Contacts of the helix formed by residues 521 - 533 (chain B) in PDB entry 2EZT
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 GLN 521 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ARG 5.3 1.7 + - - -
516B VAL* 3.4 21.8 - - + +
517B ASN* 2.8 44.7 + - - +
518B LYS* 3.0 37.2 + - + +
519B ILE 3.1 0.6 - - - -
520B GLU* 1.3 78.6 - - + +
522B LEU* 1.3 66.8 + - - +
523B PRO* 3.5 1.2 - - - -
524B ASP* 3.8 4.6 + - - +
525B VAL* 3.5 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 3.8 22.9 - - + -
375B GLN* 3.4 44.6 - - + +
376B VAL* 4.4 6.7 - - + -
378B ARG* 3.8 10.5 - - - +
379B ALA* 4.0 11.9 - - + -
516B VAL* 4.2 17.9 - - + -
518B LYS 4.4 0.9 - - - +
519B ILE* 3.4 14.6 - - - +
521B GLN* 1.3 78.1 - - - +
523B PRO* 1.4 72.9 - - + +
525B VAL* 3.3 2.9 + - - -
526B PHE* 2.9 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B GLN* 6.2 0.2 - - - +
378B ARG* 4.6 11.9 - - - +
379B ALA* 6.0 0.4 - - + -
519B ILE 4.1 2.9 - - - +
520B GLU* 3.6 18.6 - - - +
521B GLN 3.6 0.7 - - - -
522B LEU* 1.4 94.0 - - + +
524B ASP* 1.3 58.8 + - - +
526B PHE* 3.9 3.5 - - + +
527B GLU* 3.0 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B GLU 5.5 0.2 + - - -
521B GLN 3.8 4.6 + - - +
522B LEU 3.4 0.8 - - - -
523B PRO* 1.3 79.7 - - - +
525B VAL* 1.3 59.6 + - + +
527B GLU* 3.6 7.4 + - - +
528B GLN* 3.0 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B PHE* 3.7 41.0 - - + -
516B VAL* 3.6 28.7 - - + -
521B GLN* 3.5 15.6 + - + +
522B LEU 3.3 2.5 + - - +
524B ASP* 1.3 76.9 - - + +
526B PHE* 1.3 63.6 + - + +
528B GLN* 3.3 10.3 + - - +
529B ALA* 2.8 27.5 + - - +
540B ILE* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B VAL* 4.1 20.9 - - + -
379B ALA* 3.6 31.0 - - + +
380B VAL* 3.8 24.9 - - + -
383B ILE* 3.6 34.0 - - + +
442B PHE* 5.5 0.4 - + - -
468B ILE* 5.6 0.2 - - + -
470B VAL* 4.2 13.0 - - + -
522B LEU* 2.9 46.8 + - + +
523B PRO* 4.2 2.7 - - + +
525B VAL* 1.3 77.4 - - + +
527B GLU* 1.3 57.0 - - - +
529B ALA* 3.4 4.5 + - - +
530B LYS* 2.8 30.5 + - - +
540B ILE* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LYS* 4.9 4.9 - - - +
383B ILE* 3.6 18.8 - - - +
523B PRO* 3.0 23.4 + - + +
524B ASP* 3.8 11.4 - - - +
526B PHE* 1.3 76.7 - - - +
528B GLN* 1.3 60.6 + - - +
530B LYS* 3.5 18.2 + - - +
531B ALA* 3.3 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B GLN* 6.1 0.2 - - - +
514B PHE* 3.6 34.4 - - + -
524B ASP* 3.0 44.8 + - - +
525B VAL* 3.5 6.5 - - - +
527B GLU* 1.3 73.2 - - + +
529B ALA* 1.3 61.5 + - - +
531B ALA* 3.1 6.1 + - - +
532B ILE* 2.9 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ILE* 4.8 1.8 - - + -
468B ILE* 4.5 8.7 - - + -
514B PHE* 4.3 1.4 - - + -
525B VAL 2.8 20.4 + - - +
526B PHE 3.6 4.3 - - - +
528B GLN* 1.3 72.1 - - - +
530B LYS* 1.3 62.9 + - - +
532B ILE* 4.6 0.2 - - - -
533B ALA* 3.0 27.7 + - - +
538B VAL* 3.6 31.7 - - + +
540B ILE* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LYS 5.5 1.1 - - - +
383B ILE* 3.0 54.8 + - + +
384B ALA 5.0 0.4 - - - -
385B GLU* 3.6 27.7 + - - +
440B GLN* 4.4 5.5 + - - +
468B ILE* 4.7 3.8 - - - +
526B PHE 2.8 20.1 + - - +
527B GLU* 3.6 20.2 - - - +
528B GLN 3.3 0.2 - - - -
529B ALA* 1.3 73.5 - - - +
531B ALA* 1.3 60.8 + - - +
533B ALA* 3.6 11.0 + - - +
534B GLN* 3.1 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B GLU 3.3 9.3 + - - +
528B GLN* 3.1 10.1 + - - +
530B LYS* 1.3 76.7 - - - +
532B ILE* 1.3 67.9 - - + +
534B GLN* 2.9 29.0 + - + +
535B HIS* 4.4 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B GLN* 3.5 42.8 - - + +
514B PHE* 3.9 29.8 - - + -
528B GLN* 2.9 26.1 + - + +
529B ALA 3.9 3.1 - - - +
531B ALA* 1.3 75.6 - - + +
533B ALA* 1.3 57.1 + - - +
535B HIS* 3.0 21.0 + - - +
536B GLU* 3.1 27.5 + - + +
537B PRO 3.9 6.3 - - - +
538B VAL* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LYS* 5.1 2.9 + - - -
440B GLN* 6.1 0.4 - - + -
466B PRO* 3.3 25.3 - - - +
468B ILE* 3.5 30.5 - - + -
529B ALA 3.0 18.1 + - - +
530B LYS 3.9 7.2 - - - +
531B ALA 3.1 0.2 - - - -
532B ILE* 1.3 73.5 - - - +
534B GLN* 1.3 62.5 + - - +
535B HIS 3.1 0.9 - - - -
536B GLU 3.2 13.0 - - - +
538B VAL* 4.1 4.5 - - + -
----------------------------------------------------------
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