Contacts of the strand formed by residues 41 - 46 (chain C) in PDB entry 2IGT
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 TYR 41 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU 3.9 0.2 - - - +
37C GLN* 3.4 4.1 + - - -
38C TYR* 2.8 39.2 + - - +
39C GLY 3.3 0.2 - - - -
40C ASP* 1.3 90.9 - - + +
42C ARG* 1.3 61.0 + - - +
43C VAL* 3.9 6.8 + - + +
65C ASP* 3.5 16.4 - - + -
66C ALA* 5.1 0.7 - - + -
86C ALA* 3.7 21.7 - - + +
87C LEU* 3.6 29.3 + - - +
88C GLY 4.8 1.6 + - - -
90C THR 4.6 4.3 + - - -
91C TRP* 3.5 49.0 - + + +
104C PHE* 3.6 37.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ILE* 3.6 12.4 - - + +
35C LEU* 3.7 21.5 - - + -
36C GLU 3.4 6.7 - - - +
37C GLN* 3.1 25.7 + - - +
41C TYR* 1.3 72.2 - - - +
43C VAL* 1.3 61.6 + - - +
60C VAL* 3.3 28.5 + - - +
63C ASN* 3.9 11.8 + - - +
64C ALA* 3.7 12.7 - - - +
65C ASP* 2.7 43.9 + - - +
66C ALA 3.3 6.1 + - - -
289C LEU* 3.4 20.6 - - - +
1007C ACY 3.0 42.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LYS 3.6 1.2 - - - +
35C LEU* 3.5 4.8 - - - +
36C GLU* 2.8 57.9 + - + +
38C TYR* 3.8 26.0 - - + -
41C TYR* 4.4 17.0 - - + +
42C ARG* 1.3 78.2 - - - +
44C VAL* 1.3 61.8 + - - +
45C ARG* 4.2 11.2 + - + +
66C ALA* 3.2 21.5 - - + +
80C TRP* 4.4 8.5 - - + -
91C TRP* 4.8 4.3 - - + -
104C PHE* 4.3 14.1 - - + -
110C VAL* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3A TYR* 4.8 3.4 - - + +
33C LEU* 4.2 22.7 - - + -
34C LYS 3.3 7.2 - - - +
35C LEU* 3.5 26.7 - - + -
43C VAL* 1.3 70.6 - - - +
45C ARG* 1.3 69.8 + - - +
61C TRP* 3.9 28.0 - - + +
64C ALA* 3.7 15.9 - - + -
66C ALA 2.9 7.9 + - - +
67C ILE* 3.4 25.9 - - + -
68C PHE 2.9 28.0 + - - +
80C TRP* 4.1 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.4 7.3 - - - +
34C LYS* 2.8 52.8 + - - +
36C GLU* 2.9 40.8 + - - +
38C TYR* 3.3 11.5 + - - -
43C VAL* 4.3 4.9 - - + +
44C VAL* 1.3 81.5 - - - +
46C PRO* 1.3 77.2 - - + +
68C PHE* 4.3 2.2 - - + -
80C TRP* 3.8 21.5 - - + -
108C ARG* 2.9 43.1 + - + +
109C HIS* 3.8 1.0 - - - +
110C VAL* 3.9 13.6 - - - +
112C VAL 5.4 0.2 + - - -
114C PRO* 5.9 0.6 - - - +
1016C FMT 3.1 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLY 3.5 9.9 - - - +
33C LEU* 4.2 9.4 - - + -
34C LYS* 3.9 10.2 + - - -
45C ARG* 1.3 91.8 - - + +
47C GLU* 1.3 60.2 + - - +
48C ALA 4.2 2.0 - - - +
68C PHE* 3.8 40.6 - - + +
69C THR* 6.0 0.7 - - - -
70C GLY 5.9 2.5 - - - +
108C ARG* 4.4 20.1 + - - -
----------------------------------------------------------
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