Contacts of the strand formed by residues 66 - 76 (chain A) in PDB entry 1MM5
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 ASN 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TRP* 3.4 6.1 - - - +
62A ASP* 2.8 54.5 + - + +
64A LYS* 3.3 6.0 + - + +
65A GLY* 1.3 78.7 - - - +
67A TRP* 1.3 70.4 + - - +
68A HIS* 4.0 11.3 + - - +
90A TRP* 3.7 30.3 - - - +
91A GLU 4.1 3.8 - - - +
92A SER* 5.6 0.9 + - - -
93A THR* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.9 21.3 + - - -
60A ARG 3.5 8.1 - - - -
61A TRP* 4.1 25.1 - + + -
66A ASN* 1.3 83.5 + - - +
68A HIS* 1.3 73.1 + - - +
69A GLY 3.5 1.6 + - - -
90A TRP* 3.7 3.3 - - - -
91A GLU* 2.8 70.3 + - + +
93A THR* 3.1 38.1 - - + -
95A ARG* 6.4 1.8 - - + -
103A HIS* 5.8 13.2 - + + -
131A SER* 5.0 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.4 11.4 + - - -
60A ARG* 2.8 63.6 + - + +
61A TRP* 4.8 0.8 - - - +
62A ASP* 5.8 4.9 - - - +
66A ASN* 4.0 12.6 + - - +
67A TRP* 1.3 77.0 - - - +
69A GLY* 1.3 58.9 + - - +
70A LEU* 4.0 22.9 - - + -
88A TYR* 3.7 27.5 + + - -
89A GLY 4.0 8.8 + - - -
90A TRP* 5.2 1.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 4.5 4.5 - - - -
67A TRP 3.5 1.4 + - - -
68A HIS* 1.3 75.0 - - - +
70A LEU* 1.3 70.4 + - - +
71A TYR* 5.1 4.9 - - - -
87A GLY 3.3 1.0 - - - +
88A TYR* 3.3 21.3 + - - -
89A GLY 3.3 14.4 + - - -
91A GLU* 3.4 23.8 + - - -
109A THR* 3.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY* 3.8 1.0 - - - -
58A LEU* 2.9 50.6 + - + +
59A SER* 4.8 1.3 + - - -
68A HIS* 4.0 19.7 - - + -
69A GLY* 1.3 91.5 - - - +
71A TYR* 1.3 73.1 + - - +
86A ALA* 6.1 2.2 - - + -
87A GLY 2.9 20.6 - - - +
88A TYR* 3.7 29.8 - - + -
89A GLY 5.1 0.4 - - - +
159A ARG* 4.6 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 4.2 16.4 - + - +
56A PHE 4.1 1.8 - - - -
57A GLY* 4.4 0.4 - - - -
69A GLY* 5.1 1.8 - - - -
70A LEU* 1.3 87.7 - - - +
72A ALA* 1.3 64.2 + - - +
85A ILE* 3.8 9.9 - - + +
86A ALA* 3.2 23.2 - - - +
87A GLY* 3.3 30.5 + - - +
91A GLU* 4.0 10.4 + - - -
109A THR* 3.3 36.2 + - + -
111A GLY* 5.6 3.6 - - - -
129A LEU* 3.3 38.0 - - + +
140A GLN* 5.3 6.9 - - + +
159A ARG* 3.7 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.9 0.4 + - - -
56A PHE* 2.5 53.3 + - + +
57A GLY* 4.2 5.6 - - - -
58A LEU* 5.4 5.6 - - + -
71A TYR* 1.3 78.9 - - - +
73A MET* 1.3 59.3 + - - +
85A ILE 3.2 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.0 37.2 - - + +
53A GLY 6.3 0.7 - - - -
54A GLY 3.1 20.9 - - - +
55A GLY* 3.6 6.5 - - - -
56A PHE* 4.2 2.5 - - - +
72A ALA* 1.3 71.7 - - - +
74A ALA* 1.3 85.2 + - - +
75A PHE* 4.3 14.8 - - + -
83A GLU 4.2 0.9 - - - +
84A PRO* 3.3 5.4 - - - +
85A ILE* 3.0 58.3 + - + -
157A TRP* 5.4 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLY* 3.6 2.1 - - - -
54A GLY 3.3 26.3 + - - +
73A MET* 1.3 82.9 - - - +
75A PHE* 1.3 60.6 + - - +
82A TRP* 4.9 11.7 - - + -
83A GLU 3.3 16.4 - - - +
84A PRO* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PRO* 5.8 4.3 - - + -
50A ARG* 6.0 1.1 - - + -
51A PRO* 3.0 25.4 - - + -
52A TRP* 3.4 11.7 - + - -
53A GLY* 3.4 29.6 - - - -
73A MET* 4.3 15.7 - - + -
74A ALA* 1.3 74.3 - - - +
76A LYS* 1.3 77.2 + - - +
77A ASP* 3.8 13.7 - - - -
81A LYS 2.7 21.7 - - - +
82A TRP* 3.2 4.3 - - - -
83A GLU* 2.9 34.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
51A PRO* 3.1 35.8 - - + +
52A TRP 2.8 37.5 + - - +
53A GLY* 4.5 5.8 - - - -
74A ALA 4.3 0.4 + - - -
75A PHE* 1.3 86.8 - - - +
77A ASP* 1.3 66.1 - - - +
80A ASN* 6.1 0.4 - - - -
81A LYS 3.2 6.5 - - - +
82A TRP* 4.7 13.2 - - + +
----------------------------------------------------------
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