Contacts of the helix formed by residues 66 - 76 (chain A) in PDB entry 4MRE
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 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU 5.0 1.8 - - - +
65A PRO* 1.3 77.0 - - - +
67A MET* 1.3 64.6 + - - +
68A ASP* 3.4 9.0 + - - +
69A GLN* 2.9 44.6 + - - +
70A MET* 2.9 22.0 + - - +
86A ILE* 4.4 1.3 - - - -
87A GLU* 4.5 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 1.3 74.0 - - - +
68A ASP* 1.3 57.8 + - - +
70A MET* 3.2 3.4 + - - +
71A LYS* 2.9 57.4 + - + +
86A ILE* 3.7 29.0 - - + +
87A GLU 5.2 2.7 + - - +
89A ASN* 5.0 6.7 - - - +
91A VAL* 4.1 2.0 - - + -
108A VAL* 3.8 27.1 - - + -
110A ILE* 3.8 35.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
66A THR* 3.2 9.2 + - - +
67A MET* 1.3 78.6 - - - +
69A GLN* 1.3 65.1 + - + +
71A LYS* 3.3 10.5 + - - +
72A LEU* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 5.2 1.8 - - - +
37A VAL* 3.8 13.7 - - + +
63A THR* 5.0 0.3 + - - -
64A LEU 4.3 1.7 - - - +
65A PRO* 3.4 14.3 - - + +
66A THR* 2.9 45.5 + - - +
68A ASP* 1.3 79.4 - - + +
70A MET* 1.3 55.6 + - - +
72A LEU* 3.4 7.5 + - - +
73A ALA* 3.0 26.5 + - - +
124A PHE* 3.3 43.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 4.0 10.3 - - + -
65A PRO* 4.6 3.8 - - + +
66A THR 2.9 13.7 + - - +
67A MET* 3.6 12.3 - - - +
69A GLN* 1.3 76.2 - - - +
71A LYS* 1.3 58.0 + - - +
73A ALA* 3.2 4.4 + - - +
74A LEU* 2.9 27.7 + - - +
78A PHE* 3.8 23.3 - - + -
86A ILE* 3.8 14.4 - - + -
91A VAL* 4.1 7.6 - - + -
93A PRO* 4.0 12.3 - - + -
108A VAL* 3.7 27.1 - - + -
122A TYR* 3.5 49.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A MET* 2.9 47.0 + - + +
68A ASP* 3.3 8.5 + - - +
70A MET* 1.3 77.4 - - - +
72A LEU* 1.3 61.1 + - - +
74A LEU* 3.4 13.4 + - + +
75A SER* 3.0 22.2 + - - -
108A VAL* 3.9 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 4.3 18.6 - - + -
68A ASP* 3.1 14.3 + - - +
69A GLN* 3.8 10.5 - - - +
71A LYS* 1.3 72.1 - - - +
73A ALA* 1.3 65.8 + - - +
75A SER* 2.7 35.2 + - - +
76A LYS* 3.2 28.8 + - - +
130A PRO 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.2 29.2 - - + +
35A ALA* 4.2 5.1 - - - +
37A VAL* 3.7 17.5 - - + -
69A GLN 3.0 14.4 + - - +
70A MET 3.2 8.5 + - - +
72A LEU* 1.3 76.7 - - - +
74A LEU* 1.3 62.8 + - - +
76A LYS* 3.0 15.3 + - - +
77A GLY 3.2 0.9 + - - -
78A PHE* 3.2 29.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
70A MET 2.9 13.5 + - - +
71A LYS* 3.5 13.7 - - + +
72A LEU 3.3 0.2 - - - -
73A ALA* 1.3 76.3 - - - +
75A SER* 1.3 57.7 + - - +
77A GLY 3.0 17.0 + - - -
78A PHE* 3.3 27.6 + - - +
93A PRO* 4.2 6.1 - - + -
94A ARG 3.4 31.0 - - - +
95A ILE* 3.6 22.8 - - + +
107A GLY* 3.6 30.1 - - - -
108A VAL* 3.8 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS 3.0 14.2 + - - -
72A LEU* 2.7 34.7 + - - +
74A LEU* 1.3 76.8 - - - +
76A LYS* 1.3 63.6 + - - +
77A GLY 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.4 22.4 - - + -
35A ALA* 4.2 14.8 - - + -
72A LEU* 3.3 36.9 - - - +
73A ALA 3.0 9.2 + - - +
75A SER* 1.3 81.1 - - - +
77A GLY* 1.3 57.8 + - - +
78A PHE 3.8 0.4 - - - -
130A PRO 4.2 9.0 - - - +
131A GLU* 3.0 46.9 + - + +
132A GLU* 4.6 6.4 + - - +
----------------------------------------------------------
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