Contacts of the helix formed by residues 529 - 538 (chain B) in PDB entry 1PG3
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 THR 529 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B GLY 4.5 0.2 + - - -
518B ASP* 2.8 39.3 + - + +
520B LEU* 3.5 27.9 - - - +
527B LEU 3.7 1.2 + - - -
528B GLY* 1.3 73.6 - - - +
530B ALA* 1.3 62.9 + - - +
532B ILE* 3.5 3.2 + - - +
533B GLU* 3.1 38.9 + - - +
547B VAL* 3.1 31.7 + - + +
612B ARG* 3.8 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B SER 3.5 22.8 + - - +
268B THR* 3.8 19.1 - - + -
269B GLY 4.2 5.4 - - - +
518B ASP* 5.4 0.2 - - - +
528B GLY 3.2 0.2 - - - -
529B THR* 1.3 78.8 - - - +
531B GLU* 1.3 64.9 + - - +
533B GLU* 3.1 15.6 + - - +
534B SER* 3.0 25.7 + - - +
612B ARG* 5.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B SER* 2.5 33.3 + - - -
266B GLY 4.8 0.3 + - - -
269B GLY 4.1 19.7 + - - +
270B LYS* 4.8 6.5 - - - -
271B PRO* 3.7 20.7 - - + +
527B LEU* 4.9 7.0 - - - +
528B GLY* 2.8 38.7 + - - +
530B ALA* 1.3 78.6 - - - +
532B ILE* 1.3 65.7 + - + +
534B SER* 3.3 8.6 + - - +
535B ALA* 3.0 22.5 + - - +
587B ILE* 3.7 28.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
520B LEU* 4.3 16.2 - - + -
527B LEU* 4.2 16.8 - - + -
528B GLY 3.2 17.0 + - - +
529B THR 3.9 4.7 - - - +
530B ALA 3.3 0.8 - - - -
531B GLU* 1.3 83.6 - - + +
533B GLU* 1.3 62.1 + - - +
535B ALA* 3.3 2.6 + - - +
536B LEU* 3.0 32.1 + - + +
547B VAL* 3.8 22.0 - - + -
559B ILE* 4.2 9.0 - - + -
583B VAL* 4.6 7.6 - - + -
587B ILE* 4.0 7.9 - - + -
591B ALA* 4.0 39.5 - - + +
593B PRO* 4.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B THR* 3.1 20.1 - - - +
530B ALA* 3.1 12.1 + - - +
532B ILE* 1.3 74.0 - - - +
534B SER* 1.3 60.4 + - - +
536B LEU* 3.2 6.7 + - - +
537B VAL* 2.9 36.1 + - + +
545B ALA* 3.8 19.0 - - - +
546B ALA* 3.3 0.7 - - - -
547B VAL* 2.9 36.3 + - + +
612B ARG* 2.9 44.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B ALA* 3.0 13.8 + - - +
531B GLU* 3.3 10.8 + - - -
533B GLU* 1.3 76.4 - - - +
535B ALA* 1.3 62.3 + - - +
537B VAL* 3.8 5.9 - - - +
538B ALA* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B GLU 3.0 13.2 + - - +
532B ILE* 3.5 8.7 - - - +
533B GLU 3.2 0.2 - - - -
534B SER* 1.3 76.0 - - - +
536B LEU* 1.3 59.7 + - - +
538B ALA* 3.2 10.8 - - - +
582B TRP* 2.7 30.8 + - - -
583B VAL* 5.0 9.6 - - + -
586B GLU* 3.8 27.4 - - + -
587B ILE* 3.9 15.5 - - + -
----------------------------------------------------------
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 ILE* 3.0 23.2 + - + +
533B GLU 3.5 5.8 - - - +
535B ALA* 1.3 77.1 - - - +
537B VAL* 1.3 59.0 + - - +
539B HIS* 2.9 29.1 + - - +
542B ILE* 3.4 15.7 - - + +
545B ALA* 3.8 25.8 - - + -
547B VAL* 3.9 20.2 - - + -
561B ALA* 3.9 16.6 - - + -
563B VAL* 4.4 4.7 - - + -
579B VAL* 3.5 28.9 - - + +
582B TRP* 4.4 3.6 - - + -
583B VAL* 3.5 26.7 - - + -
593B PRO* 4.5 4.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
533B GLU* 2.9 26.0 + - + +
534B SER* 4.1 5.4 - - - +
536B LEU* 1.3 71.4 - - - +
538B ALA* 1.3 55.8 + - - +
539B HIS 3.1 0.4 - - - -
542B ILE* 3.7 9.9 - - - +
543B ALA* 3.8 17.0 - - - +
544B GLU* 3.8 9.9 - - + -
545B ALA* 3.7 28.5 - - + +
901B MG 2.5 29.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B SER 2.9 14.2 + - - +
535B ALA* 3.2 18.2 - - - +
536B LEU 3.0 0.6 - - - -
537B VAL* 1.3 76.4 - - - +
539B HIS* 1.3 63.0 + - - +
540B PRO* 3.5 4.7 - - - +
582B TRP* 3.8 17.3 - - + +
586B GLU* 4.6 7.0 - - - +
901B MG 4.1 1.4 - - - -
----------------------------------------------------------
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