Contacts of the strand formed by residues 59 - 67 (chain C) in PDB entry 1MPX
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 LYS 59 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C MSE 3.8 39.6 - - + +
52C ILE 3.3 6.3 - - - +
53C PRO* 4.0 23.1 - - + -
57C GLY 3.9 12.7 + - - +
58C VAL* 1.3 74.8 - - - +
60C LEU* 1.3 64.9 + - - +
126C GLU* 3.1 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C MSE 4.4 2.2 - - - -
52C ILE* 3.0 26.2 + - - +
54C MSE 3.7 30.5 - - + -
58C VAL* 4.1 13.9 - - + -
59C LYS* 1.3 80.7 - - - +
61C HIS* 1.3 60.8 + - - +
62C THR* 3.1 15.2 + - - -
79C ARG* 3.3 30.5 - - - +
117C GLN* 3.5 23.6 - - - +
118C ASP 3.8 4.0 - - - +
120C ARG* 3.8 28.5 - - + +
125C SER* 3.2 10.3 - - - +
149C ASP* 4.0 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 2.7 30.8 + - + -
50C VAL 3.8 3.4 - - - -
51C MSE 3.7 19.4 - - - -
60C LEU* 1.3 68.1 - - - +
62C THR* 1.3 67.0 + - - +
63C VAL* 3.7 15.0 - - + +
83C ASP* 5.7 0.4 - - - -
84C ALA* 4.5 0.9 - - - +
85C SER* 3.2 28.3 - - - -
116C PHE 4.3 0.2 - - - +
117C GLN* 3.4 2.4 - - - +
118C ASP* 2.7 50.8 + - - +
124C GLY* 3.4 33.8 - - - +
125C SER* 2.9 10.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
48C ARG 3.7 1.6 - - - +
49C GLU* 3.4 3.6 - - - +
50C VAL* 2.9 41.7 + - - +
52C ILE* 3.3 23.7 - - + +
60C LEU 3.1 8.1 + - - -
61C HIS* 1.3 74.1 - - - +
63C VAL* 1.3 60.1 + - - +
64C ILE* 4.5 6.7 - - + -
115C VAL* 3.4 31.9 - - + -
116C PHE 3.7 4.7 - - - +
117C GLN* 2.9 32.4 + - + +
153C THR* 5.0 2.5 - - + -
157C LEU* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LYS* 3.9 29.4 - - + -
48C ARG 3.6 4.0 - - - +
49C GLU* 4.3 6.5 - - + +
61C HIS* 3.7 32.1 - - + +
62C THR* 1.3 73.0 - - - +
64C ILE* 1.3 62.1 + - - +
65C VAL* 4.4 2.2 - - + -
84C ALA* 3.9 14.4 - - + +
85C SER* 3.9 12.1 - - - +
88C THR* 3.4 29.9 - - + +
114C ARG 3.8 1.2 - - - +
115C VAL* 3.3 5.9 - - - +
116C PHE* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE 3.5 2.1 - - - +
47C LYS* 3.4 2.9 - - - -
48C ARG* 2.8 51.5 + - + +
50C VAL* 3.9 28.0 - - + -
62C THR* 4.5 3.8 - - + +
63C VAL* 1.3 76.5 - - - +
65C VAL* 1.3 63.4 + - - +
66C LEU* 3.8 18.2 - - + +
113C ILE* 3.6 26.5 - - + -
114C ARG 3.7 2.7 - - - -
115C VAL* 4.0 19.3 - - + -
156C TRP* 4.1 8.5 - - + -
157C LEU* 3.9 18.6 - - + -
161C VAL* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TYR* 4.1 11.7 - - + -
46C ILE 3.4 5.4 - - - +
47C LYS* 3.9 26.5 - - + -
63C VAL* 4.4 2.2 - - + -
64C ILE* 1.3 75.2 - - - +
66C LEU* 1.3 61.6 + - - +
88C THR* 4.1 20.9 - - + -
96C MSE 3.7 29.5 - - + +
99C LEU* 4.1 19.5 - - + -
100C LEU* 4.2 9.6 - - + -
113C ILE* 3.5 3.4 - - - -
114C ARG* 2.8 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TYR* 3.2 5.1 - - - -
46C ILE* 2.8 50.5 + - + +
48C ARG* 4.0 26.2 - - - +
64C ILE* 3.8 25.8 - - + +
65C VAL* 1.3 74.8 - - - +
67C PRO* 1.3 75.7 - - + +
70C ALA* 4.6 1.3 - - + -
96C MSE 4.4 1.1 - - - -
113C ILE* 4.0 15.9 - - + -
161C VAL* 4.2 7.9 - - + -
163C GLU* 3.3 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ASP 3.8 8.1 - - - +
46C ILE* 5.8 0.4 - - - +
65C VAL 4.3 0.9 - - - +
66C LEU* 1.3 88.7 - - + +
68C LYS* 1.3 68.2 + - - +
69C GLY 3.4 0.2 + - - -
70C ALA* 3.1 30.4 + - + +
96C MSE 4.0 16.8 - - - -
108C VAL 5.7 1.3 - - - +
111C GLY* 3.8 22.7 - - - +
112C TYR 3.4 28.9 - - - +
113C ILE* 4.2 2.2 - - + -
----------------------------------------------------------
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