Contacts of the helix formed by residues 68 - 79 (chain A) in PDB entry 2KSP
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 THR 68 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 4.3 17.7 - - + -
66A LYS 5.0 0.2 - - - +
67A ILE* 1.3 78.6 - - - +
69A GLY* 1.3 64.9 + - - +
70A ALA* 3.3 11.9 + - - +
71A ASN* 2.8 41.3 + - - +
72A ALA* 3.5 14.0 + - - +
90A TRP* 4.4 2.8 - - - -
100A LEU* 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 1.3 75.3 - - - +
70A ALA* 1.3 56.6 + - - +
72A ALA 3.9 0.3 - - - -
73A LYS* 2.9 32.3 + - - +
90A TRP* 3.5 23.5 - - - -
99A GLY 3.9 9.8 + - - -
100A LEU* 4.4 0.8 - - - +
150B PRO* 3.7 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 3.2 10.1 + - - +
69A GLY* 1.3 75.3 - - - +
71A ASN* 1.3 69.5 + - - +
73A LYS* 3.2 15.5 + - - +
74A LYS* 3.1 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.9 35.4 + - + +
61A SER 4.1 4.8 - - - +
63A VAL* 5.2 2.3 - - - +
67A ILE* 3.4 17.9 - - + +
68A THR* 2.8 39.4 + - - +
69A GLY 3.4 0.2 - - - -
70A ALA* 1.3 80.8 - - - +
72A ALA* 1.3 59.7 + - - +
74A LYS* 3.0 32.2 - - - +
75A GLU* 3.2 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.4 2.7 - - - -
67A ILE* 4.0 14.4 - - + -
68A THR 3.5 6.2 + - - +
71A ASN* 1.3 78.1 - - - +
73A LYS* 1.3 59.7 + - - +
75A GLU* 3.4 8.2 - - - +
76A MET* 2.8 43.2 + - - +
90A TRP* 3.5 25.8 - - + -
101A LEU* 4.0 13.7 - - + -
106A PHE* 4.6 4.5 - - + -
151B PHE* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 2.9 21.2 + - - +
70A ALA* 3.2 15.5 + - - +
72A ALA* 1.3 78.0 - - - +
74A LYS* 1.3 61.5 + - - +
76A MET* 3.3 3.6 + - - +
77A VAL* 3.1 34.1 + - + +
150B PRO* 3.2 26.7 - - + +
151B PHE* 3.5 24.4 - - + -
153B GLU* 2.8 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 5.2 5.6 - - + -
70A ALA* 3.1 27.1 + - - +
71A ASN* 3.0 28.1 - - - +
73A LYS* 1.3 74.1 - - - +
75A GLU* 1.3 62.3 + - - +
77A VAL* 3.1 19.6 - - + +
78A LYS* 2.9 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 4.2 16.4 - - + +
59A THR* 5.5 0.5 + - - -
60A LEU* 3.3 29.0 - - + +
71A ASN 3.2 15.6 + - - +
72A ALA* 3.4 10.1 - - - +
73A LYS 3.2 0.2 - - - -
74A LYS* 1.3 76.7 - - - +
76A MET* 1.3 64.8 + - - +
78A LYS* 2.7 52.4 + - - +
79A SER* 3.0 18.3 + - - +
106A PHE* 4.4 13.2 - - + -
110A ASN* 4.8 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 2.8 37.9 + - + +
73A LYS 3.5 1.6 - - - +
75A GLU* 1.3 79.6 - - - +
77A VAL* 1.3 56.3 + - - +
79A SER* 3.1 26.4 + - - -
80A LYS 3.7 2.8 + - - -
81A LEU 4.2 0.3 + - - -
86A LEU* 3.5 32.2 - - + +
89A ILE* 4.2 10.3 - - + -
90A TRP* 4.4 18.2 - - + +
101A LEU* 4.8 2.2 - - + -
106A PHE* 5.6 1.3 - - + -
109A ALA* 3.6 31.9 - - + -
110A ASN* 5.2 3.4 - - - +
113A ILE* 3.7 25.6 - - + -
151B PHE* 3.4 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 3.1 20.0 + - + +
74A LYS* 3.1 29.8 - - + +
76A MET* 1.3 73.9 - - - +
78A LYS* 1.3 64.8 + - + +
80A LYS* 3.3 23.8 + - - +
81A LEU 5.5 2.5 - - - -
83A ASN* 5.0 8.5 - - - +
86A LEU* 4.1 16.2 - - + -
151B PHE* 5.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.1 8.7 - - - +
74A LYS* 2.9 24.5 + - + +
75A GLU* 2.7 58.2 + - - +
77A VAL* 1.3 76.4 - - + +
79A SER* 1.3 60.1 + - - +
80A LYS* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 3.0 18.7 + - - +
76A MET* 3.1 17.1 + - - -
78A LYS* 1.3 76.4 - - - +
80A LYS* 1.3 64.0 + - - +
81A LEU* 3.1 29.1 - - - +
110A ASN* 5.7 0.9 + - - -
113A ILE* 3.9 23.0 - - - +
117A LEU* 4.4 10.8 - - - +
----------------------------------------------------------
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