Contacts of the strand formed by residues 87 - 94 (chain E) in PDB entry 2IAN
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 87 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ARG* 3.1 23.0 + - - -
37E GLN 3.0 13.2 + - - -
38E ASP* 2.8 26.9 + - - +
39E PRO* 6.0 1.3 - - - -
85E GLN 3.1 2.4 + - - -
86E THR* 1.3 75.8 - - - +
88E VAL* 1.3 63.2 + - - +
89E TYR* 3.6 21.3 - - - -
105E SER 3.5 1.2 - - - +
106E TRP* 3.9 0.5 - - - -
107E LEU 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ARG* 3.4 1.9 - - - -
37E GLN* 2.8 45.6 + - + +
87E SER* 1.3 76.5 - - - +
89E TYR* 1.3 64.7 + - - +
90E PHE* 3.5 32.6 - - + -
105E SER 3.1 12.8 - - - +
106E TRP* 3.3 50.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLN* 3.3 5.0 - - - +
21E LEU* 4.1 22.7 - - + -
34E TRP* 4.1 5.6 - - + -
35E TYR 3.4 5.6 - - - +
36E ARG* 4.1 5.5 + - + -
46E ILE* 3.6 25.1 - - + -
64E TYR* 2.8 47.5 + + - -
76E LEU* 4.0 11.4 - - + -
78E LEU* 4.4 5.9 - - + +
85E GLN* 2.8 33.0 + - - +
87E SER* 3.6 24.7 - - - -
88E VAL* 1.3 73.4 - - - +
90E PHE* 1.3 66.1 + - - +
104E GLY* 3.6 1.0 - - - -
105E SER 2.7 38.5 + - - +
107E LEU* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLN* 4.1 4.7 - - - -
40D GLY* 2.9 34.1 - - - -
41D GLN* 5.1 1.1 - - - -
42D LEU* 3.9 16.8 - - + -
6E GLN* 3.7 1.8 - - - +
33E TYR 3.8 0.2 - - - +
34E TRP* 3.4 4.8 - - - -
35E TYR* 2.5 51.4 + - + +
37E GLN* 3.7 19.7 - - - -
43E LEU* 4.1 15.7 - - + -
88E VAL* 3.5 33.9 - - + -
89E TYR* 1.3 76.2 - - - +
91E CYS* 1.3 59.3 + - - +
101E PHE* 3.8 18.8 - + + -
102E GLY 3.7 19.7 - - - -
103E GLU 4.3 2.0 - - - -
104E GLY* 3.6 17.5 - - - -
106E TRP* 4.6 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E VAL* 4.5 2.0 - - + +
6E GLN* 3.1 13.6 - - - +
23E CYS* 2.0 51.1 - - + -
32E MET* 4.1 10.1 - - - -
33E TYR 3.1 12.3 - - - -
34E TRP* 3.7 24.0 - - + -
74E PHE* 4.6 3.1 - - - -
90E PHE* 1.3 73.5 - - - +
92E ALA* 1.3 65.8 + - - +
101E PHE* 3.2 7.5 - - - -
102E GLY 3.0 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 4.8 6.3 - - + -
4E VAL* 4.7 3.4 - - - -
32E MET* 3.1 9.2 - - - +
33E TYR* 2.8 37.4 + - + -
35E TYR* 4.1 12.3 - - + -
91E CYS* 1.3 78.4 - - - +
93E SER* 1.3 63.5 + - - +
99E GLY 5.7 0.2 - - - -
100E TYR 3.0 14.6 - - - +
101E PHE* 3.6 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E VAL* 3.9 5.4 - - - +
25E GLN* 3.5 11.0 - - - +
27E MET* 3.5 17.3 - - - +
29E HIS* 2.7 31.1 + - - -
31E TYR 3.3 13.0 - - - -
32E MET* 3.8 11.7 - - - -
33E TYR* 4.5 2.0 - - - -
92E ALA* 1.3 77.3 - - - +
94E THR* 1.3 62.7 + - - +
98E THR 3.8 0.5 - - - +
99E GLY* 3.4 0.5 - - - -
100E TYR* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLN* 3.9 7.2 - - - +
89D LEU* 4.5 10.3 - - + +
96D LEU* 4.7 8.2 - - + +
29E HIS* 3.1 23.4 - - - +
31E TYR* 3.2 20.9 + - - +
33E TYR* 3.5 20.8 + - - -
93E SER* 1.3 70.5 - - - +
95E TYR* 1.3 66.8 + - - +
97E GLY 3.6 10.8 - - - +
98E THR 2.9 11.9 - - - +
99E GLY* 2.8 39.3 - - - +
----------------------------------------------------------
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