Contacts of the helix formed by residues 551 - 562 (chain B) in PDB entry 2JGN
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 ILE 551 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B LEU* 4.7 7.6 - - + -
518B PRO* 3.5 24.0 - - + +
519B SER 4.1 7.0 - - - +
520B ASP 3.8 6.3 - - - +
521B ILE* 3.8 48.9 - - + +
524B TYR* 4.3 10.5 - - + -
544B PHE* 4.0 15.0 - - + -
548B ASN* 3.0 22.1 + - + +
550B ASN* 1.3 84.5 + - - +
552B THR* 1.3 65.0 + - - +
553B LYS 3.3 2.2 + - - -
554B ASP* 3.4 6.9 + - + +
555B LEU* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B PHE* 3.4 13.5 - - - -
548B ASN 3.6 1.7 + - - -
549B ILE* 2.9 37.1 + - - +
550B ASN 3.5 0.4 - - - -
551B ILE* 1.3 75.9 - - - +
553B LYS* 1.3 56.3 + - - +
555B LEU* 3.7 1.4 - - - +
556B LEU* 2.8 34.0 + - - +
570B LEU* 3.8 23.6 - - + +
573B MET* 3.9 7.9 - - + +
574B ALA* 3.4 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ILE 5.8 0.7 - - - +
550B ASN 5.4 0.4 + - - -
551B ILE 3.4 0.4 - - - -
552B THR* 1.3 77.3 - - - +
554B ASP* 1.3 62.7 + - - +
556B LEU* 3.5 4.9 + - - +
557B ASP* 3.0 39.8 + - - +
573B MET 5.5 0.7 - - - -
574B ALA* 3.5 35.8 + - + +
575B TYR* 4.8 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ILE* 3.6 39.7 + - + +
550B ASN 5.4 3.3 - - - +
551B ILE* 3.4 9.5 + - + +
553B LYS* 1.3 81.2 - - - +
555B LEU* 1.3 57.8 + - - +
557B ASP* 3.6 10.7 + - - +
558B LEU* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLN* 4.9 0.2 - - - +
418B VAL* 4.0 24.7 - - + -
517B LEU* 4.4 11.0 - - + -
521B ILE* 3.8 13.3 - - + +
524B TYR* 3.8 41.3 - - + +
544B PHE* 3.9 31.0 - - + -
551B ILE* 2.9 24.1 + - + +
552B THR* 3.7 2.9 - - - +
554B ASP* 1.3 74.5 - - - +
556B LEU* 1.3 66.9 + - - +
558B LEU* 3.2 4.5 + - + +
559B LEU* 3.0 32.4 + - + +
570B LEU* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B THR 2.8 22.4 + - - +
553B LYS* 3.7 3.6 - - - +
555B LEU* 1.3 75.0 - - - +
557B ASP* 1.3 73.1 + - - +
559B LEU* 3.3 1.9 + - - +
560B VAL* 3.1 34.9 + - + +
566B VAL* 3.3 34.3 - - + -
570B LEU* 3.8 19.4 - - + +
571B GLU* 4.1 17.7 - - + -
574B ALA* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B LYS* 3.0 31.2 + - - +
554B ASP* 3.6 11.6 + - - +
555B LEU 3.3 0.2 - - - -
556B LEU* 1.3 81.3 - - - +
558B LEU* 1.3 56.9 + - - +
560B VAL* 3.4 5.8 + - - +
561B GLU* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B SER* 4.3 14.1 - - - +
416B GLN* 3.2 39.0 - - - +
521B ILE* 4.0 15.0 - - + -
524B TYR* 4.0 11.4 - - + -
525B VAL* 3.4 33.0 - - + -
528B ILE* 5.5 0.2 - - + -
554B ASP 3.1 17.3 + - - +
555B LEU* 3.6 6.1 - - + +
556B LEU 3.2 0.2 - - - -
557B ASP* 1.3 78.2 - - - +
559B LEU* 1.3 59.4 + - + +
561B GLU* 3.4 5.2 + - - +
562B ALA* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLN* 3.5 42.4 - - + +
418B VAL* 3.8 24.7 - - + -
524B TYR* 4.7 0.2 - - - +
555B LEU* 3.0 18.0 + - + +
556B LEU 3.7 5.6 - - - +
558B LEU* 1.3 74.0 - - - +
560B VAL* 1.3 65.9 + - - +
562B ALA 3.3 0.9 + - - -
563B LYS 3.1 4.2 + - - -
564B GLN* 2.9 43.6 + - + -
565B GLU 4.0 12.8 - - - +
566B VAL* 4.1 12.1 - - + -
567B PRO* 4.4 4.5 - - + -
570B LEU* 3.4 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B LEU* 3.1 30.7 + - + +
557B ASP* 3.8 5.8 - - - +
559B LEU* 1.3 75.7 - - - +
561B GLU* 1.3 76.3 + - - +
563B LYS* 3.2 17.3 + - - +
564B GLN 5.2 0.4 - - - -
566B VAL* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ASP* 2.9 24.0 + - + +
558B LEU* 4.0 4.3 - - - +
560B VAL* 1.3 90.5 - - - +
562B ALA* 1.3 56.0 + - - +
563B LYS* 3.2 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A TRP* 4.0 7.3 - - - +
411B SER* 3.7 26.5 - - - +
412B GLU* 5.5 8.0 - - - +
416B GLN* 3.9 6.3 - - - +
558B LEU 3.0 18.4 + - - +
559B LEU 3.3 0.2 + - - -
560B VAL 3.2 0.2 - - - -
561B GLU* 1.3 73.2 - - - +
563B LYS* 1.3 67.8 - - - +
564B GLN* 3.1 29.6 - - + +
----------------------------------------------------------
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