Contacts of the helix formed by residues 57 - 68 (chain A) in PDB entry 2LUC
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 PRO 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 5.3 2.0 - - + +
44A ASN* 4.8 10.1 - - - +
51A THR* 5.1 4.5 - - + -
55A LYS 4.8 0.2 - - - +
56A ASP* 1.3 84.2 - - + +
58A GLY* 1.3 61.0 + - - +
59A VAL* 3.0 7.0 - - + -
60A LEU* 3.0 40.1 + - + +
61A ASP* 3.7 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP* 2.9 19.3 + - - -
57A PRO* 1.3 79.8 - - - +
59A VAL* 1.3 57.0 + - - +
60A LEU 3.3 0.2 - - - -
61A ASP* 3.0 28.2 - - - +
62A ARG* 3.2 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 4.4 11.2 - - + -
51A THR* 4.6 7.2 - - - +
54A GLN* 3.8 36.8 - - + +
56A ASP* 3.0 22.6 + - - +
57A PRO* 4.3 0.7 - - + -
58A GLY* 1.3 74.6 - - - +
60A LEU* 1.3 75.7 + - + +
61A ASP 2.9 4.7 - - - -
62A ARG* 2.8 19.5 + - + +
63A MET* 2.8 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 4.1 4.5 - - + -
40A LEU* 3.6 36.2 - - + +
43A MET* 3.3 33.0 - - + -
44A ASN* 3.1 33.4 - - - +
51A THR* 3.3 27.4 - - + +
57A PRO* 3.0 20.8 + - + +
59A VAL* 1.3 85.1 - - + +
61A ASP* 1.3 56.7 + - - +
63A MET* 3.6 7.7 - - - +
64A MET* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 2.6 38.4 + - - +
40A LEU* 5.0 0.8 - - + +
57A PRO 3.7 1.5 + - - +
58A GLY* 3.0 23.0 + - - +
60A LEU* 1.3 80.4 - - - +
62A ARG* 1.3 61.9 + - - +
64A MET* 3.7 1.0 - - - +
65A LYS* 3.2 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN* 5.8 4.2 - - - +
58A GLY 3.2 17.0 - - - +
59A VAL* 2.8 19.7 + - + +
61A ASP* 1.3 78.3 - - + +
63A MET* 1.3 66.3 + - - +
65A LYS* 3.6 2.8 + - - +
66A LYS* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 3.8 13.5 - - + -
43A MET* 3.8 10.8 - - + -
50A PHE* 3.9 26.2 - - + -
59A VAL* 2.8 37.8 + - + +
60A LEU* 3.6 14.1 - - - +
62A ARG* 1.3 75.1 - - - +
64A MET* 1.3 67.8 + - - +
66A LYS* 3.0 26.4 + - - +
67A LEU* 2.9 34.0 + - + +
83A LEU* 3.6 26.7 - - + +
86A GLY 6.4 1.1 - - - -
87A LEU* 5.2 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU 3.4 23.8 - - - +
36A LYS* 3.7 37.7 - - + -
39A PHE* 3.6 30.0 - - + -
60A LEU 2.9 18.8 + - - +
61A ASP 3.7 4.5 - - - +
63A MET* 1.3 77.5 - - - +
65A LYS* 1.3 65.4 + - + +
67A LEU 3.5 0.2 - - - -
68A ASP* 2.6 40.1 + - - +
73A GLY* 3.6 23.8 - - - +
74A GLN 3.7 0.2 - - - -
75A LEU* 3.5 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 5.7 3.4 - - + +
61A ASP* 3.2 27.7 + - - +
62A ARG* 4.4 2.9 - - - +
64A MET* 1.3 90.9 - - + +
66A LYS* 1.3 60.2 + - - +
68A ASP* 2.7 38.3 + - - +
71A SER* 4.9 4.8 - - - +
73A GLY* 4.5 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG 3.0 16.5 + - - +
63A MET* 3.0 28.0 + - - +
65A LYS* 1.3 79.4 - - - +
67A LEU* 1.3 80.9 + - + +
68A ASP 4.8 1.6 - - - -
69A THR* 4.8 3.3 + - - -
86A GLY* 5.8 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 4.1 2.2 - - + -
63A MET* 2.9 26.3 + - + +
66A LYS* 1.3 96.5 - - + +
68A ASP* 1.3 51.8 + - - +
69A THR* 2.6 24.5 + - - -
75A LEU* 3.3 32.1 - - + -
79A GLU* 3.2 24.5 - - - +
82A ASN* 3.8 17.0 + - + +
83A LEU* 3.3 56.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET* 2.6 31.4 + - - +
65A LYS* 2.7 40.7 + - - +
66A LYS 3.5 1.5 - - - -
67A LEU* 1.3 66.5 - - - +
69A THR* 1.3 58.5 + - - +
70A ASN 3.2 0.9 - - - -
71A SER* 3.1 24.6 + - - -
72A ASP* 2.7 9.7 + - - +
73A GLY* 2.7 29.6 + - - -
74A GLN 3.2 13.9 - - - +
75A LEU* 3.3 3.8 - - - +
79A GLU* 3.2 5.8 - - - +
----------------------------------------------------------
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