Contacts of the helix formed by residues 526 - 537 (chain B) in PDB entry 3NG8
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 526 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLN* 5.4 0.2 + - - -
518B ILE* 4.5 4.3 - - - -
524B ASN 3.4 3.6 + - - -
525B LEU* 1.3 73.7 - - - +
527B LEU* 1.3 59.8 + - - +
528B ALA* 3.5 11.3 + - - +
529B ASP* 3.0 34.1 + - - -
530B VAL* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B GLU* 3.8 37.5 - - + +
471B TYR* 3.8 23.1 - - - +
472B GLY* 3.8 16.2 - - - +
516B PHE* 3.9 27.6 - - + +
517B ARG* 4.2 10.5 - - + -
518B ILE* 4.4 15.0 - - + +
526B SER* 1.3 70.5 - - - +
528B ALA* 1.3 61.0 + - - +
530B VAL* 2.9 8.3 - - + +
531B THR* 2.9 33.3 + - - +
554B VAL* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLN* 3.5 43.6 - - + +
526B SER* 3.5 10.5 - - - +
527B LEU* 1.3 79.9 - - - +
529B ASP* 1.3 57.0 + - - +
531B THR* 3.2 7.8 + - - -
532B GLN* 3.0 33.1 + - - +
554B VAL* 4.7 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLN* 5.4 2.9 + - - -
524B ASN 3.6 11.4 - - - +
525B LEU* 3.5 25.5 - - + +
526B SER* 3.0 38.2 + - - +
528B ALA* 1.3 81.3 - - - +
530B VAL* 1.3 58.2 + - - +
532B GLN* 3.4 13.8 + - - +
533B GLN* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B LEU* 4.0 11.0 - - + +
497B VAL* 4.8 4.7 - - + -
504B PHE* 4.6 15.0 - - + -
516B PHE* 3.7 30.1 - - + -
518B ILE* 4.2 12.1 - - + -
525B LEU* 3.7 28.3 - - + -
526B SER 2.9 13.5 + - - +
527B LEU* 2.9 32.8 - - + +
529B ASP* 1.3 77.2 - - - +
531B THR* 1.3 56.3 + - + +
533B GLN* 3.2 8.2 + - - +
534B ALA* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B GLY* 4.5 7.6 - - - -
473B TYR 4.7 2.9 - - - +
474B ILE* 6.2 0.7 - - + -
516B PHE* 4.6 7.0 - - + -
527B LEU 2.9 21.9 + - - +
528B ALA* 3.2 11.4 + - - -
530B VAL* 1.3 78.4 - - + +
532B GLN* 1.3 64.2 + - - +
534B ALA* 3.2 9.7 + - + +
535B GLY* 3.1 18.2 + - - -
552B THR* 4.2 11.9 + - - -
553B GLY* 3.5 38.6 - - - +
554B VAL* 4.2 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ALA* 4.1 25.9 - - + +
529A ASP* 4.2 19.2 + - - +
532A GLN* 4.4 12.1 + - - -
528B ALA 3.0 17.7 + - - +
529B ASP* 3.6 13.1 + - - +
531B THR* 1.3 74.6 + - - +
533B GLN* 1.3 64.5 + - - +
535B GLY* 3.1 4.8 + - - -
536B LEU* 3.0 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B LEU* 3.8 10.5 - - + -
496B HIS* 3.8 22.0 + - + +
497B VAL* 3.5 29.9 - - + +
529B ASP 2.9 14.9 + - - +
530B VAL 3.2 8.3 + - - +
532B GLN* 1.3 78.4 - - - +
534B ALA* 1.3 60.7 + - - +
536B LEU* 3.1 25.4 + - - +
537B VAL* 3.0 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B ILE* 4.4 13.5 - - + -
493B LEU* 3.8 22.1 - - + +
530B VAL 2.9 13.6 + - - +
531B THR* 3.2 12.7 + - + +
533B GLN* 1.3 76.4 - - - +
535B GLY* 1.3 56.8 + - - +
538B LYS* 3.1 28.4 + - - +
541B LEU* 3.6 18.2 - - + +
549B ILE* 5.3 0.5 - - - +
552B THR* 4.4 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A GLU* 5.2 10.1 - - - +
531B THR 3.1 8.3 + - - -
532B GLN* 3.1 8.2 + - - -
534B ALA* 1.3 74.8 - - - +
536B LEU* 1.3 65.4 + - - +
538B LYS* 3.2 21.3 + - - +
552B THR* 4.8 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B GLN* 3.0 35.2 + - + +
533B GLN* 3.1 35.2 + - - +
535B GLY* 1.3 77.2 - - - +
537B VAL* 1.3 61.1 - - + +
538B LYS 3.8 0.2 + - - -
539B SER 5.2 0.3 + - - -
540B GLU* 4.1 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B ILE* 5.3 0.2 - - + -
493B LEU* 4.5 7.6 - - + -
496B HIS* 3.4 47.1 - - + +
533B GLN* 3.0 34.9 + - - +
534B ALA* 3.7 1.3 - - - -
536B LEU* 1.3 79.5 - - + +
538B LYS* 1.3 64.5 + - - +
539B SER 3.2 3.1 - - - -
540B GLU* 3.0 23.1 + - + +
541B LEU* 2.9 39.8 + - + +
----------------------------------------------------------
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