Contacts of the helix formed by residues 649 - 657 (chain A) in PDB entry 1P4J
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 ARG 649 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 3.2 19.5 - - - +
93A ARG* 4.8 8.5 - - - +
128A ASP* 3.9 14.3 + - + +
167A ASN* 5.0 3.6 - - - -
548A TYR* 4.4 12.7 + - - -
553A TYR* 4.7 8.3 + - - -
608A LYS* 4.8 5.2 - - - +
646A GLU 4.4 1.0 + - - -
647A ASN* 2.8 54.9 + - - +
648A TYR* 1.3 77.4 - - - +
650A VAL* 1.3 68.3 + - - +
651A SER* 3.0 26.5 + - - +
652A LEU* 3.0 21.5 + - - +
653A ALA* 2.9 21.1 + - - +
655A LYS* 6.2 0.6 - - - +
999A PLP 3.4 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 3.4 45.1 + - + +
92A GLY* 4.0 16.6 - - - -
93A ARG 5.1 0.4 - - - +
128A ASP* 3.6 7.1 + - - +
138A ARG* 4.5 9.0 - - + +
490A ARG* 4.4 9.0 - - - +
491A TRP* 4.3 12.6 - - + -
649A ARG* 1.3 74.3 - - - +
651A SER* 1.3 64.6 + - - +
653A ALA* 3.1 14.9 + - - +
654A GLU* 3.1 31.8 + - - +
999A PLP 3.4 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 3.7 29.1 + - - +
128A ASP* 2.9 31.0 + - - -
649A ARG* 3.0 33.7 + - - -
650A VAL* 1.3 73.9 - - - +
652A LEU* 1.3 60.9 + - - +
654A GLU* 3.6 21.3 + - - +
655A LYS* 3.7 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A PHE* 4.5 14.8 - - + -
548A TYR* 4.0 32.3 - - + +
553A TYR* 5.7 3.1 - - + +
645A LEU* 4.5 16.6 - - + -
646A GLU 3.5 24.9 - - - +
647A ASN 4.0 1.6 - - - +
648A TYR* 3.7 25.4 - - + -
649A ARG* 3.0 27.1 + - - +
651A SER* 1.3 78.1 + - - +
653A ALA* 1.3 66.3 + - - +
655A LYS* 2.9 17.9 + - + +
656A VAL* 2.9 18.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A TRP* 3.9 21.2 - - + -
648A TYR* 3.5 31.8 - - - +
649A ARG 2.9 12.2 + - - +
650A VAL 3.1 8.9 + - - +
652A LEU* 1.3 77.7 - - - +
654A GLU* 1.3 62.0 + - - +
656A VAL* 3.9 4.0 - - - -
657A ILE* 3.0 35.6 + - + +
999A PLP 3.9 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 5.3 7.8 + - - +
490A ARG* 2.8 40.8 + - + -
491A TRP* 3.9 18.2 - - + -
494A LEU* 3.8 19.6 - - + +
495A CYS* 3.3 28.3 - - + +
650A VAL* 3.1 21.0 + - - +
651A SER* 3.7 16.5 - - - +
652A LEU 3.2 0.2 - - - -
653A ALA* 1.3 76.2 - - - +
655A LYS* 1.3 58.6 + - + +
658A PRO* 3.2 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 4.1 9.1 - - - +
124A GLU* 2.8 39.6 + - - -
541A ASN* 5.4 0.5 - - - +
545A PHE* 3.8 22.7 - - + +
548A TYR* 3.5 46.9 - - + +
649A ARG* 6.2 0.4 - - - +
651A SER* 3.7 19.3 + - - +
652A LEU* 2.9 11.5 + - + +
654A GLU* 1.3 82.9 - - + +
656A VAL* 1.3 64.3 + - - +
658A PRO* 3.6 8.4 - - - +
659A ALA* 4.0 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A PHE* 3.8 34.8 - - + -
565A VAL* 4.0 25.4 - - + -
567A VAL* 4.5 9.9 - - + -
604A MET* 4.4 0.9 - - + -
645A LEU* 4.0 17.9 - - + -
648A TYR* 4.4 11.7 - - + -
652A LEU* 2.9 21.7 + - + +
653A ALA* 3.9 10.1 - - - +
655A LYS* 1.3 76.0 - - - +
657A ILE* 1.3 76.2 + - + +
659A ALA* 3.1 12.4 + - + +
660A ALA* 3.2 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A TRP* 4.3 5.8 - - + -
495A CYS* 6.1 0.2 - - - -
538A LYS* 4.1 4.0 + - - -
567A VAL* 4.9 1.6 - - + -
648A TYR* 4.5 5.4 - - - +
653A ALA* 3.0 31.2 + - + +
656A VAL* 1.3 80.8 - - + +
658A PRO* 1.3 67.3 - - + +
659A ALA 3.0 0.9 + - - -
660A ALA* 3.1 14.4 + - - +
677A GLY* 5.0 1.3 - - - +
680A LYS* 3.6 61.2 - - + +
681A PHE* 3.8 38.7 - - + -
684A ASN* 4.0 13.0 - - + +
----------------------------------------------------------
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