Contacts of the helix formed by residues 67 - 74 (chain X) in PDB entry 1KKC
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 67 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.9 0.2 + - - -
62X ALA* 2.9 16.5 + - - +
65X ALA* 3.1 10.3 - - + +
66X THR* 1.3 73.8 - - - +
68X VAL* 1.3 57.9 + - - +
69X PRO* 3.1 14.2 - - - +
70X LYS* 2.8 42.8 + - + +
71X LEU* 3.0 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.3 38.8 - - + -
52A LEU* 4.0 19.5 - - + -
82A GLY* 3.7 16.6 - - - +
85A HIS* 4.4 9.2 - - + +
86A ILE* 3.5 24.2 - - + -
66X THR 3.4 3.9 + - - +
67X ASP* 1.3 69.0 - - - +
69X PRO* 1.3 76.1 - - + +
71X LEU* 3.2 8.3 + - + +
72X VAL* 2.9 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 69 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 3.5 26.9 - - + -
163A PRO* 6.1 0.9 - - + -
165A THR* 5.8 2.1 - - - +
213A LYS 5.3 10.1 - - - +
66X THR 5.3 0.2 - - - +
67X ASP* 3.1 13.2 - - - +
68X VAL* 1.3 94.0 - - + +
70X LYS* 1.3 61.5 + - - +
72X VAL* 3.4 2.6 + - + +
73X SER* 3.1 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58X ALA* 4.4 24.0 - - - +
62X ALA* 3.6 16.8 - - + -
67X ASP* 2.8 34.1 + - + +
69X PRO* 1.3 71.0 - - - +
71X LEU* 1.3 63.7 + - - +
73X SER* 2.7 26.3 + - - +
74X VAL* 3.3 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.7 19.3 - - + +
52A LEU* 5.8 1.8 - - + -
56A LEU* 4.2 22.7 - - + -
78A ILE* 4.6 7.9 - - + -
59X GLN* 3.0 42.2 - - + +
62X ALA* 3.5 8.1 - - + -
63X ALA* 3.3 28.7 - - + +
67X ASP 3.0 25.5 + - - +
68X VAL* 3.2 9.4 + - + +
70X LYS* 1.3 77.6 - - - +
72X VAL* 1.3 63.0 + - + +
74X VAL* 3.3 18.1 - - - +
75X GLN* 3.3 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 5.9 0.2 - - + -
78A ILE* 4.0 12.3 - - + +
79A LYS* 4.2 21.5 - - + +
82A GLY* 3.9 34.1 - - - -
83A GLY 4.0 0.4 - - - +
86A ILE* 4.0 4.5 - - + -
163A PRO* 3.8 31.6 - - + -
165A THR* 5.9 1.3 - - + -
68X VAL* 2.9 22.0 + - + +
69X PRO 3.8 3.8 - - - +
71X LEU* 1.3 75.3 - - + +
73X SER* 1.3 65.5 + - - +
75X GLN* 3.1 22.6 - - - +
76X GLN 4.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A THR* 4.9 18.4 - - - +
69X PRO 3.1 13.2 + - - -
70X LYS* 2.7 38.6 + - - +
72X VAL* 1.3 79.3 - - - +
74X VAL* 1.3 59.6 + - - +
75X GLN 3.1 1.4 + - - -
76X GLN* 3.5 15.2 + - - +
77X ALA 4.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55X ALA* 3.3 39.0 - - + +
58X ALA* 4.3 12.6 - - + -
59X GLN* 4.0 26.9 - - + -
70X LYS* 3.6 15.7 - - - +
71X LEU 3.3 17.9 - - - +
73X SER* 1.3 79.5 + - - +
75X GLN* 1.3 66.0 + - - +
76X GLN 3.2 0.7 - - - -
77X ALA* 3.1 17.9 + - + +
78X ILE* 3.2 13.2 + - + +
----------------------------------------------------------
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