Contacts of the helix formed by residues 65 - 75 (chain A) in PDB entry 4K71
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 SER 65 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 5.3 5.8 - - - -
63A ASP 3.6 2.4 + - - -
64A LYS* 1.3 76.8 - - - +
66A LEU* 1.3 64.3 + - - +
67A HIS* 3.7 12.2 + - - +
68A THR* 2.9 39.0 + - - -
69A LEU* 3.2 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 3.9 24.1 - - + +
7A VAL* 3.6 46.7 - - + +
10A ARG* 4.2 8.5 - - + -
64A LYS 5.1 0.4 - - - +
65A SER* 1.3 73.1 - - - +
67A HIS* 1.3 64.6 + - + +
69A LEU* 4.5 7.9 - - + +
70A PHE* 2.9 45.9 + - + -
251A LEU* 3.7 27.1 - - + -
252A GLU* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 4.4 6.4 + - - -
65A SER* 3.2 11.1 + - - +
66A LEU* 1.3 79.6 - - + +
68A THR* 1.3 57.1 + - - +
70A PHE* 4.2 4.3 - + - +
71A GLY 3.0 23.4 + - - -
95A GLU* 3.3 24.9 + - + +
96A PRO* 6.0 4.4 - - - +
99A ASN* 3.1 41.6 + - + +
100A GLU* 5.9 0.2 - - - -
247A HIS* 4.2 12.7 + + - -
248A GLY 5.8 0.2 - - - -
249A ASP* 2.7 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 4.1 23.1 - - + +
65A SER* 2.9 27.1 + - - -
67A HIS* 1.3 76.0 - - - +
69A LEU* 1.3 59.6 + - - +
72A ASP* 2.8 51.0 + - - +
95A GLU* 3.7 18.9 - - + +
98A ARG* 3.2 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.1 22.4 - - + -
46A VAL* 5.5 10.5 - - + -
49A PHE* 3.5 41.1 - - + -
61A ASN* 4.6 1.8 - - + +
64A LYS* 3.8 37.0 - - + +
65A SER 3.2 13.4 + - - +
66A LEU* 3.9 9.9 - - + +
67A HIS 3.4 0.2 - - - -
68A THR* 1.3 76.3 - - - +
70A PHE* 1.3 70.4 + - + +
72A ASP* 3.3 10.2 + - - +
73A LYS* 3.1 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 5.9 0.7 - - + -
19A PHE* 5.9 0.2 - + - -
23A VAL* 4.0 15.0 - - + -
26A ALA* 3.9 28.9 - - + -
27A PHE* 3.7 24.4 - + + -
30A TYR* 4.3 23.3 - + + -
46A VAL* 4.3 22.0 - - + -
66A LEU* 2.9 39.9 + - + +
67A HIS* 4.2 5.6 - + - +
69A LEU* 1.3 81.3 - - + +
71A GLY* 1.3 59.1 + - - +
73A LYS* 3.2 3.1 + - - +
74A LEU* 2.8 35.2 + - + +
248A GLY 5.5 4.3 - - - -
250A LEU* 6.2 1.8 - - + -
251A LEU* 4.0 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS 3.0 13.9 + - - -
70A PHE* 1.3 74.9 - - - +
72A ASP* 1.3 64.5 + - - +
74A LEU* 3.3 1.5 + - - +
75A CYS* 3.0 30.5 + - - +
95A GLU* 4.2 1.3 - - - -
98A ARG* 3.4 26.2 - - - -
102A PHE* 4.2 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 4.1 15.8 + - - +
68A THR* 2.8 35.8 + - - +
69A LEU* 3.4 11.0 - - - +
71A GLY* 1.3 76.1 - - - +
73A LYS* 1.3 65.8 + - + +
75A CYS* 3.7 7.1 + - - +
76A THR* 3.6 17.5 + - - +
98A ARG* 3.2 20.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
27A PHE* 3.9 15.5 - - + -
42A LEU* 3.5 21.3 - - + +
45A GLU* 2.5 49.2 + - + +
46A VAL* 3.9 24.2 - - + +
49A PHE* 6.5 0.2 - - - -
69A LEU* 3.1 13.7 + - + +
70A PHE 3.6 6.5 - - - +
72A ASP* 1.3 78.8 - - + +
74A LEU* 1.3 62.5 + - - +
76A THR* 2.7 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.4 27.1 - - + +
30A TYR* 3.4 41.7 - - + -
31A LEU* 3.4 35.2 - - + +
39A HIS* 4.2 6.7 - - + -
42A LEU* 4.4 5.6 - - + -
70A PHE 2.8 24.3 + - - +
71A GLY 3.9 3.1 - - - +
73A LYS* 1.3 72.2 - - - +
75A CYS* 1.3 58.1 + - - +
76A THR 3.2 0.4 - - - -
77A VAL* 3.3 8.1 + - - +
78A ALA* 3.0 28.0 + - + +
102A PHE* 4.3 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY 3.0 18.9 + - - +
72A ASP* 4.2 4.3 - - - +
73A LYS 3.2 0.2 - - - -
74A LEU* 1.3 72.0 - - - +
76A THR* 1.3 63.4 + - - +
77A VAL 3.2 1.7 + - - -
78A ALA 4.2 1.1 - - - +
79A THR* 3.6 20.8 + - + +
91A CYS* 2.1 59.0 - - + +
98A ARG* 4.0 15.3 - - - +
102A PHE* 3.8 14.1 - - - -
----------------------------------------------------------
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