Contacts of the helix formed by residues 686 - 703 (chain A) in PDB entry 1CJY
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 PRO 686 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A SER* 4.7 8.7 - - - +
677A PRO* 5.2 4.5 - - + -
684A GLN* 3.3 24.7 - - + +
685A TYR* 1.3 89.1 - - - +
687A ASN* 1.3 67.5 + - - +
688A GLN* 3.3 5.4 - - + +
689A ALA* 3.0 17.9 + - + +
690A PHE 3.0 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 687 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A MET* 3.7 34.8 + - - +
257A LYS* 5.3 1.0 - - - +
260A SER* 3.5 26.5 - - - -
685A TYR 4.6 0.4 + - - -
686A PRO* 1.3 71.9 - - - +
688A GLN* 1.3 61.9 + - - +
690A PHE* 3.2 6.6 + - - +
691A LYS* 2.9 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A ILE* 5.8 7.0 - - + -
686A PRO* 3.3 4.3 - - + +
687A ASN* 1.3 79.2 - - - +
689A ALA* 1.3 64.7 + - - +
691A LYS* 3.4 6.5 + - - +
692A ARG* 3.0 70.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A PRO* 3.9 29.8 - - + -
678A PHE* 3.4 22.2 - - + -
685A TYR* 4.4 6.5 - - + -
686A PRO* 3.0 26.9 + - + +
688A GLN* 1.3 81.2 - - - +
690A PHE* 1.3 62.3 + - - +
692A ARG* 3.5 3.8 + - - +
693A LEU* 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 690 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 3.5 42.2 - - + +
206A SER* 4.2 7.2 - - - -
252A ASN* 3.8 20.9 - - + -
255A LEU* 4.0 20.6 - - + -
256A MET* 3.7 45.1 - - + +
259A VAL* 4.9 5.6 - - + -
685A TYR* 4.4 16.3 - - + +
686A PRO 3.0 12.1 + - - +
687A ASN* 3.5 11.2 - - - +
689A ALA* 1.3 77.3 - - - +
691A LYS* 1.3 61.5 + - + +
694A HIS* 2.9 53.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 691 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A MET* 3.9 31.7 - - - +
687A ASN* 2.9 28.5 + - - +
688A GLN* 3.8 5.8 - - - +
690A PHE* 1.3 77.7 - - + +
692A ARG* 1.3 56.2 + - + +
694A HIS* 4.2 5.6 - - + -
695A ASP* 2.6 54.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 692 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A PHE* 4.3 3.9 - - + -
664A GLU 3.6 15.4 + - - -
665A ILE* 2.8 36.1 + - + +
667A ASP 4.1 5.9 + - - -
668A PHE* 3.2 49.0 - - + +
678A PHE* 4.3 8.6 - - + -
688A GLN* 3.0 57.1 + - + +
689A ALA* 3.7 7.9 - - - +
690A PHE 3.3 0.2 - - - -
691A LYS* 1.3 77.4 - - + +
693A LEU* 1.3 53.8 + - - +
695A ASP* 3.8 2.4 - - - +
696A LEU* 2.8 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 693 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ARG* 3.4 43.1 - - + +
203A VAL* 4.1 10.5 - - + -
204A GLY* 4.0 19.0 - - - +
642A LEU* 3.5 35.7 - - + -
668A PHE* 5.3 0.9 - - - -
670A ILE* 5.6 3.6 - - + -
678A PHE* 3.6 32.3 - - + -
685A TYR* 4.1 1.8 - - + -
689A ALA 3.2 5.9 + - - +
690A PHE 4.3 1.8 - - - +
692A ARG* 1.3 78.8 - - - +
694A HIS* 1.3 61.4 + - - +
696A LEU* 4.2 7.6 - - + -
697A MET* 3.3 20.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 694 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 4.0 11.8 - - + +
206A SER* 3.1 17.2 + - - -
207A GLY* 3.3 22.2 - - - -
210A LYS* 3.8 26.1 + - + +
252A ASN* 3.1 36.0 - - + +
690A PHE* 2.9 38.1 + + + +
691A LYS* 3.7 2.9 - - + +
693A LEU* 1.3 77.2 - - - +
695A ASP* 1.3 84.2 + - - +
696A LEU 3.4 0.2 + - - -
698A HIS* 3.0 31.0 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A PHE* 3.8 21.4 - - + -
665A ILE* 6.0 2.3 - - - +
691A LYS* 2.6 42.5 + - - +
692A ARG* 4.9 0.2 - - - -
694A HIS* 1.3 89.4 - - - +
