Contacts of the strand formed by residues 29 - 34 (chain C) in PDB entry 1I3R
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 ASP 29 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASP* 3.1 5.7 + - - -
26C PHE* 2.6 39.7 + - - +
27C ASP* 4.5 1.0 - - - +
28C GLY* 1.3 80.3 - - - +
30C GLU* 1.3 62.3 + - - +
31C ILE 3.4 0.2 + - - -
149D TYR* 3.7 24.6 + - - -
175D ARG* 3.3 32.3 + - - +
177D GLY* 4.4 8.8 - - - +
179D TRP* 3.4 46.6 + - + +
181D PHE* 4.8 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C MET* 3.8 5.6 - - + +
24C PHE 3.4 8.1 - - - +
25C ASP* 4.1 0.6 + - - -
28C GLY 4.4 0.4 + - - -
29C ASP* 1.3 72.1 - - - +
31C ILE* 1.3 61.3 + - - +
32C PHE* 3.4 16.0 - - - +
33C HIS* 2.5 46.0 + - - +
44C ARG* 3.0 39.8 + - + +
135C THR* 4.3 3.6 - - - +
136C VAL* 3.7 23.3 + - - +
138C LEU* 3.8 24.4 - - + +
177D GLY 5.5 3.7 + - - +
179D TRP* 3.0 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 5.3 0.2 - - + -
24C PHE* 2.9 18.4 + - + +
25C ASP 4.0 8.1 - - - +
26C PHE* 3.7 32.8 - - + +
30C GLU* 1.3 72.6 - - - +
32C PHE* 1.3 78.9 + - + +
43C TRP* 3.8 16.7 - - + -
44C ARG* 2.9 22.8 + - - +
48C PHE* 3.8 14.0 - - + -
112D PHE* 3.5 41.3 - - + -
115D PHE* 5.3 1.1 - - + -
116D LEU* 3.7 20.2 - - + -
179D TRP* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 4.4 10.3 - + - -
23C MET* 3.3 4.5 - - - +
24C PHE* 3.0 61.9 + + + +
30C GLU* 3.4 9.7 - - - +
31C ILE* 1.3 94.7 - - + +
33C HIS* 1.3 67.9 + - - +
34C VAL* 4.4 2.9 - - + -
41C THR* 3.9 15.7 - - + -
42C ILE 2.9 24.7 - - - +
43C TRP* 3.7 16.4 - + + -
44C ARG 4.2 1.3 - - - +
54C PHE* 3.7 43.5 - + + -
5D ILE* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLU* 6.3 1.6 - - + -
22C PHE 3.1 13.9 - - - +
23C MET* 3.7 8.5 - - + -
30C GLU* 2.5 25.9 + - - +
32C PHE* 1.3 77.2 - - - +
34C VAL* 1.3 77.8 + - - +
35C ASP* 4.1 10.5 + - - -
41C THR* 3.9 0.5 - - - -
42C ILE* 2.9 64.1 + - + +
43C TRP 6.2 0.2 - - - -
44C ARG* 6.3 0.6 - - - -
134C GLU 6.1 0.2 - - - -
135C THR* 6.1 0.7 - - - -
136C VAL* 3.5 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLU* 4.8 2.9 - - - +
22C PHE* 2.8 27.7 + - + +
32C PHE* 4.4 2.9 - - + -
33C HIS* 1.3 83.7 - - - +
35C ASP* 1.3 68.0 + - - +
36C ILE* 3.1 15.9 + - - +
40C GLU 3.6 9.4 - - - +
41C THR* 4.1 15.9 - - - +
54C PHE* 4.0 17.0 - - + -
56C ALA* 3.9 26.2 - - + +
59C ALA* 3.6 27.6 - - + -
60C LEU* 4.3 11.9 - - + -
----------------------------------------------------------
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