Contacts of the helix formed by residues 42 - 60 (chain P) in PDB entry 3LUE
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 ALA 42 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P TRP* 1.3 77.6 + - - +
44P GLU* 3.1 5.9 + - - +
45P LYS* 3.2 10.6 + - - +
46P GLN* 2.7 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 43 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G ARG 6.0 1.8 - - - -
92G ASN 4.6 9.2 - - - -
93G GLU* 4.2 23.8 - - - +
42P ALA* 1.3 87.9 - - - +
44P GLU* 1.3 89.5 + - + +
46P GLN* 3.3 8.5 + - - +
47P GLN* 2.8 77.3 + - - +
135P LYS* 4.7 27.1 - - + -
138P LEU* 5.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P ALA 3.1 4.0 - - - +
43P TRP* 1.3 108.5 + - + +
45P LYS* 1.3 62.0 - - - +
47P GLN* 4.6 1.1 - - - -
48P ARG* 3.1 25.1 + - - +
134P LEU* 3.2 37.6 - - + +
135P LYS* 3.7 30.4 + - + +
138P LEU* 3.9 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P ALA* 3.2 6.5 + - - +
44P GLU* 1.3 78.8 - - - +
46P GLN* 1.3 77.4 + - - +
48P ARG* 3.5 11.0 + - - +
49P LYS* 3.2 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P ALA* 2.7 40.1 + - + +
43P TRP* 3.6 7.0 - - - +
45P LYS* 1.3 91.2 - - - +
47P GLN* 1.3 67.1 + - - +
49P LYS* 2.9 19.1 + - - +
50P THR* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G ASN 4.3 1.4 + - - +
93G GLU 4.4 2.2 + - - -
95G ARG* 2.3 61.0 + - + +
43P TRP* 2.8 55.9 + - - +
44P GLU* 4.0 3.1 - - - +
46P GLN* 1.3 73.5 - - - +
48P ARG* 1.3 56.6 + - - +
50P THR* 4.6 3.6 - - - +
51P PHE* 2.9 52.2 + - + -
138P LEU* 4.0 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P GLU 3.1 18.2 + - - +
45P LYS* 3.6 12.2 + - - +
46P GLN 3.1 0.8 - - - -
47P GLN* 1.3 76.6 - - - +
49P LYS* 1.3 55.7 + - - +
51P PHE* 4.2 0.3 - - - +
52P THR* 2.5 41.0 + - - +
67P GLU 4.6 2.1 + - - -
68P ASN* 3.0 30.2 - - - +
69P ILE* 3.7 17.6 - - + +
70P GLU* 2.5 43.0 + - - -
134P LEU* 4.2 16.2 - - + -
138P LEU* 3.9 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P LYS* 3.2 9.6 + - + +
46P GLN* 2.9 19.9 + - - +
48P ARG* 1.3 81.5 - - - +
50P THR* 1.3 73.7 + - - +
52P THR* 3.6 4.6 - - - -
53P ALA* 3.0 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P GLN* 2.9 17.9 + - - +
47P GLN* 4.1 4.3 - - - -
49P LYS* 1.3 89.4 + - - +
51P PHE* 1.3 69.8 + - + +
53P ALA* 3.3 6.9 + - - +
54P TRP* 2.9 30.3 + - + +
145P ILE* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 51 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ARG* 0.9 147.6 - - + -
47P GLN* 2.9 41.0 + - + +
50P THR* 1.3 83.3 - - + +
52P THR* 1.3 58.7 + - - +
54P TRP* 3.2 6.9 + - - +
55P CYS* 2.8 33.4 + - - -
69P ILE* 4.0 15.9 - - + -
138P LEU* 3.3 29.4 - - + -
141P ILE* 4.0 13.2 - - + -
142P TRP* 3.7 3.4 - + + -
145P ILE* 3.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 52 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P ARG* 2.5 28.3 + - - +
49P LYS* 3.6 4.9 - - - -
