Contacts of the helix formed by residues 55 - 73 (chain A) in PDB entry 1MRA
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 55 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 3.7 4.7 - - - -
53A ALA* 2.3 40.0 + - - +
54A TYR* 1.3 73.6 - - + +
56A PRO* 1.3 76.5 - - - +
57A VAL* 3.1 23.5 + - + +
58A ALA* 3.2 22.6 + - + +
59A LEU 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 4.4 18.2 - - - +
31A THR* 6.2 0.7 - - - +
33A PRO* 3.8 13.2 - - + -
54A TYR 4.7 0.7 - - - +
55A THR* 1.3 90.0 - - - +
57A VAL* 1.3 67.4 + - + +
59A LEU* 3.0 21.9 + - + +
60A LYS* 4.5 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 3.0 18.5 - - + +
56A PRO* 1.3 82.4 - - + +
58A ALA* 1.3 59.2 + - + +
59A LEU 3.7 0.3 + - - -
60A LYS* 4.9 3.1 + - - +
61A SER* 5.0 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA* 4.4 10.5 - - + +
55A THR* 3.2 19.7 + - + +
56A PRO 3.1 0.8 - - - -
57A VAL* 1.3 77.9 - - + +
59A LEU* 1.3 59.2 + - - +
60A LYS 3.7 0.7 - - - -
61A SER* 3.5 8.6 + - - -
62A LEU* 2.9 31.2 + - - +
99A LEU* 4.9 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 3.9 17.7 - - + -
14A VAL 3.8 16.2 - - - +
15A ASN* 4.5 5.2 - - - +
33A PRO* 4.0 19.7 - - + -
34A LEU* 3.5 23.6 - - - +
35A VAL* 3.4 31.0 - - + -
53A ALA* 4.2 7.6 - - + -
55A THR 3.7 1.6 + - - -
56A PRO* 3.0 18.0 + - + +
57A VAL 3.4 0.2 - - - -
58A ALA* 1.3 75.3 - - - +
60A LYS* 1.3 67.5 + - + +
62A LEU* 3.3 1.3 + - - +
63A LYS* 3.2 19.6 + - - +
359A VAL* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO 4.5 3.5 + - - +
57A VAL 4.9 2.5 + - - +
58A ALA 3.7 0.2 - - - -
59A LEU* 1.3 78.2 - - + +
61A SER* 1.3 62.7 + - - +
63A LYS* 3.2 7.1 + - - +
64A GLN* 3.0 25.7 + - + +
359A VAL* 4.1 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL 5.0 4.1 + - - -
58A ALA* 3.5 15.5 + - - -
59A LEU 3.1 0.4 - - - -
60A LYS* 1.3 78.3 - - - +
62A LEU* 1.3 63.2 + - - +
64A GLN* 3.3 6.7 + - - +
65A LEU* 3.0 25.1 + - - +
99A LEU* 3.9 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.7 9.6 - - + -
51A LEU* 3.9 30.1 - - + -
52A PHE 5.0 3.4 - - - +
53A ALA* 5.2 8.1 - - + -
58A ALA* 2.9 18.9 + - + +
59A LEU* 4.1 2.7 - - - +
61A SER* 1.3 76.0 - - - +
63A LYS* 1.3 64.8 + - - +
65A LEU* 3.4 7.3 + - + +
66A LEU* 3.3 25.8 + - + +
99A LEU* 3.2 43.5 - - + +
102A MET* 4.0 21.8 - - + -
103A ALA* 3.9 16.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
11A THR* 3.4 35.3 + - - +
12A ARG* 4.5 0.9 - - - +
13A ALA* 4.0 27.4 - - + +
35A VAL* 4.4 17.8 - - + +
59A LEU 3.2 12.8 + - - +
60A LYS* 3.6 8.3 - - - +
61A SER 3.2 0.2 - - - -
62A LEU* 1.3 75.4 - - - +
64A GLN* 1.3 68.7 + - - +
66A LEU* 2.9 16.1 + - - +
67A ASP* 2.9 38.6 + - - +
359A VAL 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS 3.0 18.4 + - - +
61A SER* 3.7 7.0 - - - +
63A LYS* 1.3 78.6 - - - +
65A LEU* 1.3 61.7 + - - +
67A ASP* 3.4 13.2 + - - +
68A ASP* 2.7 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A SER* 3.0 17.6 + - - +
