Contacts of the helix formed by residues 53 - 67 (chain A) in PDB entry 3K4H
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 53 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 1.3 80.6 - - + +
54A GLU* 1.3 66.3 + - - +
55A GLU* 3.2 9.7 + - - +
56A GLU* 2.9 46.0 + - - +
57A ILE* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU 4.2 0.4 + - - -
53A THR* 1.3 75.5 - - - +
55A GLU* 1.3 65.6 + - - +
57A ILE* 3.3 10.6 + - + +
58A PHE* 3.1 18.2 + - - +
79A ARG* 5.4 10.3 - - - +
83A ARG* 2.7 44.6 + - - -
84A ILE* 5.7 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A THR* 3.2 6.9 + - - +
54A GLU* 1.3 86.9 + - - +
56A GLU* 1.3 67.7 + - + +
58A PHE* 3.1 2.4 + - - +
59A ASN* 2.9 46.0 + - - +
83A ARG* 4.2 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 4.5 0.2 + - - -
51A GLY* 3.7 18.8 - - - -
52A GLU* 3.1 24.3 + - - +
53A THR* 2.9 34.7 + - + +
55A GLU* 1.3 83.0 - - + +
57A ILE* 1.3 56.8 + - - +
59A ASN* 3.6 10.3 + - - +
60A GLY* 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.0 27.1 - - + -
15A MSE 4.1 5.2 - - + +
16A PRO 4.1 6.3 - - - +
17A SER* 3.4 43.1 - - - +
18A SER 4.3 0.7 - - - +
49A SER* 5.0 4.5 + - - +
51A GLY* 3.2 21.5 - - - +
52A GLU 4.4 2.5 - - - +
53A THR 2.8 20.9 + - - +
54A GLU* 3.8 7.4 - - - +
56A GLU* 1.3 69.8 - - - +
58A PHE* 1.3 67.4 + - - +
60A GLY* 3.1 3.5 + - - +
61A VAL* 3.1 19.6 + - + +
77A TYR* 5.5 1.1 - - - +
84A ILE* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 3.1 13.6 + - - +
55A GLU 3.1 8.3 + - - +
57A ILE* 1.3 73.4 - - - +
59A ASN* 1.3 75.9 + - - +
61A VAL* 2.8 16.1 + - + +
62A VAL* 3.0 35.2 + - + +
83A ARG* 3.2 59.9 - - + +
84A ILE* 3.7 23.3 - - + +
87A TYR* 3.9 30.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 2.9 39.9 + - - +
56A GLU* 3.9 8.8 - - - +
58A PHE* 1.3 82.0 - - - +
60A GLY* 1.3 64.9 + - - +
62A VAL* 3.1 9.5 + - - +
63A LYS* 2.9 37.8 + - + +
83A ARG* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 4.9 1.9 + - - -
49A SER* 3.7 30.2 - - - -
56A GLU 3.0 11.4 + - - -
57A ILE 3.1 5.1 + - - -
58A PHE 3.0 1.6 + - - -
59A ASN* 1.3 77.8 - - - +
61A VAL* 1.3 62.1 + - - +
63A LYS* 3.4 7.2 + - - +
64A MSE 3.2 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.3 36.6 - - + -
49A SER* 6.5 0.2 - - - -
57A ILE 3.1 13.0 + - - +
58A PHE* 2.8 11.7 + - + +
60A GLY* 1.3 70.5 - - - +
62A VAL* 1.3 66.6 + - + +
64A MSE 3.0 14.7 - - - +
65A VAL* 3.0 21.1 + - - +
73A ILE* 4.1 5.6 - - + -
84A ILE* 3.8 29.2 - - + -
87A TYR* 4.3 9.9 - - + -
88A LEU* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.0 42.7 + - + +
59A ASN* 3.5 11.7 - - - +
61A VAL* 1.3 78.0 - - + +
63A LYS* 1.3 59.7 + - + +
65A VAL* 3.2 2.1 + - - +
66A GLN* 2.8 63.1 + - - +
87A TYR* 3.8 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 5.5 7.9 - - - +
59A ASN* 2.9 29.0 + - + +
60A GLY* 3.9 6.5 - - - +
62A VAL* 1.3 74.7 - - + +
64A MSE 1.3 60.8 + - - +
66A GLN* 3.9 8.9 - - - +
67A GLY* 2.8 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY* 3.2 33.9 - - - -
13A LEU 4.8 4.5 - - - +
14A VAL* 4.7 7.2 - - - -
47A TYR* 3.3 35.8 + - + -
49A SER* 5.4 4.7 - - - -
60A GLY 3.2 15.1 + - - +
61A VAL* 3.0 26.0 - - - +
63A LYS* 1.3 76.9 - - - +
65A VAL* 1.3 62.7 + - - +
67A GLY* 3.5 6.6 + - - -
68A ARG 4.0 5.2 + - - -
69A GLN* 4.5 0.3 + - - +
70A ILE* 3.3 48.4 + - + +
73A ILE* 3.3 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL 3.0 14.3 + - - +
62A VAL 3.8 1.6 - - - +
64A MSE 1.3 76.0 - - - +
66A GLN* 1.3 64.1 + - + +
67A GLY 3.3 0.9 + - - -
68A ARG* 3.4 22.6 + - - +
73A ILE* 4.3 6.3 - - + -
87A TYR* 3.6 36.6 - - + +
88A LEU* 3.8 19.7 - - + -
91A GLN* 4.7 9.0 - - + -
93A PHE* 3.7 38.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 2.8 43.9 + - - +
63A LYS* 3.9 9.1 + - - +
65A VAL* 1.3 78.5 - - + +
67A GLY* 1.3 59.3 + - - +
68A ARG* 3.1 28.1 + - - +
87A TYR* 4.1 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS 2.8 16.9 + - - -
64A MSE 3.5 2.2 + - - -
65A VAL 3.2 0.8 - - - -
66A GLN* 1.3 76.3 - - - +
68A ARG* 1.3 56.4 + - - +
69A GLN* 2.8 44.4 + - - +
----------------------------------------------------------
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