51P PHE* 1.3 76.7 - - - +
53P ALA* 1.3 62.7 + - - +
55P CYS* 3.2 2.8 + - - +
56P ASN* 2.9 38.8 + - - +
66P ILE* 4.0 17.5 - - + +
67P GLU 4.0 19.6 + - - +
69P ILE* 3.6 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P LYS* 3.0 19.2 + - + +
50P THR* 3.6 6.7 - - - +
52P THR* 1.3 77.7 - - - +
54P TRP* 1.3 63.0 + - - +
56P ASN* 3.4 6.8 + - - +
57P SER* 3.0 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 54 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50P THR* 2.9 17.6 + - + +
51P PHE* 3.5 9.4 - - - +
53P ALA* 1.3 77.9 - - - +
55P CYS* 1.3 86.0 + - - +
57P SER* 2.7 25.7 + - - -
58P HIS* 3.5 35.3 + + - -
82P LEU* 4.1 25.8 - - + -
86P ILE* 4.1 25.6 - - + -
141P ILE* 4.9 1.1 - - + -
144P ILE* 4.2 5.6 - - + -
145P ILE* 3.6 46.8 - - + +
149P ALA* 4.2 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 55 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P PHE 2.8 26.5 + - - +
52P THR 3.6 3.8 - - - +
54P TRP* 1.3 83.3 - - - +
56P ASN* 1.3 59.1 + - - +
58P HIS* 3.1 5.9 + - - +
59P LEU* 2.9 34.4 + - + +
66P ILE* 4.1 14.6 - - + -
69P ILE* 4.7 2.0 - - - -
73P PHE* 3.9 13.9 - - + -
82P LEU* 3.7 25.3 - - + +
141P ILE* 3.8 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 56 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P THR* 2.9 26.7 + - - +
53P ALA* 3.7 6.4 - - - +
55P CYS* 1.3 72.9 - - - +
57P SER* 1.3 56.3 + - - +
58P HIS 3.0 5.2 - - - -
59P LEU* 4.2 3.5 - - - +
60P ARG* 3.0 20.3 + - - +
65P GLN* 2.7 48.9 + - - +
66P ILE* 2.7 54.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P ALA 3.0 13.4 + - - -
54P TRP* 2.7 25.5 + - - -
56P ASN* 1.3 76.2 - - - +
58P HIS* 1.3 65.5 + - - +
60P ARG* 2.9 43.8 + - - +
61P LYS* 3.5 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 58 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P TRP* 3.5 56.2 + + - -
55P CYS 3.1 6.4 + - - +
56P ASN 3.0 0.4 - - - -
57P SER* 1.3 84.2 + - - +
59P LEU* 1.3 66.2 + - - +
60P ARG 3.1 1.8 - - - -
61P LYS* 3.0 49.0 + - - +
62P ALA 4.1 0.3 + - - -
82P LEU* 3.8 14.1 - - + -
85P VAL* 3.6 17.1 - - + +
86P ILE* 3.5 20.4 - - + +
149P ALA* 5.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55P CYS 2.9 22.6 + - - +
56P ASN* 4.2 11.2 - - - +
58P HIS* 1.3 76.0 - - - +
60P ARG* 1.3 53.5 + - - +
62P ALA* 2.7 28.6 + - - +
63P GLY 3.3 6.4 + - - -
64P THR* 3.3 36.4 + - + +
65P GLN* 4.2 1.3 - - - +
66P ILE* 3.8 29.2 - - + +
73P PHE* 4.4 14.1 - - + -
78P LYS* 3.6 12.1 - - + +
81P LEU* 4.3 8.5 - - + -
82P LEU* 3.6 35.4 - - + +
85P VAL* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P ASN 3.0 18.5 + - - +
57P SER* 2.9 37.2 + - - +
59P LEU* 1.3 77.1 - - - +
61P LYS* 1.3 67.0 + - + +
63P GLY* 3.1 17.6 + - - +
64P THR 3.3 10.7 + - - +
65P GLN* 3.5 12.8 - - - +
----------------------------------------------------------
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