Contacts of the strand formed by residues 57 - 68 (chain A) in PDB entry 2MPR
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 SER 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 3.9 23.1 + - - +
51A TRP* 3.2 17.4 - - - -
52A LYS* 4.2 12.7 + - - -
55A ASP 4.0 1.2 + - - -
56A LYS* 1.3 77.9 - - - +
58A PHE* 1.3 66.6 + - - +
59A TYR* 4.2 0.6 - - - +
87A GLN 3.7 0.6 - - - +
88A GLY* 3.3 4.3 - - - -
89A LYS* 2.9 53.7 + - - +
91A LEU* 4.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 3.6 5.5 - - - +
50A VAL* 2.9 30.3 + - + -
51A TRP* 3.0 44.2 + + + +
57A SER* 1.3 74.4 - - - +
59A TYR* 1.3 60.3 + - - +
86A VAL* 3.9 13.9 - - + -
87A GLN 3.3 3.8 - - - -
88A GLY* 4.0 8.1 - - - -
91A LEU* 3.5 34.3 - - + -
329B ILE* 5.4 1.6 - - + -
361B TRP 4.1 12.3 - - - -
362B GLN* 3.6 23.6 - - - -
363B ALA* 3.6 24.2 - - + -
371B PRO* 3.6 30.7 - - + -
373B ILE* 4.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASP* 2.7 39.8 + - - +
4A HIS* 4.9 5.5 + - - -
47A GLY* 3.6 3.3 - - - -
48A GLN 3.5 23.9 + - - -
49A GLU* 3.5 18.8 - - + -
50A VAL* 5.0 0.2 - - - -
57A SER* 4.2 0.6 - - - +
58A PHE* 1.3 75.2 - - - +
60A PHE* 1.3 75.8 + - - +
61A ASP* 3.9 22.2 + - + -
85A ASN 3.9 0.5 - - - +
86A VAL* 3.3 5.8 - - - -
87A GLN* 2.8 45.4 + - + +
89A LYS* 4.0 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU 5.1 0.4 - - - -
47A GLY* 3.1 3.3 - - - -
48A GLN* 2.8 40.7 + - + +
50A VAL* 4.2 8.1 - - + -
58A PHE 4.2 0.4 + - - -
59A TYR* 1.3 75.5 - - - +
61A ASP* 1.3 66.7 + - - +
62A THR* 3.3 31.9 - - + -
84A ALA* 4.9 0.9 - - - -
85A ASN 3.6 10.3 - - - -
86A VAL* 4.1 5.8 - - + +
3B PHE* 4.3 12.3 - + - -
7B ALA* 4.1 7.4 - - + -
44B LEU* 5.2 0.4 - - + -
423B MET* 4.1 14.6 - - + -
425B ILE* 3.7 43.1 - - + -
427B TRP* 3.3 47.3 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
4A HIS* 6.1 0.7 - - - -
45A LYS* 2.7 38.0 + - - +
46A LEU 4.3 0.5 - - - -
47A GLY* 3.9 14.4 + - - -
59A TYR* 3.9 20.2 + - + -
60A PHE* 1.3 76.5 - - - +
62A THR* 1.3 72.7 + - - +
83A GLU* 4.5 5.5 - - - +
84A ALA* 3.3 5.0 + - - -
85A ASN* 3.1 47.5 + - - +
87A GLN* 4.7 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU 4.9 1.0 + - - -
45A LYS* 3.2 26.7 + - - +
46A LEU* 2.8 30.4 + - - +
60A PHE* 3.3 39.0 - - + -
61A ASP* 1.3 75.7 + - - +
63A ASN* 1.3 65.3 + - - +
64A VAL* 5.5 0.7 - - - +
81A PHE* 4.9 6.3 - - + -
83A GLU* 3.3 15.9 - - - +
84A ALA* 4.7 3.4 - - + -
3B PHE* 5.1 0.7 - - + -
44B LEU* 4.4 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 3.3 32.3 + - - +
44A LEU 3.7 6.0 + - - -
45A LYS* 3.7 16.0 - - + +
62A THR* 1.3 82.2 - - - +
64A VAL* 1.3 72.7 + - - +
65A ALA* 4.1 0.5 + - - +
81A PHE* 3.8 2.5 - - - -
82A ARG* 3.0 28.3 + - - -
83A GLU* 3.0 43.5 + - + +
106A PHE* 3.3 26.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 3.6 0.5 - - - -
44A LEU* 3.0 35.2 + - + +
62A THR* 5.5 0.4 - - - +
63A ASN* 1.3 81.0 + - - +
65A ALA* 1.3 61.3 + - - +
66A TYR* 3.5 37.5 - - + +
79A PRO* 3.8 15.7 - - + -
80A ALA 3.5 6.3 - - - +
81A PHE* 3.7 23.6 - - + -
44B LEU* 4.5 11.7 - - + -
66B TYR* 3.9 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 3.6 24.5 - - + +
42A ALA 3.3 7.2 - - - +
43A GLU* 4.0 6.7 - - + +
63A ASN* 4.1 1.1 + - - +
64A VAL* 1.3 73.8 - - - +
66A TYR* 1.3 62.6 + - - +
78A ASP 4.8 0.3 - - - +
79A PRO* 3.2 9.4 - - - +
80A ALA* 2.9 31.5 + - - +
82A ARG* 3.7 22.4 - - - -
74B TRP* 4.1 11.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR 3.9 0.6 - - - +
41A TYR* 3.4 8.6 - - - -
42A ALA 2.8 38.5 + - - +
44A LEU* 4.3 21.1 - - + +
64A VAL* 3.5 38.4 - - + +
65A ALA* 1.3 76.2 - - - +
67A SER* 1.3 60.7 + - - +
68A VAL 4.2 0.4 - - - -
77A THR* 4.0 18.4 - - + -
78A ASP 5.9 0.2 - - - -
79A PRO* 3.7 22.5 - - + +
66B TYR* 4.0 8.8 + - - -
64C VAL* 4.0 34.5 - - + +
66C TYR* 4.1 4.3 + - - -
79C PRO* 4.4 7.1 - - + +
81C PHE* 3.9 40.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU* 4.3 13.7 - - - +
40A THR 3.5 6.6 + - - -
41A TYR* 4.0 18.5 - - - -
66A TYR* 1.3 76.2 - - - +
68A VAL* 1.3 61.4 + - - +
77A THR* 3.3 21.5 + - - -
78A ASP 6.0 0.2 + - - -
74B TRP* 4.6 14.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU* 3.5 6.0 - - - +
40A THR* 2.9 49.8 + - + +
67A SER* 1.3 81.3 + - - +
69A ASN* 1.3 63.5 + - - +
70A GLN 3.3 1.0 + - - -
75A GLU* 3.5 42.0 - - + +
76A SER 4.6 1.6 - - - +
77A THR* 3.9 24.5 - - + -
81C PHE* 4.0 26.0 - - + +
104C LYS* 4.4 4.0 - - + -
----------------------------------------------------------
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