Contacts of the strand formed by residues 81 - 90 (chain C) in PDB entry 2E3V
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 THR 81 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 3.4 5.0 - - - -
50C VAL* 2.9 36.9 + - + +
80C THR* 1.3 77.1 - - - +
82C TYR* 1.3 62.3 + - - +
102C GLU* 3.5 33.9 - - + +
103C PHE 3.3 14.4 - - - +
104C LYS* 3.7 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C TRP* 4.0 17.5 - + + -
48C ARG 3.4 5.2 - - - -
49C ALA* 3.4 33.0 - - + -
50C VAL* 4.7 1.3 - - - -
56C HIS* 5.8 3.4 - + - -
76C LEU* 3.6 24.0 - - + -
77C LYS* 2.7 48.0 + - - +
80C THR* 3.4 34.9 - - + +
81C THR* 1.3 74.4 - - - +
83C ALA* 1.3 62.0 + - - +
101C SER 3.8 0.2 - - - +
102C GLU* 3.3 10.1 - - - +
103C PHE* 2.8 68.1 + + + -
105C THR* 4.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C TRP* 3.1 7.4 - - - +
48C ARG* 2.8 41.1 + - + +
50C VAL* 4.7 5.6 - - + +
55C TRP* 3.8 22.8 - - + -
82C TYR* 1.3 74.6 - - - +
84C VAL* 1.3 59.3 + - - +
100C ALA* 4.2 9.9 - - + -
101C SER 3.3 7.9 - - - +
102C GLU* 4.5 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 3.6 19.8 - - + +
18C VAL* 4.6 7.9 - - + -
27C VAL* 4.3 7.6 - - + -
46C GLU 3.3 11.0 - - - +
47C TRP* 4.3 1.3 - - + -
73C ILE* 3.5 28.7 - - + -
83C ALA* 1.3 75.8 - - - +
85C ARG* 1.3 69.3 + - - +
86C LEU* 4.6 5.2 - - + -
100C ALA* 3.3 2.7 - - - -
101C SER* 2.7 53.4 + - - +
103C PHE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 4.1 2.7 - - - -
46C GLU* 2.8 63.6 + - + +
55C TRP* 3.5 60.5 - - + +
84C VAL* 1.3 76.0 - - - +
86C LEU* 1.3 69.2 + - - +
97C ILE* 3.5 28.9 - - + +
98C SER* 3.4 27.4 - - - +
99C ALA 4.0 2.7 - - - +
100C ALA* 4.2 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 3.4 23.1 - - + +
15C ILE* 3.7 20.9 - - + -
27C VAL* 4.1 10.8 - - + -
29C PHE* 3.6 45.1 - - + -
43C TYR* 5.7 4.0 - - + -
44C LYS 3.3 5.4 - - - +
45C ALA* 3.4 26.7 - - + +
71C VAL* 3.9 14.6 - - + -
84C VAL* 4.6 4.5 - - + -
85C ARG* 1.3 84.1 - - - +
87C ALA* 1.3 60.9 + - - +
97C ILE* 3.6 3.6 - - - -
98C SER* 2.7 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 3.8 8.3 - - - -
43C TYR* 3.4 8.0 - - - +
44C LYS* 2.8 34.7 + - + +
86C LEU* 1.3 74.5 - - - +
88C ALA* 1.3 59.9 + - - +
94C LEU* 3.8 18.4 - - + -
95C GLY 3.7 20.2 - - - +
96C GLU 4.1 2.5 - - - -
97C ILE* 3.7 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PRO* 3.4 12.7 - - + +
11C SER 4.2 4.0 + - - +
13C PRO* 3.9 3.6 - - + +
31C GLU* 3.6 24.2 - - - +
40C ILE* 3.9 8.1 - - + -
42C LYS 3.6 4.5 - - - -
43C TYR* 3.6 24.5 - - + -
87C ALA* 1.3 74.7 - - - +
89C LEU* 1.3 60.2 + - - +
94C LEU* 3.6 3.6 - - - +
95C GLY* 2.9 28.5 + - - +
96C GLU 4.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 5.5 5.2 - - + +
10C PRO* 4.0 1.3 - - - -
40C ILE* 3.5 2.8 - - - +
41C LEU* 2.5 39.9 + - + -
42C LYS* 2.7 40.1 + - + +
59C TRP* 3.7 29.6 - - + -
88C ALA* 1.3 74.0 - - - +
90C ASN* 1.3 62.0 + - - +
93C GLY* 3.4 28.3 - - - -
94C LEU* 3.4 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLY* 3.6 6.3 - - - -
10C PRO* 3.5 31.6 - - + +
38C VAL* 3.5 21.3 + - + +
39C PRO 3.4 24.0 - - - +
40C ILE* 4.4 1.5 - - + +
41C LEU* 3.6 10.8 - - - +
89C LEU* 1.3 82.9 - - - +
91C GLY* 1.3 64.8 + - - +
92C LYS* 2.9 20.7 + - - +
93C GLY* 3.0 32.9 + - - +
----------------------------------------------------------
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