Contacts of the helix formed by residues 571 - 582 (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 SER 571 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387L TRP* 3.2 26.9 - - - -
438L ALA* 3.5 11.5 - - - +
441L GLU* 3.6 9.7 + - - -
567L ARG* 3.2 25.6 - - - -
568L ILE 3.1 9.6 + - - -
569L ILE 3.6 0.2 - - - -
570L GLN* 1.3 79.2 - - - +
572L GLY* 1.3 64.7 + - - +
573L ILE* 3.2 9.1 + - - +
574L ALA* 3.2 15.8 + - - +
575L LEU* 3.6 2.6 + - - +
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Residues in contact with GLY 572 (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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368L LEU* 4.6 3.0 - - - +
438L ALA* 3.4 23.1 + - - +
441L GLU* 2.8 21.0 + - - +
442L LEU* 3.6 25.4 - - - +
571L SER* 1.3 70.2 - - - +
573L ILE* 1.3 65.7 + - - +
575L LEU* 3.3 2.6 + - - -
576L LEU* 3.1 18.5 + - - +
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Residues in contact with ILE 573 (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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368L LEU* 3.3 49.6 - - + +
371L ARG* 4.1 19.5 - - + +
372L MET* 3.5 34.3 - - + -
375L MET* 4.4 12.1 - - + -
376L PHE* 4.7 0.2 - - + -
387L TRP* 3.6 25.6 - - + -
441L GLU* 4.6 4.5 - - - +
571L SER* 3.2 7.4 - - - +
572L GLY* 1.3 77.2 - - - +
574L ALA* 1.3 60.9 + - - +
576L LEU* 3.3 6.8 + - - +
577L LEU* 3.2 22.1 + - + +
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Residues in contact with ALA 574 (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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387L TRP* 3.9 11.0 - - + +
390L GLY 5.5 0.4 - - - -
391L VAL* 3.8 9.1 - - + +
394L LEU* 3.9 17.7 - - + +
568L ILE* 3.0 40.6 - - + +
571L SER* 3.2 9.7 + - - +
572L GLY 3.1 0.2 - - - -
573L ILE* 1.3 76.7 - - - +
575L LEU* 1.3 64.7 + - - +
577L LEU* 3.2 18.9 + - - +
578L MET* 3.2 9.5 + - - +
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Residues in contact with LEU 575 (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* 4.0 18.2 - - + -
401L MET* 5.5 0.4 - - + -
405L VAL* 4.7 3.6 - - + -
435L LEU* 4.2 16.2 - - + -
438L ALA* 3.5 35.9 - - + +
439L LEU* 3.5 34.5 - - + +
442L LEU* 3.6 19.7 - - + -
571L SER 3.6 1.1 + - - +
572L GLY 3.3 5.3 + - - +
574L ALA* 1.3 76.7 - - - +
576L LEU* 1.3 59.0 + - - +
578L MET* 3.1 32.9 + - + +
579L LEU* 2.9 33.8 + - - +
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Residues in contact with LEU 576 (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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365L PHE* 3.5 39.3 - - + +
368L LEU* 3.5 28.0 - - + +
369L LEU* 3.5 17.0 - - + -
372L MET* 3.5 28.0 - - - -
442L LEU* 3.8 10.0 - - + +
572L GLY 3.1 12.8 + - - +
573L ILE* 3.4 10.1 - - - +
574L ALA 3.1 0.2 - - - -
575L LEU* 1.3 77.6 - - - +
577L LEU* 1.3 62.2 + - - +
579L LEU* 3.0 5.8 + - + +
580L ILE* 3.0 43.7 + - + +
588L PHE* 5.4 0.9 - - + -
596L ILE* 6.0 1.1 - - + -
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Residues in contact with LEU 577 (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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372L MET* 3.4 31.9 - - + -
376L PHE* 4.6 2.0 - - + -
384L ILE* 4.3 9.9 - - + -
387L TRP* 3.6 35.4 - - + +
388L MET* 3.5 33.0 - - + +
391L VAL* 3.9 4.7 - - + -
573L ILE 3.2 11.2 + - - +
574L ALA* 3.2 9.7 + - - +
576L LEU* 1.3 79.7 - - - +
578L MET* 1.3 57.8 - - - +
580L ILE* 3.5 7.7 + - + +
581L TRP* 3.1 29.6 + - - +
599L TRP* 4.9 0.7 - - + -
603L LEU* 3.6 27.6 - - + +
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Residues in contact with MET 578 (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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391L VAL* 3.5 39.4 - - + +
394L LEU* 4.4 10.8 - - + -
395L HIS* 4.5 6.3 - - - -
401L MET* 3.5 25.4 - - + -
402L ASP* 3.7 22.4 - - + +
405L VAL* 3.5 32.8 - - + -
574L ALA 3.2 9.0 + - - +
575L LEU* 3.1 29.0 + - + +
577L LEU* 1.3 77.9 - - - +
579L LEU* 1.3 60.9 + - + +
581L TRP* 4.4 1.8 - - - -
582L TYR* 3.4 29.2 + - + +
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Residues in contact with LEU 579 (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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365L PHE* 3.5 29.2 - - + -
402L ASP* 4.5 4.9 - - - +
405L VAL* 3.5 31.0 - - + -
406L TYR* 4.6 2.9 - - + +
409L LEU* 3.9 14.4 - - + -
442L LEU* 3.8 29.4 - - + -
575L LEU 2.9 14.5 + - - +
576L LEU* 3.0 7.8 + - + +
578L MET* 1.3 81.8 - - + +
580L ILE* 1.3 57.8 + - - +
581L TRP 3.4 0.2 - - - -
583L ARG* 3.2 47.6 + - + +
588L PHE* 3.4 17.0 - - + -
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Residues in contact with ILE 580 (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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369L LEU* 3.9 28.3 - - + -
372L MET* 5.4 0.2 - - - -
576L LEU* 3.0 33.1 + - + +
577L LEU* 4.1 12.1 - - + +
579L LEU* 1.3 77.6 - - - +
581L TRP* 1.3 58.2 + - - +
583L ARG 4.6 1.1 - - - -
588L PHE* 4.4 12.1 - - + -
596L ILE* 3.6 39.0 - - + +
599L TRP* 4.1 21.3 - - + +
600L LYS* 2.7 41.3 + - + +
603L LEU* 5.0 5.8 - - + -
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Residues in contact with TRP 581 (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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388L MET* 3.5 27.8 - - + -
391L VAL* 5.2 1.3 - - + -
577L LEU 3.1 19.9 + - - +
578L MET* 4.1 1.6 - - - +
580L ILE* 1.3 80.3 - - - +
582L TYR* 1.3 91.8 + + + +
600L LYS* 4.2 4.7 + - - -
603L LEU* 3.6 40.1 - - + +
604L ASP* 5.1 7.9 - - - -
607L PHE* 3.8 26.7 - - + -
608L SER 3.8 9.4 - - - -
609L LEU* 4.6 17.9 - - + +
612L TYR* 3.4 48.2 - + + -
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Residues in contact with TYR 582 (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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391L VAL* 4.5 0.4 - - + -
395L HIS* 3.3 28.6 - + - -
402L ASP* 3.2 32.1 - - + +
578L MET* 3.4 24.4 + - + +
581L TRP* 1.3 97.8 - + + +
583L ARG* 1.3 68.7 - - + +
584L PRO* 3.4 6.6 - - - +
600L LYS* 4.6 1.7 + - - -
612L TYR* 2.8 42.3 + + - -
613L GLN* 5.1 1.5 + - - -
616L LYS* 3.3 19.6 + - - -
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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