4 - - + -
401L MET* 3.8 35.0 - - + -
404L VAL* 6.4 1.6 - - + -
405L VAL* 5.5 1.1 - - + -
424L PHE* 3.5 28.3 - - + -
431L GLY 2.9 15.8 + - - +
434L THR* 1.3 75.8 - - - +
436L ALA* 1.3 63.1 + - - +
437L ALA 2.9 6.5 + - - -
438L ALA* 3.1 2.1 + - + +
439L LEU* 2.9 51.3 + - + +
545L ILE* 5.6 2.0 - - + -
547L PHE* 3.6 15.7 - - + -
569L ILE 5.4 0.2 - - - -
575L LEU* 4.2 20.4 - - + -
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Residues in contact with ALA 436 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424L PHE* 3.8 14.0 - - + -
432L LYS 2.7 20.1 + - - +
433L THR* 4.6 0.2 - - - -
435L LEU* 1.3 73.7 - - - +
437L ALA* 1.3 57.6 + - - +
439L LEU* 4.3 6.9 - - - +
440L LEU* 3.7 13.9 + - - +
471L VAL* 3.7 23.3 - - + +
473L GLU* 3.8 12.8 - - - +
525L ILE* 4.6 7.9 - - + +
527L THR* 3.7 27.4 - - + -
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Residues in contact with ALA 437 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504K SER* 3.0 34.2 - - - +
505K VAL* 3.8 11.2 - - + -
433L THR 3.1 22.8 + - - +
434L THR 4.1 3.1 - - - +
435L LEU 2.9 0.4 - - - -
436L ALA* 1.3 78.8 - - - +
438L ALA* 1.3 66.2 + - - +
439L LEU 3.2 0.2 - - - -
440L LEU* 3.1 21.0 + - - +
441L GLU* 3.4 6.2 + - - +
570L GLN* 4.3 8.7 - - + +
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Residues in contact with ALA 438 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394L LEU* 5.8 0.4 - - + -
434L THR 3.5 11.3 + - - +
435L LEU* 3.1 5.3 + - + +
437L ALA* 1.3 78.5 - - - +
439L LEU* 1.3 57.7 + - - +
441L GLU* 3.1 3.0 + - - -
442L LEU* 2.9 24.6 + - - +
569L ILE 4.4 3.6 - - - +
570L GLN* 3.7 21.5 + - - -
571L SER 3.5 19.7 - - - +
572L GLY* 3.4 9.0 - - - +
575L LEU* 3.5 22.7 - - + -
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Residues in contact with LEU 439 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405L VAL* 4.5 15.3 - - + -
408L PHE* 4.4 26.7 - - + -
424L PHE* 3.6 20.2 - - + -
435L LEU* 2.9 34.2 + - + +
436L ALA 4.4 3.1 - - - +
438L ALA* 1.3 77.1 - - - +
440L LEU* 1.3 62.8 + - - +
442L LEU* 3.6 13.3 - - + +
443L CYS* 3.0 29.0 + - - +
469L LEU* 4.7 2.5 - - + +
525L ILE* 3.5 28.3 - - + -
575L LEU* 3.5 20.9 - - + -
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Residues in contact with LEU 440 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505K VAL* 4.5 14.4 - - + -
506K LYS* 4.8 10.1 - - + +
436L ALA 3.7 11.2 + - - +
437L ALA 3.1 14.2 + - - +
439L LEU* 1.3 79.3 - - - +
441L GLU* 1.3 55.3 + - + +
444L GLY* 2.8 30.5 + - - -
445L GLY 3.4 32.2 + - - +
446L LYS* 3.4 8.1 - - - +
447L ALA* 3.8 29.8 - - + +
469L LEU* 3.5 25.6 - - + -
471L VAL* 3.5 13.0 - - + -
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Residues in contact with GLU 441 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506K LYS* 5.2 11.3 + - - -
364L ARG* 2.8 49.4 + - - +
368L LEU* 3.7 7.0 - - + +
371L ARG* 3.4 23.3 + - - +
437L ALA 3.4 5.3 + - - +
438L ALA* 3.1 8.6 + - - +
440L LEU* 1.3 78.1 - - - +
442L LEU* 1.3 60.1 + - - +
443L CYS 3.3 0.4 - - - -
570L GLN 5.0 1.0 - - - +
571L SER* 3.6 12.0 + - - -
572L GLY* 2.8 30.2 + - - +
573L ILE* 4.1 2.8 + - - +
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Residues in contact with LEU 442 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364L ARG* 3.5 7.1 - - - +
365L PHE* 3.9 13.8 - - + -
368L LEU* 3.5 26.7 - - + +
405L VAL* 3.7 24.5 - - + -
409L LEU* 4.4 10.3 - - + -
438L ALA 2.9 16.2 + - - +
439L LEU* 3.6 10.5 - - + +
441L GLU* 1.3 78.1 - - - +
443L CYS* 1.3 60.8 + - - +
572L GLY* 3.6 19.9 - - - +
575L LEU* 3.6 26.9 - - + -
576L LEU* 3.8 12.1 - - + +
579L LEU* 3.8 23.1 - - + -
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Residues in contact with CYS 443 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360L MET 5.4 0.3 - - - +
361L LEU* 3.7 24.6 - - + +
364L ARG* 3.2 20.3 - - - +
408L PHE* 3.9 14.6 - - - -
409L LEU* 3.5 31.0 - - - -
412L MET* 5.2 0.4 - - - -
439L LEU* 3.0 15.6 + - - +
442L LEU* 1.3 83.3 - - - +
444L GLY* 1.3 58.7 + - - +
468L PHE* 3.8 10.1 - - + +
469L LEU* 3.5 29.4 - - + -
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Residues in contact with GLY 444 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364L ARG* 4.2 17.3 - - - -
440L LEU 2.8 22.4 + - - -
441L GLU 4.1 0.6 + - - -
442L LEU 3.8 0.2 - - - -
443L CYS* 1.3 75.1 - - - +
445L GLY* 1.3 58.4 + - - -
468L PHE* 3.4 23.8 - - - +
469L LEU* 3.4 13.6 - - - +
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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