Contacts of the strand formed by residues 57 - 68 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 3.8 23.5 + - - -
51C TRP* 3.1 17.0 - - - -
52C LYS* 4.2 12.3 + - - -
55C ASP 4.6 1.2 + - - -
56C LYS* 1.3 79.1 - - - +
58C PHE* 1.3 67.8 + - - +
59C TYR* 4.2 0.4 - - - +
87C GLN 3.7 0.2 - - - +
88C GLY* 3.3 4.2 - - - -
89C LYS* 2.9 54.1 + - - +
91C LEU* 4.6 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ILE* 5.4 1.1 - - + -
361A TRP* 4.1 11.2 - - + -
362A GLN* 3.7 23.3 - - - -
363A ALA* 3.5 26.0 - - + -
371A PRO* 3.6 31.6 - - + -
373A ILE* 4.5 11.2 - - + -
49C GLU* 3.5 6.8 - - - +
50C VAL* 2.9 29.0 + - + -
51C TRP* 2.9 43.9 + + + +
57C SER* 1.3 74.7 - - - +
59C TYR* 1.3 60.3 + - - +
86C VAL* 3.8 13.9 - - + -
87C GLN 3.3 4.0 - - - -
88C GLY* 4.0 7.9 - - - -
91C LEU* 3.5 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ASP* 2.8 39.4 + - - +
4C HIS* 4.9 5.7 - - - -
47C GLY* 3.6 6.4 - - - -
48C GLN 3.5 20.6 - - - -
49C GLU* 3.6 19.7 - - + +
50C VAL* 5.0 0.4 - - - -
57C SER 4.2 0.4 - - - -
58C PHE* 1.3 74.1 - - - +
60C PHE* 1.3 71.1 + - - +
61C ASP* 3.9 23.5 + - + -
85C ASN 3.9 0.7 - - - +
86C VAL* 3.3 5.9 - - - -
87C GLN* 2.9 44.8 + - + +
89C LYS* 4.0 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 4.3 11.9 - + - -
7A ALA* 4.1 13.2 - - + -
44A LEU* 5.1 0.2 - - + -
423A MET* 4.1 7.2 - - + -
425A ILE* 3.7 43.5 - - + -
427A TRP* 3.3 48.0 - + - -
47C GLY* 3.1 4.0 - - - -
48C GLN* 2.8 39.7 + - + +
50C VAL* 4.2 7.8 - - + +
58C PHE 4.2 0.2 - - - -
59C TYR* 1.3 75.5 - - - +
61C ASP* 1.3 73.7 + - - +
62C THR* 3.3 27.6 - - + -
84C ALA* 4.8 1.6 - - - -
85C ASN 3.4 11.7 - - - -
86C VAL* 4.2 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C HIS* 6.1 0.5 - - - -
45C LYS* 2.8 38.4 + - - +
46C LEU 4.1 0.7 - - - +
47C GLY* 3.9 14.0 + - - -
59C TYR* 3.9 21.1 + - + -
60C PHE* 1.3 76.4 - - - +
62C THR* 1.3 72.4 + - - +
83C GLU* 4.5 5.5 - - - +
84C ALA* 3.3 5.5 + - - -
85C ASN* 3.1 48.3 + - - +
87C GLN* 4.7 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 5.1 0.7 - - + -
44A LEU* 4.3 26.7 - - + +
44C LEU 4.9 1.2 + - - -
45C LYS* 3.2 27.0 + - - +
46C LEU* 2.7 31.6 + - - +
60C PHE* 3.3 39.0 - - + -
61C ASP* 1.3 75.1 + - - +
63C ASN* 1.3 65.9 + - - +
64C VAL* 5.6 1.1 - - - +
81C PHE* 4.9 5.6 - - + -
83C GLU* 3.3 14.8 - - - +
84C ALA* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLU* 3.3 32.5 + - - +
44C LEU 3.8 6.4 + - - -
45C LYS* 3.7 15.0 - - - +
62C THR* 1.3 80.5 - - - +
64C VAL* 1.3 72.8 + - - +
65C ALA* 4.1 0.9 + - - +
81C PHE* 3.8 3.1 - - - -
82C ARG* 3.0 25.9 + - - -
83C GLU* 3.0 43.1 + - + +
106C PHE* 3.3 26.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.6 11.0 - - + -
66A TYR* 4.0 24.2 - - + +
43C GLU* 3.6 0.5 - - - -
44C LEU* 3.0 35.1 + - + +
62C THR* 5.6 0.9 - - - +
63C ASN* 1.3 80.0 + - - +
65C ALA* 1.3 59.9 + - - +
66C TYR* 3.5 37.9 - - + +
79C PRO* 3.8 17.3 - - + -
80C ALA 3.5 5.6 - - - +
81C PHE* 3.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 4.0 11.4 - - + -
41C TYR* 3.5 25.6 - - + +
42C ALA 3.3 6.3 - - - +
43C GLU* 4.0 6.5 - - + +
63C ASN* 4.1 0.8 + - - +
64C VAL* 1.3 73.0 - - - +
66C TYR* 1.3 62.1 + - - +
79C PRO* 3.2 8.8 - - - +
80C ALA* 2.9 32.8 + - - +
82C ARG* 3.7 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 4.1 8.7 + - - -
74A TRP* 5.3 0.4 - - - -
64B VAL* 4.0 33.2 - - + +
66B TYR* 4.1 4.5 + - - -
79B PRO* 4.3 7.4 - - + +
81B PHE* 3.9 40.7 - + + -
40C THR 3.9 0.6 - - - +
41C TYR* 3.4 8.4 - - - -
42C ALA 2.8 37.5 + - - +
44C LEU* 4.3 21.0 - - + +
64C VAL* 3.5 38.5 - - + +
65C ALA* 1.3 76.0 - - - +
67C SER* 1.3 60.7 + - - +
68C VAL 4.2 0.2 - - - -
77C THR* 3.9 22.0 - - + -
79C PRO* 3.7 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 4.6 14.5 - - - -
39C GLU* 4.2 14.0 - - - +
40C THR 3.5 6.4 + - - -
41C TYR* 4.0 19.4 - - - -
66C TYR* 1.3 76.3 - - - +
68C VAL* 1.3 61.7 + - - +
77C THR* 3.2 22.8 + - - -
78C ASP 5.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 4.0 21.3 - - + -
104B LYS* 4.5 4.3 - - + +
39C GLU* 3.5 5.6 - - - +
40C THR* 3.0 55.2 + - + +
67C SER* 1.3 79.6 - - - +
69C ASN* 1.3 62.8 + - - +
70C GLN 3.3 1.2 + - - -
75C GLU* 3.6 47.6 - - + +
76C SER 4.5 1.6 - - - +
77C THR* 3.9 19.3 - - + -
----------------------------------------------------------
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