Contacts of the strand formed by residues 80 - 89 (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 ALA 80 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 3.4 50.0 - - + +
75A GLU 3.2 13.0 - - - +
76A SER* 4.0 0.7 - - - +
64C VAL* 3.5 2.5 - - - -
65C ALA* 2.9 32.3 + - + +
78C ASP 3.6 1.2 + - - -
79C PRO* 1.3 74.1 - - - +
81C PHE* 1.3 58.8 + - - +
82C ARG* 3.3 16.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 3.7 14.8 - - + -
42A ALA* 3.5 27.8 - - + -
44A LEU* 4.9 4.0 - - + -
66A TYR* 3.9 37.0 - + + -
68A VAL* 4.0 31.7 - - + +
73A ASP 4.0 0.8 - - - +
75A GLU 3.0 10.1 + - - +
77A THR* 4.7 1.3 - - + +
62C THR* 4.9 11.2 - - + -
63C ASN 3.9 3.8 - - - -
64C VAL* 3.8 27.4 - - + +
79C PRO 3.8 1.8 + - - -
80C ALA* 1.3 67.3 - - - +
82C ARG* 1.3 53.6 - - - +
83C GLU 3.9 8.3 - - - -
84C ALA* 3.6 29.8 - - + -
104C LYS* 2.8 31.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASP* 2.7 57.1 + - - +
74A TRP* 3.5 28.5 - - + +
41C TYR* 2.9 24.0 + - - -
43C GLU* 3.4 2.0 + - - -
63C ASN* 3.0 11.8 + - + +
65C ALA* 3.7 15.9 - - + -
80C ALA* 3.3 18.1 + - + +
81C PHE* 1.3 75.0 - - - +
83C GLU* 1.3 65.9 + - + +
104C LYS* 3.4 20.9 - - - +
105C ARG 4.4 1.4 + - - -
106C PHE* 3.5 28.1 - - + -
109C ARG* 4.6 0.6 - - - +
121C ASP* 5.6 1.2 + - - -
124C GLY* 5.6 1.2 - - - -
1F BGC 3.1 41.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS* 2.8 28.8 + - - -
61C ASP* 4.5 2.8 - - - +
62C THR* 3.3 9.3 - - - +
63C ASN* 3.0 48.1 + - + +
81C PHE* 3.7 9.4 - - - -
82C ARG* 1.3 82.6 - - - +
84C ALA* 1.3 64.8 + - - +
85C ASN* 4.1 9.5 + - - +
104C LYS* 3.4 8.1 - - - +
105C ARG* 3.8 6.8 - - - +
106C PHE* 3.0 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 5.1 5.8 - - + -
9A SER* 3.4 7.8 - - - +
40A THR* 4.3 11.4 - - + -
423A MET* 3.7 14.1 - - + -
60C PHE* 4.8 2.2 - - + -
61C ASP 3.3 9.4 + - - -
62C THR* 4.4 4.7 - - + +
81C PHE* 3.6 27.6 - - + -
83C GLU* 1.3 76.7 - - - +
85C ASN* 1.3 59.6 + - - +
103C GLY* 3.4 4.9 - - - -
104C LYS* 2.9 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A MET* 3.9 4.4 - - - +
60C PHE* 3.4 6.8 - - - -
61C ASP* 3.1 39.6 + - - +
83C GLU* 4.1 9.1 + - - +
84C ALA* 1.3 76.5 - - - +
86C VAL* 1.3 65.9 + - - +
87C GLN* 2.9 32.8 + - - +
101C TRP* 4.8 1.1 - - + -
102C ALA 3.3 16.6 - - - +
103C GLY* 3.8 5.8 - - - -
104C LYS 2.9 21.3 + - - +
105C ARG* 3.4 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PRO* 3.9 24.9 - - + -
373A ILE* 3.9 13.7 - - + +
423A MET* 3.7 33.8 - - + +
424A GLU 5.2 0.2 - - - +
425A ILE* 4.5 5.4 - - + -
58C PHE* 3.8 28.5 - - + -
59C TYR 3.3 9.6 - - - +
60C PHE* 4.2 13.0 - - + -
85C ASN* 1.3 79.6 - - - +
87C GLN* 1.3 64.7 + - - +
101C TRP* 3.2 24.9 - - - +
102C ALA 3.2 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C SER 3.7 1.0 - - - +
58C PHE* 3.3 3.5 - - - -
59C TYR* 2.9 45.4 + - + +
61C ASP* 4.7 12.7 + - - +
85C ASN* 2.9 23.8 + - - +
86C VAL* 1.3 78.4 - - - +
88C GLY* 1.3 59.4 + - - +
89C LYS* 3.9 21.2 + - - +
99C THR* 3.8 15.9 - - + +
100C ILE 3.5 4.5 - - - -
101C TRP* 3.9 13.2 - - + -
105C ARG* 3.9 28.9 + - - +
130C GLU* 4.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ILE* 4.1 3.2 - - - +
57C SER 3.3 7.6 - - - -
58C PHE* 4.0 8.3 - - - -
87C GLN* 1.3 72.6 - - - +
89C LYS* 1.3 62.2 + - - -
90C ASN 4.0 0.3 + - - -
91C LEU* 3.7 24.6 + - - +
98C SER 4.1 0.5 - - - +
99C THR* 3.4 2.7 - - - -
100C ILE* 2.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 5.6 2.2 + - - -
55C ASP 4.8 2.2 - - - +
56C LYS* 3.4 2.4 - - - -
57C SER* 2.9 52.9 + - - +
59C TYR* 4.0 22.3 - - - +
87C GLN* 3.9 32.7 + - - +
88C GLY* 1.3 72.5 - - - -
90C ASN* 1.3 79.8 + - - +
91C LEU* 3.4 3.7 + - - +
97C GLY 5.8 1.3 - - - +
98C SER 4.0 4.5 - - - -
99C THR* 3.7 18.2 - - - +
----------------------------------------------------------
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