Contacts of the helix formed by residues 571 - 582 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C TRP* 3.2 26.4 - - - -
438C ALA* 3.5 10.7 - - - +
441C GLU* 3.5 9.4 + - - -
567C ARG* 3.2 24.9 - - - -
568C ILE 3.1 10.0 + - - -
570C GLN* 1.3 80.3 - - - +
572C GLY* 1.3 66.5 + - - +
573C ILE* 3.3 8.8 + - - +
574C ALA* 3.2 15.6 + - - +
575C LEU* 3.6 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 572 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C LEU* 4.6 3.4 - - - +
438C ALA* 3.4 23.5 + - - +
441C GLU* 2.8 20.6 + - - +
442C LEU* 3.6 26.1 - - - +
571C SER* 1.3 70.7 - - - +
573C ILE* 1.3 66.6 + - - +
575C LEU* 3.3 2.4 + - - -
576C LEU* 3.1 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 573 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C LEU* 3.3 49.6 - - + +
371C ARG* 4.1 18.8 - - + +
372C MET* 3.5 34.5 - - + -
375C MET* 4.4 11.9 - - + -
376C PHE* 4.7 0.2 - - + -
387C TRP* 3.5 26.5 - - + -
441C GLU* 4.6 4.5 - - - +
571C SER* 3.2 7.6 - - - +
572C GLY* 1.3 76.5 - - - +
574C ALA* 1.3 60.9 + - - +
576C LEU* 3.3 6.1 + - - +
577C LEU* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 574 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C TRP* 3.9 10.6 - - - +
390C GLY 5.5 0.4 - - - -
391C VAL* 3.8 9.8 - - + +
394C LEU* 3.9 17.9 - - + +
568C ILE* 3.0 41.3 - - + +
571C SER* 3.2 9.4 + - - +
572C GLY 3.1 0.2 - - - -
573C ILE* 1.3 77.1 - - - +
575C LEU* 1.3 65.2 + - - +
577C LEU* 3.2 18.8 + - - +
578C MET* 3.2 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 575 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LEU* 4.0 18.2 - - + -
401C MET* 5.5 0.4 - - + -
405C VAL* 4.7 4.9 - - + -
435C LEU* 4.3 15.5 - - + -
438C ALA* 3.5 34.3 - - + +
439C LEU* 3.5 35.0 - - + +
442C LEU* 3.6 19.5 - - + -
571C SER 4.1 0.9 - - - +
572C GLY 3.3 5.6 + - - +
574C ALA* 1.3 76.4 - - - +
576C LEU* 1.3 60.6 + - - +
578C MET* 3.1 31.9 + - + +
579C LEU* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 576 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C PHE* 3.5 39.9 - - + +
368C LEU* 3.5 27.8 - - + +
369C LEU* 3.5 16.2 - - + -
372C MET* 3.5 28.3 - - - -
442C LEU* 3.8 9.8 - - + +
572C GLY 3.1 12.7 + - - +
573C ILE* 3.4 10.1 - - - +
574C ALA 3.1 0.4 - - - -
575C LEU* 1.3 77.4 - - - +
577C LEU* 1.3 61.5 + - - +
579C LEU* 3.1 6.1 + - + +
580C ILE* 3.0 44.7 + - + +
588C PHE* 5.4 1.1 - - + -
596C ILE* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 577 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C MET* 3.4 32.3 - - + -
376C PHE* 4.6 2.2 - - + -
384C ILE* 4.3 10.3 - - + -
387C TRP* 3.6 35.7 - - + +
388C MET* 3.5 32.3 - - + +
391C VAL* 3.9 4.7 - - + -
573C ILE 3.2 10.3 + - - +
574C ALA* 3.2 8.8 + - - +
576C LEU* 1.3 78.8 - - - +
578C MET* 1.3 57.3 + - - +
580C ILE* 3.9 8.4 - - + +
581C TRP* 3.1 30.0 + - - +
599C TRP* 4.9 0.4 - - + -
603C LEU* 3.6 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 578 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C VAL* 3.5 38.1 - - + +
394C LEU* 4.4 10.8 - - + -
395C HIS* 4.5 6.7 - - - -
401C MET* 3.5 26.5 - - + -
402C ASP* 3.7 23.2 - - + +
405C VAL* 3.5 32.3 - - + -
574C ALA 3.2 9.2 + - - +
575C LEU* 3.1 27.5 + - + +
577C LEU* 1.3 78.6 - - - +
579C LEU* 1.3 61.8 + - + +
581C TRP* 3.9 2.2 - - - -
582C TYR* 3.4 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 579 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C PHE* 3.5 28.3 - - + -
402C ASP* 4.5 5.2 - - - +
405C VAL* 3.5 28.9 - - + -
406C TYR* 4.6 2.9 - - + +
409C LEU* 3.9 14.8 - - + -
442C LEU* 3.8 30.1 - - + -
575C LEU 2.9 12.5 + - - +
576C LEU* 3.1 8.0 + - + +
578C MET* 1.3 81.5 - - + +
580C ILE* 1.3 57.4 + - + +
583C ARG* 3.2 48.6 + - + +
588C PHE* 3.4 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 580 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C LEU* 3.9 28.9 - - + -
372C MET* 5.4 0.4 - - - -
576C LEU* 3.0 31.5 + - + +
577C LEU* 4.1 11.7 - - + +
579C LEU* 1.3 76.1 - - - +
581C TRP* 1.3 57.1 + - - +
583C ARG 4.6 1.1 - - - -
588C PHE* 4.4 12.6 - - + -
596C ILE* 3.6 39.5 - - + +
599C TRP* 4.1 21.5 - - + +
600C LYS* 2.7 40.6 + - + +
603C LEU* 5.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 581 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C MET* 3.5 26.9 - - + -
391C VAL* 5.2 1.3 - - + -
577C LEU 3.1 18.4 + - - +
578C MET* 3.7 2.2 + - - +
579C LEU 3.4 0.2 - - - -
580C ILE* 1.3 79.8 - - - +
582C TYR* 1.3 90.8 + + + +
600C LYS* 4.2 4.3 + - - -
603C LEU* 3.6 39.5 - - + -
604C ASP* 5.0 9.0 - - - -
607C PHE* 3.8 26.7 - - + -
608C SER 3.8 10.3 - - - -
609C LEU* 4.6 15.9 - - + +
612C TYR* 3.4 48.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 582 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C VAL* 4.5 0.2 - - + -
395C HIS* 3.3 27.5 - + - -
402C ASP* 3.2 30.7 - - + +
578C MET* 3.4 25.1 + - + +
581C TRP* 1.3 97.7 - + + +
583C ARG* 1.3 67.4 + - - +
584C PRO* 3.4 7.8 - - - +
600C LYS* 4.6 1.7 + - - -
612C TYR* 2.8 42.1 + + - -
613C GLN* 5.1 1.3 + - - -
616C LYS* 3.3 18.2 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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