Contacts of the helix formed by residues 1030 - 1035 (chain B) in PDB entry 6CNB
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 MET1030 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B ILE* 6.3 0.4 - - + -
726B TYR* 4.7 13.0 - - + -
785B CYS* 4.4 3.4 - - + -
904B ARG* 3.3 59.5 - - + +
905B ARG 4.5 5.6 - - - +
906B PRO* 4.8 0.2 - - + -
907B GLU* 5.8 1.3 - - + -
910B ASP* 3.3 28.3 - - - +
1026B LYS* 2.5 37.9 - - - +
1027B LEU 4.3 11.4 - - - +
1028B LYS 3.1 2.1 + - - -
1029B HIS* 1.3 79.7 - - - +
1031B VAL* 1.3 67.4 + - + +
1032B LEU* 4.6 3.6 - - + +
1033B ASP* 3.4 19.8 + - - +
1034B LYS* 3.7 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1031 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A THR* 4.5 8.3 - - + -
380A VAL* 3.5 27.4 - - + +
496A ARG* 4.1 22.0 - - + +
907B GLU* 3.9 19.1 - - + +
908B LEU 3.6 15.5 - - - +
909B GLY 3.1 16.4 - - - +
910B ASP* 2.9 17.7 + - - +
1029B HIS 3.4 2.8 + - - -
1030B MET* 1.3 73.0 - - + +
1032B LEU* 1.3 59.1 + - - +
1034B LYS* 2.5 31.3 + - + +
1035B MET* 3.1 14.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1032 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ARG* 3.7 39.1 + - - +
876B PRO* 3.5 32.6 - - + +
877B GLU* 3.9 37.2 - - + +
902B GLN* 4.3 2.0 - - - +
904B ARG* 4.2 28.9 - - + +
907B GLU* 4.2 13.5 - - - +
1030B MET* 3.3 2.5 - - + +
1031B VAL* 1.3 80.9 - - - +
1033B ASP* 1.3 61.5 + - - +
1035B MET* 4.7 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1033 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B TYR* 3.0 25.3 + - - -
789B ARG* 3.8 13.9 + - - -
904B ARG* 2.4 40.7 + - - +
1028B LYS* 5.6 0.2 - - - +
1029B HIS* 5.5 1.9 + - - -
1030B MET* 3.5 13.8 + - - +
1031B VAL 2.8 0.8 + - - -
1032B LEU* 1.3 81.4 - - - +
1034B LYS* 1.3 62.4 + - + +
1035B MET 3.5 5.7 + - - +
1054B ARG* 3.3 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1034 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG* 3.6 11.8 - - - +
379A THR* 5.3 1.6 - - - -
380A VAL* 4.1 23.8 - - + +
514A GLY 5.6 1.3 - - - +
516A GLU* 3.0 35.1 + - + +
1028B LYS* 5.4 1.6 - - - +
1029B HIS* 3.4 49.5 + - - +
1030B MET 4.1 5.4 - - - +
1031B VAL* 2.5 20.6 + - + +
1033B ASP* 1.3 72.9 - - + +
1035B MET* 1.3 63.3 + - - +
1036B HIS* 3.6 5.8 + - - +
1054B ARG* 4.6 8.2 - - - +
25Y T 5.9 0.4 + - - -
26Y T 5.5 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1035 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG 3.5 5.4 - - - -
379A THR* 3.6 24.7 - - + +
395A PRO* 4.3 8.3 - - - -
397A ARG* 4.3 15.0 - - + +
398A VAL* 3.6 28.9 - - + -
496A ARG* 3.3 61.9 - - + +
876B PRO* 6.0 1.8 - - + -
1031B VAL* 3.1 12.3 + - + +
1032B LEU 4.7 3.2 + - - +
1033B ASP 3.5 8.4 - - - +
1034B LYS* 1.3 78.9 - - - +
1036B HIS* 1.3 65.4 + - - +
1054B ARG* 5.1 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