696A LEU* 1.3 58.7 + - - +
698A HIS* 3.3 12.1 - - + +
699A PHE* 2.8 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A LEU* 3.9 24.9 - - + -
643A ALA 3.9 19.5 - - - +
644A ASN* 3.9 18.4 - - + +
647A PHE* 3.5 42.6 - - + -
668A PHE* 4.3 6.7 - - + -
670A ILE* 4.2 11.9 - - + -
692A ARG 2.8 20.2 + - - +
693A LEU* 3.7 7.9 - - + +
694A HIS 3.2 0.2 - - - -
695A ASP* 1.3 78.1 - - - +
697A MET* 1.3 62.5 + - - +
699A PHE* 3.2 1.2 + - - +
700A ASN* 2.9 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 697 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLY* 3.5 21.5 - - - +
207A GLY 4.4 1.8 - - - -
208A VAL* 3.7 15.7 - - + +
574A PHE* 4.2 13.7 - - + -
575A ASP 5.6 1.1 - - - +
576A PHE* 3.7 31.6 - - + -
640A PHE* 4.9 7.0 - - + -
641A VAL 4.4 14.1 - - - +
642A LEU* 3.6 31.4 - - + -
693A LEU 3.3 15.5 + - - +
694A HIS 4.2 0.7 - - - +
696A LEU* 1.3 77.7 - - - +
698A HIS* 1.3 61.6 + - - +
700A ASN* 3.9 19.4 - - + +
701A THR* 2.6 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 698 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLY* 3.6 16.0 + - - +
210A LYS* 4.1 19.2 - - + +
211A ALA* 3.6 20.8 + - - +
214A GLU* 3.4 25.5 + - - -
694A HIS* 3.0 22.3 + + - +
695A ASP* 3.3 14.4 - - + +
696A LEU 3.1 0.2 - - - -
697A MET* 1.3 79.5 - - - +
699A PHE* 1.3 67.4 + - + +
701A THR* 3.2 2.9 + - - -
702A LEU* 3.1 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A GLU* 4.1 3.1 - - - -
646A ASN* 3.8 11.9 - - + -
647A PHE* 3.5 35.2 - + + -
650A TYR* 3.7 28.9 - + + -
651A LYS 4.0 4.5 - - - +
652A ALA* 3.2 45.5 - - - -
653A PRO* 3.4 6.1 - - + -
695A ASP 2.8 19.8 + - - +
696A LEU 3.5 2.9 - - - +
698A HIS* 1.3 79.5 - - + +
700A ASN* 1.3 67.6 + - - +
702A LEU* 2.9 6.5 + - - +
703A ASN* 2.5 66.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 700 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A GLU* 3.8 30.5 + - + +
640A PHE* 3.5 15.0 - - + -
641A VAL 4.2 14.1 + - - -
643A ALA 3.1 25.1 + - - +
645A ILE 5.4 0.2 + - - -
647A PHE* 4.3 1.0 - - - +
696A LEU* 2.9 34.7 + - - +
697A MET* 4.0 20.2 - - + +
699A PHE* 1.3 87.5 - - - +
701A THR* 1.3 61.4 + - - +
703A ASN* 4.3 2.9 - - - -
704A ASN* 3.5 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 3.7 8.1 - - - +
211A ALA* 3.6 20.9 - - + -
212A LEU* 3.8 29.4 - - + +
215A SER* 6.1 0.2 - - - +
217A ILE* 6.3 0.2 - - + -
574A PHE* 3.5 25.7 - - + -
640A PHE* 3.8 12.3 - - + -
697A MET* 2.6 24.0 + - - +
698A HIS 3.5 4.3 - - - -
699A PHE 3.1 0.6 - - - -
700A ASN* 1.3 76.6 - - - +
702A LEU* 1.3 64.3 + - + +
704A ASN* 3.2 12.3 + - - +
705A ILE* 3.4 10.9 + - - -
708A ILE* 5.0 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ALA* 3.6 33.2 - - + +
214A GLU* 5.0 3.6 - - + +
215A SER* 4.3 14.1 - - - +
653A PRO* 3.8 27.8 - - + +
698A HIS* 3.1 39.4 + - + +
699A PHE* 2.9 7.3 + - - +
701A THR* 1.3 74.9 - - + +
703A ASN* 1.3 57.1 + - - +
704A ASN 2.9 11.4 + - - -
705A ILE* 3.4 18.5 + - + +
706A ASP* 4.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A GLU* 3.0 26.3 + - - +
646A ASN* 4.2 12.2 + - - +
653A PRO* 3.4 34.8 - - + +
699A PHE* 2.5 44.7 + - + +
700A ASN 4.1 1.6 - - - +
701A THR 3.3 0.2 - - - -
702A LEU* 1.3 71.7 - - - +
704A ASN* 1.3 66.5 + - - +
705A ILE 3.8 0.2 - - - -
706A ASP* 4.1 9.2 - - - +
----------------------------------------------------------
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