Contacts of the strand formed by residues 59 - 66 (chain C) in PDB entry 2NUP
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 MET 59 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TYR* 3.1 50.0 - - + +
55C GLU* 4.1 0.3 - - - -
56C ALA* 3.0 27.9 + - + +
57C GLY 2.8 8.3 - - - +
58C ALA* 1.3 113.0 - - + +
60C THR* 1.3 69.9 + - - +
74C LEU* 4.0 16.6 - - + -
75C CYS* 3.6 17.3 - - - +
76C GLU* 3.9 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C THR* 3.8 7.9 - - + -
54C LEU 3.3 16.6 + - - +
55C GLU* 4.5 9.2 - - + +
56C ALA 4.5 0.4 - - - +
59C MET* 1.3 81.7 + - - +
61C PHE* 1.3 59.0 + - - +
62C HIS* 3.0 42.4 - - + +
74C LEU* 3.9 5.3 - - - +
75C CYS* 3.0 26.3 + - - +
77C ALA* 2.9 34.0 - - - +
81C LYS* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 4.6 1.6 - - + -
33C TYR* 3.8 29.6 - + - -
36C GLN* 3.5 20.9 - - + -
37C ALA* 4.3 6.7 - - + -
40C LEU* 5.2 1.6 - - + -
52C CYS 4.9 0.2 - - - -
53C THR* 3.3 6.1 - - - +
54C LEU* 2.8 51.8 + - + +
56C ALA* 4.4 9.9 - - + -
60C THR* 1.3 73.4 - - - +
62C HIS* 1.3 61.7 + - - +
63C TYR* 6.1 0.9 - - + -
72C LEU* 3.5 36.8 - - + -
73C VAL 3.4 6.7 - - - -
74C LEU* 3.3 33.9 - - + -
153C ILE* 3.4 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C CYS 3.8 3.4 - - - -
53C THR* 3.1 40.0 + - + +
60C THR* 3.0 31.5 - - + +
61C PHE* 1.3 71.8 - - - +
63C TYR* 1.3 61.9 + - - +
72C LEU* 4.1 0.9 - - - +
73C VAL* 2.8 54.2 + - + +
75C CYS* 4.0 13.7 - - - -
77C ALA 5.5 0.4 + - - -
79C PHE 4.9 4.9 + - - -
81C LYS* 3.6 33.7 + - + +
84C ALA* 3.7 20.6 - - + +
85C PHE* 3.4 14.8 - - + -
88C LEU* 3.4 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.9 28.0 - - + -
44C LEU* 3.4 29.4 - - + +
49C PRO* 2.7 37.9 + - - +
50C THR 4.0 2.5 - - - -
51C ARG* 3.5 0.9 - - - -
52C CYS* 3.1 58.8 + - + +
54C LEU* 5.0 5.4 - - + -
61C PHE 6.1 0.4 - - - -
62C HIS* 1.3 75.4 - - - +
64C ILE* 1.3 80.8 + - - +
65C ILE* 3.9 15.7 - - + -
70C CYS* 4.1 9.0 - - - -
71C TYR 3.0 16.2 - - - +
72C LEU* 3.9 11.9 - - + -
85C PHE* 3.3 7.0 - - - -
88C LEU* 3.5 2.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
50C THR 3.1 8.7 - - - -
51C ARG* 3.7 25.8 - - - +
63C TYR* 1.3 82.4 - - - +
65C ILE* 1.3 70.8 + - - +
66C GLU* 4.3 4.5 - - + -
70C CYS* 3.5 1.2 - - - -
71C TYR* 2.9 48.3 + - + -
85C PHE* 3.7 16.8 - - + +
88C LEU* 3.6 36.8 - - + +
89C GLU* 3.1 29.6 - - - +
92C HIS* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 3.8 26.0 - - + -
44C LEU* 4.0 22.7 - - + -
45C ASN 5.1 2.2 - - - +
48C SER* 4.9 6.7 - - - +
49C PRO 4.1 8.1 - - - +
50C THR* 2.9 32.4 + - + +
51C ARG* 5.1 1.0 + - - -
63C TYR* 3.9 23.1 - - + -
64C ILE* 1.3 81.7 - - - +
66C GLU* 1.3 84.2 + - - +
67C GLN 5.1 0.2 - - - +
68C GLY* 4.6 5.8 - - - +
69C VAL 3.3 11.4 - - - +
70C CYS* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C THR* 5.9 0.3 - - - +
51C ARG* 2.9 29.1 + - - +
64C ILE* 4.3 6.5 - - + -
65C ILE* 1.3 89.3 - - - +
67C GLN* 1.3 76.1 + - - +
68C GLY 3.2 1.1 - - - -
69C VAL* 3.0 24.5 + - - +
71C TYR* 4.5 4.7 + - + -
92C HIS* 3.3 46.1 + - + +
----------------------------------------------------------
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