Contacts of the helix formed by residues 702 - 716 (chain F) in PDB entry 5G04
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 ASN 702 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669F SER* 3.4 21.8 + - - +
673F CYS* 5.7 0.7 - - - -
695F ALA 3.6 5.1 + - - -
699F ASP* 2.8 48.2 + - - +
700F PRO 3.1 5.2 - - - +
701F LYS* 1.3 71.7 - - - +
703F PRO* 1.3 71.1 - - + +
704F LEU* 4.8 1.3 - - + +
705F CYS* 3.3 42.1 - - + +
706F LYS* 3.4 9.7 + - - +
732F ILE* 5.0 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 703 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701F LYS 3.2 10.3 - - - +
702F ASN* 1.3 83.8 - - + +
704F LEU* 1.3 68.2 + - + +
705F CYS 3.3 0.3 + - - -
706F LYS 3.4 0.2 + - - -
707F PHE* 3.1 23.0 + - - +
729F LEU* 3.4 18.5 - - + +
732F ILE* 4.2 5.4 - - + +
733F VAL* 3.4 30.5 - - + -
492R SER* 5.8 5.2 - - - -
493R LEU* 3.9 18.4 - - + +
496R GLN* 6.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 704 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670F VAL* 4.0 27.8 - - + -
673F CYS* 4.3 16.6 - - + -
674F HIS* 4.7 10.5 - - + +
702F ASN* 5.4 1.8 - - + -
703F PRO* 1.3 82.1 - - + +
705F CYS* 1.3 62.2 + - - +
707F PHE* 3.5 6.6 + - + +
708F HIS* 3.0 55.1 + - + +
493R LEU* 3.8 11.4 - - + +
494R ILE* 3.4 39.3 - - + +
496R GLN* 5.2 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 705 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673F CYS* 3.5 28.4 - - - -
692F LEU* 4.3 5.6 - - + +
695F ALA* 4.6 6.7 - - + -
696F ILE* 3.2 33.4 - - + +
699F ASP 4.6 0.7 - - - -
702F ASN* 3.3 44.0 + - + +
703F PRO 3.3 0.4 - - - -
704F LEU* 1.3 79.6 - - - +
706F LYS* 1.3 78.8 - - - +
708F HIS* 3.1 5.6 + - - +
709F ARG* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 706 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696F ILE* 3.9 43.9 - - + +
700F PRO* 4.7 2.4 - - - +
701F LYS* 3.6 22.4 - - - +
702F ASN 3.7 11.4 - - - +
703F PRO 3.4 3.9 + - - +
705F CYS* 1.3 88.1 - - - +
707F PHE* 1.3 61.8 + - - +
709F ARG* 3.4 5.2 + - - +
710F ALA* 3.3 19.9 + - - +
725F GLU* 4.3 24.3 - - + +
728F GLU* 4.8 18.1 + - + +
729F LEU* 4.0 13.0 - - + +
732F ILE* 3.8 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 707 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703F PRO 3.1 15.4 + - - +
704F LEU* 3.7 6.3 - - - +
706F LYS* 1.3 76.8 - - - +
708F HIS* 1.3 88.7 + + - +
710F ALA* 3.1 9.3 + - - +
711F SER* 3.0 22.1 + - - -
726F LEU* 4.5 8.5 - - + -
729F LEU* 3.4 29.3 - - + +
736F GLU* 6.5 0.4 - - + -
738F LEU* 4.0 37.2 - - + -
739F VAL* 4.7 6.5 - - + -
742F LEU* 3.4 42.8 - - + -
777F GLU* 6.1 1.1 - - + -
494R ILE* 4.4 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 708 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673F CYS* 4.0 12.3 - - + -
674F HIS* 6.0 1.6 - - - -
677F VAL* 3.5 38.5 - - + +
692F LEU* 3.9 17.7 - - + -
704F LEU* 3.0 49.3 + - + +
705F CYS 3.6 4.5 - - - +
707F PHE* 1.3 94.6 - + - +
709F ARG* 1.3 67.0 + - - +
711F SER* 3.0 10.6 + - - -
712F VAL* 2.9 27.5 + - + +
494R ILE* 5.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 709 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689F LEU* 3.4 30.0 - - + +