62A LEU* 3.6 9.9 - - + +
63A LYS 3.0 0.8 - - - -
64A GLN* 1.3 78.0 - - - +
66A LEU* 1.3 56.9 + - - +
68A ASP* 3.6 7.2 + - + +
69A MET* 2.8 45.3 + - + +
91A PHE* 5.2 5.2 - - + -
99A LEU* 3.6 34.5 - - + +
100A ILE* 3.8 28.5 - - + +
103A ALA* 3.9 8.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
9A LEU* 3.3 17.3 - - + +
11A THR* 4.0 11.9 - - + -
35A VAL* 4.0 24.0 - - + -
37A ILE* 4.1 17.9 - - + -
51A LEU* 4.1 20.0 - - + -
62A LEU* 3.3 21.9 + - + +
63A LYS 2.9 6.4 + - - +
65A LEU* 1.3 74.6 - - - +
67A ASP* 1.3 66.7 + - - +
68A ASP 3.2 0.2 - - - -
69A MET* 3.1 6.5 + - - +
70A ALA 3.0 18.9 + - - -
103A ALA* 3.8 22.0 - - + +
107A ILE* 3.9 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 5.3 3.2 - - - +
11A THR* 2.9 26.5 + - - +
63A LYS* 2.9 38.2 + - - +
64A GLN* 3.5 22.4 - - - +
66A LEU* 1.3 77.2 - - - +
68A ASP* 1.3 63.3 + - - +
70A ALA* 3.5 17.4 + - - +
71A ALA 4.7 1.0 + - - -
----------------------------------------------------------
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 GLN* 2.7 44.6 + - - +
65A LEU* 3.9 8.2 - - + +
66A LEU 3.2 0.2 - - - -
67A ASP* 1.3 80.1 - - - +
69A MET* 1.3 60.0 + - + +
70A ALA 3.3 0.2 - - - -
71A ALA* 4.2 11.5 + - - +
72A MET* 5.0 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.9 0.9 - - - -
65A LEU* 2.8 33.0 - - + +
66A LEU* 3.1 8.7 + - - +
68A ASP* 1.3 76.4 - - + +
70A ALA* 1.3 65.8 + - - +
71A ALA 3.1 3.6 - - - -
72A MET* 3.0 28.8 + - - +
73A ILE* 3.5 8.7 + - + +
87A LEU* 3.7 32.5 - - + -
91A PHE* 4.1 24.0 - - + -
100A ILE* 4.8 3.1 - - - +
103A ALA* 3.8 24.9 - - - -
104A ALA* 4.8 9.4 - - + +
107A ILE* 4.2 21.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
9A LEU* 3.6 41.3 - - + +
66A LEU 3.0 4.6 + - - +
67A ASP* 3.5 15.7 - - - +
68A ASP 3.3 1.4 - - - -
69A MET* 1.3 78.1 - - - +
71A ALA* 1.3 62.1 + - - +
73A ILE* 3.1 5.8 + - - +
74A VAL* 3.0 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP 4.7 1.2 + - - -
68A ASP 4.2 10.4 + - - +
69A MET 3.1 0.6 - - - -
70A ALA* 1.3 79.9 - - - +
72A MET* 1.3 61.6 + - + +
73A ILE 3.3 0.3 + - - -
74A VAL* 3.7 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP 5.1 2.2 - - - +
69A MET* 3.0 21.3 + - - +
71A ALA* 1.3 78.2 - - + +
73A ILE* 1.3 65.7 + - + +
74A VAL 4.4 0.9 - - - +
76A GLU* 3.6 14.7 - - - +
86A MET* 3.7 11.3 - - - +
87A LEU* 4.3 9.6 - - + -
90A ARG* 2.8 76.0 + - + +
91A PHE* 4.0 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.7 20.6 - - + +
9A LEU* 4.2 12.1 - - + -
39A LEU* 3.7 26.0 - - + -
69A MET* 3.8 10.5 - - + +
70A ALA* 3.4 13.2 - - - +
72A MET* 1.3 86.1 - - + +
74A VAL* 1.3 70.0 + - + +
75A ASN 3.5 0.2 + - - -
76A GLU* 3.0 23.7 + - - +
83A LEU* 4.7 7.4 - - + -
86A MET* 4.5 7.2 - - + -
87A LEU* 4.3 20.0 - - + -
107A ILE* 3.2 40.4 - - + -
----------------------------------------------------------
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