Contacts of the helix formed by residues 624 - 632 (chain B) in PDB entry 6CNC
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 624 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLU* 5.9 1.0 - - - +
38B ILE* 3.0 32.2 + - - +
40B THR* 3.0 32.3 + - + +
43B ASP* 2.8 27.7 - - - +
622B VAL* 3.0 17.1 - - - +
623B LYS* 1.3 76.2 - - - +
625B ILE* 1.3 61.6 + - - +
626B HIS 3.4 2.2 + - - -
627B LEU* 3.6 12.6 + - - +
628B ARG* 3.8 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 625 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B VAL 4.4 0.4 - - - +
623B LYS* 2.5 21.5 + - + +
624B ASP* 1.3 73.3 - - - +
626B HIS* 1.3 85.2 + - + +
628B ARG* 3.4 37.0 + - + +
629B LYS* 2.9 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 626 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B ARG* 4.1 4.2 + - - -
622B VAL* 2.8 31.8 + - + +
623B LYS* 5.3 1.8 - - - +
624B ASP 3.4 0.8 - - - -
625B ILE* 1.3 91.3 - - + +
627B LEU* 1.3 52.2 + - + +
629B LYS* 3.0 28.1 - - + +
630B LEU* 2.6 29.6 + - - +
635B LEU* 3.1 11.2 - - + +
640B PHE* 4.2 18.4 - + + -
643B LEU* 4.1 24.1 - - + +
645B LEU* 3.4 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 627 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.7 3.1 - - + -
40B THR* 6.2 0.7 - - + -
43B ASP* 3.1 59.9 - - + +
44B LYS* 3.9 7.2 - - + +
46B HIS* 5.2 2.2 - - + -
47B LEU* 3.7 31.4 - - + +
622B VAL* 4.1 25.4 - - + -
624B ASP* 3.6 10.2 + - - +
625B ILE 3.2 0.8 - - - -
626B HIS* 1.3 75.8 - - - +
628B ARG* 1.3 60.8 + - - +
630B LEU* 2.8 28.1 + - + +
631B LEU* 3.0 24.1 + - + +
640B PHE* 5.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 628 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP 5.9 3.1 - - - -
38B ILE* 4.4 21.2 - - + +
624B ASP 3.8 4.3 + - - +
625B ILE* 3.4 34.7 + - + +
627B LEU* 1.3 76.4 - - - +
629B LYS* 1.3 58.4 + - - +
630B LEU 3.1 0.9 + - - -
631B LEU* 4.9 8.7 - - + +
632B ASP* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 629 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B ILE* 2.9 24.1 + - + +
626B HIS* 3.0 33.4 - - + +
628B ARG* 1.3 73.8 - - - +
630B LEU* 1.3 52.5 + - - +
632B ASP* 2.7 26.5 - - - +
634B GLU 3.0 22.4 + - - +
635B LEU* 3.1 26.2 - - + +
643B LEU* 5.0 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 630 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS* 3.9 24.7 - - + +
47B LEU* 4.1 14.8 - - + -
50B ALA* 4.6 12.1 - - + -
626B HIS 2.6 14.3 + - - +
627B LEU* 2.8 31.5 + - + +
628B ARG 3.0 0.4 - - - -
629B LYS* 1.3 73.8 - - - +
631B LEU* 1.3 60.8 + - - +
632B ASP* 2.8 15.0 - - - +
633B GLY* 2.8 15.6 + - - -
634B GLU 4.0 0.2 + - - -
635B LEU* 3.6 8.1 + - + -
636B ASP* 3.3 45.7 + - - +
640B PHE* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 631 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.7 19.3 - - + -
43B ASP* 5.9 0.2 - - + -
46B HIS* 3.7 44.6 - - + +
627B LEU* 3.0 19.1 + - + +
628B ARG* 4.9 7.2 - - + +
630B LEU* 1.3 75.5 - - + +
632B ASP* 1.3 62.4 + - - +
633B GLY* 3.0 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 632 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B ARG* 3.0 24.7 + - + +
629B LYS* 2.7 32.4 - - - +
630B LEU 2.8 3.3 - - - +
631B LEU* 1.3 80.3 - - - +
633B GLY* 1.3 73.4 + - - +
634B GLU* 3.2 23.2 + - - +
----------------------------------------------------------
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