Contacts of the helix formed by residues 699 - 709 (chain K) in PDB entry 6D6Q
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 TYR 699 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694K PRO* 2.9 43.6 - - + +
695K PRO 4.3 1.1 - - - -
696K PRO* 3.4 22.0 + - + +
698K ASN* 1.3 76.5 - - + +
700K GLU* 1.3 65.5 + - - +
701K ILE 3.1 0.2 - - - -
702K LEU* 2.9 24.4 + - + +
703K VAL* 2.9 12.4 + - - +
715K THR* 3.5 41.1 - - + +
717K THR 5.5 1.6 - - - -
721K LEU* 3.1 30.7 - - + -
744K ALA* 5.3 6.3 - - + -
747K CYS* 4.5 15.5 - - + -
748K MET* 5.1 8.6 - - + +
765K TYR* 2.4 30.1 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 700 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696K PRO 3.8 8.2 + - - +
697K SER* 3.5 22.5 - - - +
699K TYR* 1.3 77.7 - - - +
701K ILE* 1.3 81.6 + - + +
703K VAL* 3.6 9.5 - - - +
704K LYS* 2.9 68.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 701 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697K SER 4.4 4.3 - - - +
698K ASN* 3.4 21.1 - - - +
699K TYR 3.0 0.6 + - - -
700K GLU* 1.3 107.6 - - + +
702K LEU* 1.3 59.3 + - - +
704K LYS* 3.3 7.8 + - + +
705K ALA* 2.9 29.6 + - + +
743K LEU* 5.8 4.3 - - + -
747K CYS* 5.8 1.8 - - - -
853K LEU 6.1 0.4 - - - +
854K PHE* 4.0 31.0 - - + -
892K PRO* 5.4 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 702 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698K ASN 4.7 0.6 + - - +
699K TYR* 2.9 19.9 + - + +
701K ILE* 1.3 80.5 - - - +
703K VAL* 1.3 64.4 + - + +
705K ALA* 3.3 6.5 + - - +
706K ALA* 2.9 21.1 + - - +
713K ILE* 3.1 41.3 - - + -
715K THR* 5.8 1.3 - - + -
721K LEU* 6.3 2.2 - - + -
725K LEU* 5.5 6.3 - - + -
740K LEU* 3.2 43.2 - - + +
743K LEU* 3.7 20.6 - - + +
744K ALA* 3.5 25.6 - - + +
747K CYS* 5.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 703 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699K TYR 2.9 20.8 + - - +
700K GLU* 3.6 10.1 - - - +
702K LEU* 1.3 79.0 - - + +
704K LYS* 1.3 60.5 + - + +
706K ALA* 3.4 1.9 + - - +
707K ARG* 2.8 35.1 + - + +
711K LEU 5.0 0.5 - - - +
712K GLU* 5.9 2.0 - - - +
713K ILE* 4.8 22.4 - - + +
715K THR* 3.3 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 704 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700K GLU* 2.9 42.9 + - + +
701K ILE* 3.7 6.1 - - - +
703K VAL* 1.3 76.4 - - + +
705K ALA* 1.3 57.4 + - - +
707K ARG* 3.3 7.5 + - - +
708K SER* 2.9 30.0 + - - -
889K ASP 2.6 26.3 + - - -
890K GLU* 3.1 24.8 + - - +
891K ILE* 5.4 4.5 - - + +
892K PRO* 4.1 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 705 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701K ILE* 2.9 15.9 + - + +
702K LEU* 3.4 12.6 - - + +
704K LYS* 1.3 76.2 - - - +
706K ALA* 1.3 64.6 + - - +
708K SER* 2.6 24.9 + - - -
709K ARG* 2.9 12.8 + - - +
740K LEU* 6.4 1.1 - - + -
743K LEU* 4.8 14.1 - - + -
892K PRO* 4.9 6.2 - - + +
903K VAL* 4.1 23.7 - - + +
904K PHE* 5.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 706 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702K LEU 2.9 10.3 + - - +
703K VAL 4.1 1.8 - - - +
705K ALA* 1.3 76.4 - - - +
707K ARG* 1.3 50.0 + - - +
709K ARG* 2.9 7.9 - - - +
710K ASN 2.7 10.9 + - - -
711K LEU* 2.5 59.9 + - + +
713K ILE* 3.6 25.6 - - + -
740K LEU* 4.2 12.5 - - + +
904K PHE* 5.9 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 707 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703K VAL* 2.8 22.9 + - + +
704K LYS* 3.4 10.8 - - - +
705K ALA 3.0 0.2 - - - -
706K ALA* 1.3 73.9 - - - +
708K SER* 1.3 56.6 + - - +
709K ARG 3.0 4.3 - - - -
710K ASN* 2.7 52.5 + - - +
711K LEU 4.1 2.4 + - - -
712K GLU* 3.2 30.4 + - - +
891K ILE* 5.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 708 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704K LYS 2.9 14.9 + - - -
705K ALA* 2.6 23.0 + - - -
707K ARG* 1.3 75.3 - - - +
709K ARG* 1.3 68.8 + - - +
710K ASN* 3.4 1.5 - - - +
891K ILE* 4.1 29.0 - - - +
892K PRO* 5.3 3.0 - - - +
902K HIS* 5.7 6.5 - - - +
903K VAL* 4.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 709 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705K ALA 2.9 16.6 + - - +
706K ALA* 2.9 11.2 - - - +
707K ARG 3.0 0.2 - - - -
708K SER* 1.3 88.7 + - - +
710K ASN* 1.3 77.3 + - - +
711K LEU* 2.8 16.6 + - + +
733K PHE* 3.2 37.9 - - - -
736K LEU* 5.7 5.4 - - + +
902K HIS* 4.3 9.5 - - - +
903K VAL* 2.1 35.5 + - + +
904K PHE* 3.3 31.4 + - + +
905K ASP* 3.0 24.2 + - - -
----------------------------------------------------------
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