692F LEU* 3.7 19.3 - - + +
693F ASN* 2.8 44.0 + - - +
696F ILE* 3.8 21.0 - - + +
705F CYS 3.1 11.2 + - - +
706F LYS 3.6 5.6 - - - +
708F HIS* 1.3 76.8 - - - +
710F ALA* 1.3 60.8 + - - +
712F VAL* 3.4 2.4 + - - +
713F LEU* 3.0 31.3 + - - +
721F SER* 5.4 2.8 + - - -
725F GLU* 3.2 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 710 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706F LYS 3.3 9.3 + - - +
707F PHE* 3.1 11.5 + - - +
709F ARG* 1.3 77.4 - - - +
711F SER* 1.3 53.0 + - - +
713F LEU* 3.3 5.8 + - - +
714F PHE* 2.9 34.5 + - - +
722F ALA* 4.0 15.8 - - - +
725F GLU* 3.6 10.9 + - + -
726F LEU* 3.7 36.3 - - + +
729F LEU* 6.1 0.2 - - + -
742F LEU* 4.5 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 711 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680F HIS* 4.6 6.6 + - - -
707F PHE* 3.0 17.0 + - - -
708F HIS* 3.0 20.6 + - - -
710F ALA* 1.3 75.1 - - - +
712F VAL* 1.3 65.1 + - - +
714F PHE* 3.5 9.4 + - - +
715F ALA* 3.5 18.4 + - - +
742F LEU* 4.1 25.7 - - - +
781F LYS* 4.4 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 712 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676F GLY 5.2 2.0 - - - +
677F VAL* 5.6 4.5 - - + -
680F HIS* 3.9 37.9 - - + -
685F SER* 3.9 17.9 - - - +
688F ALA* 4.3 6.5 - - + -
689F LEU* 4.2 14.4 - - + +
692F LEU* 3.5 22.0 - - + -
708F HIS* 2.9 19.3 + - + +
709F ARG 3.9 2.2 - - - +
711F SER* 1.3 78.3 - - - +
713F LEU* 1.3 61.7 - - - +
715F ALA* 3.3 7.6 + - - +
716F ASN* 3.3 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 713 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689F LEU* 3.7 38.6 - - + -
709F ARG* 3.0 22.4 + - - +
710F ALA 3.7 4.3 - - - +
712F VAL* 1.3 74.7 - - - +
714F PHE* 1.3 63.3 + - - +
716F ASN* 3.2 5.8 + - + +
717F GLU 3.2 16.8 + - - -
718F LYS* 3.4 46.2 + - + +
721F SER* 3.8 26.5 - - - +
722F ALA* 4.3 12.6 - - + -
725F GLU* 3.5 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 714 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710F ALA 2.9 16.3 + - - +
711F SER* 3.5 12.6 - - - +
712F VAL 3.3 0.2 - - - -
713F LEU* 1.3 77.4 - - - +
715F ALA* 1.3 64.6 + - + +
717F GLU* 3.3 15.1 + - - +
719F TYR* 3.9 13.7 - + - -
722F ALA* 4.4 5.8 - - + +
742F LEU* 4.8 11.2 - - + -
745F LYS* 3.5 49.6 - - + -
746F VAL* 3.5 27.1 - - + -
749F LYS* 4.1 29.3 - - + -
781F LYS* 5.4 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 715 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680F HIS* 3.6 27.1 - - + +
685F SER* 5.9 2.2 - - - -
711F SER 3.5 4.9 + - - +
712F VAL 3.3 10.4 + - - +
714F PHE* 1.3 78.6 - - + +
716F ASN* 1.3 59.9 + - - +
717F GLU* 3.2 16.4 + - - +
781F LYS 4.8 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 716 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685F SER* 4.0 26.5 + - - -
686F GLU* 4.1 11.2 - - - +
689F LEU* 4.3 15.2 - - - +
712F VAL* 3.3 31.3 + - - +
713F LEU* 3.2 11.8 + - + +
715F ALA* 1.3 75.7 - - - +
717F GLU* 1.3 61.4 + - - +
718F LYS* 3.1 35.9 + - - +
----------------------------------------------------------
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