Contacts of the helix formed by residues 604 - 613 (chain A) in PDB entry 1JSC
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 ASP 604 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A PRO* 1.3 69.4 - - - +
605A PHE* 1.3 51.3 + - - +
606A ILE* 3.6 2.1 - - - +
607A LYS* 2.9 61.8 + - + +
608A LEU* 2.7 35.8 + - - +
618A ARG* 2.9 32.0 + - - +
611B ALA* 2.9 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ASP* 4.2 12.8 - - + -
553A PHE* 3.7 26.9 - + - -
554A ASN* 4.0 8.7 - - - -
557A LEU* 5.0 0.2 - - + -
574A ILE* 3.9 27.1 - - + -
576A ASN* 3.8 19.1 - - - -
602A ASN* 3.8 31.2 - - + -
603A PRO* 3.0 32.3 + - + -
604A ASP* 1.3 70.5 + - - +
606A ILE* 1.3 68.4 + - + +
608A LEU* 3.4 7.2 - - + +
609A ALA* 2.9 29.1 + - - +
618A ARG* 4.1 3.2 - - - +
640A LEU* 4.2 16.7 - - + +
642A GLU* 3.6 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ASP* 3.2 9.0 + - - +
605A PHE* 1.3 78.8 - - + +
607A LYS* 1.3 67.1 + - + +
609A ALA* 3.3 7.0 + - - +
610A GLU* 3.0 46.1 + - - +
616A GLY* 3.9 10.5 - - - +
617A LEU* 3.3 41.7 - - - +
618A ARG* 3.6 33.0 - - + +
640A LEU* 4.3 4.0 - - + -
642A GLU* 3.8 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ASP* 2.9 41.9 + - + +
606A ILE* 1.3 79.7 - - + +
608A LEU* 1.3 58.0 + - - +
610A GLU* 3.5 16.0 + - - +
611A ALA* 2.9 28.8 + - - +
607B LYS* 4.7 3.1 - - - +
610B GLU* 5.4 5.6 + - + +
611B ALA* 3.9 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A PHE* 4.1 9.9 - - + -
557A LEU* 3.7 32.5 - - + -
560A LEU* 3.9 17.5 - - + -
603A PRO* 4.3 13.0 - - + -
604A ASP 2.7 18.1 + - - +
605A PHE* 3.4 9.2 - - + +
606A ILE 3.2 0.2 - - - -
607A LYS* 1.3 73.6 - - - +
609A ALA* 1.3 66.4 + - - +
611A ALA* 3.0 5.6 + - - +
612A MET* 2.8 34.7 + - + +
640A LEU* 5.5 0.2 - - + -
608B LEU* 3.4 32.5 - - + -
611B ALA* 3.7 10.7 - - + +
612B MET* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A LEU* 4.6 4.3 - - - -
605A PHE 2.9 13.8 + - - +
606A ILE 3.5 8.1 - - - +
608A LEU* 1.3 78.0 - - - +
610A GLU* 1.3 62.4 + - - +
612A MET* 3.0 3.1 + - - -
613A GLY 2.9 7.1 + - - -
614A LEU* 2.9 37.1 + - + +
615A LYS 4.2 4.5 - - - +
616A GLY* 4.2 13.5 - - - -
640A LEU* 4.0 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A ILE* 3.0 33.6 + - + +
607A LYS* 3.8 15.5 - - - +
609A ALA* 1.3 74.6 - - - +
611A ALA* 1.3 63.4 + - - +
613A GLY* 3.1 13.0 + - - -
614A LEU 3.4 15.0 - - - +
616A GLY 4.5 12.2 + - - +
604B ASP* 5.6 0.3 - - - +
607B LYS* 5.3 8.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A LYS 2.9 18.1 + - - +
608A LEU* 3.0 8.0 + - - +
610A GLU* 1.3 77.7 - - - +
612A MET* 1.3 60.3 + - - +
613A GLY 3.6 0.3 + - - -
603B PRO* 3.4 3.2 - - - +
604B ASP* 2.9 32.6 + - - +
607B LYS* 3.7 19.9 - - + +
608B LEU* 3.7 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 4.0 17.3 - - + +
558A THR* 4.1 12.8 - - - +
560A LEU* 3.5 19.5 - - + -
561A SER* 3.6 35.1 - - - +
564A VAL* 3.6 15.4 - - - +
608A LEU* 2.8 32.1 + - + +
609A ALA 3.0 2.2 + - - +
611A ALA* 1.3 76.9 - - + +
613A GLY* 1.3 58.3 + - - +
614A LEU* 3.5 21.3 - - + -
557B LEU* 4.5 11.0 - - + -
601B LEU* 5.4 3.1 - - - +
602B ASN 5.6 0.3 - - - +
603B PRO* 3.6 27.0 - - + +
608B LEU* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A VAL* 3.7 21.0 - - - +
609A ALA 2.9 1.8 + - - -
610A GLU 3.1 11.3 + - - -
611A ALA 3.3 0.4 + - - -
612A MET* 1.3 80.7 - - - +
614A LEU* 1.3 61.2 + - - +
638A PRO* 4.9 2.4 - - - +
----------------------------------------------------------
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