Contacts of the strand formed by residues 10 - 17 (chain C) in PDB entry 3IKH
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 10 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASN* 3.7 24.2 - - - +
9C ILE* 1.3 80.4 - - - +
11C VAL* 1.3 64.8 + - - +
12C ASP* 2.8 25.3 + - - -
36C ILE* 3.6 10.6 - - - +
37C GLY 2.8 31.9 + - - +
38C GLY* 4.2 1.1 - - - -
69C ILE* 3.8 8.5 - - - +
91C ASP* 3.2 28.0 - - + +
92C THR* 4.0 6.3 - - - +
93C SER* 4.2 5.8 - - - +
107C THR* 4.3 1.6 - - + -
501C GOL 3.1 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C THR* 1.3 76.8 - - - +
12C ASP* 1.3 68.5 + - - +
13C GLU* 3.9 8.1 + - + +
34C GLN* 4.6 10.1 - - + -
35C ASP 3.3 6.1 - - - +
36C ILE* 4.5 0.4 - - + -
65C ASN* 3.5 39.7 - - + +
68C TRP* 3.6 34.5 - - + -
69C ILE* 4.0 12.8 - - + -
91C ASP 3.4 3.8 + - - +
92C THR* 3.3 17.1 - - + -
93C SER 3.1 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C THR* 2.8 17.2 + - - -
11C VAL* 1.3 70.8 - - - +
13C GLU* 1.3 61.1 + - - +
14C THR* 4.2 2.1 + - - +
33C SER 3.7 0.7 - - - +
34C GLN* 3.0 6.1 - - - +
35C ASP* 2.6 37.3 + - + +
37C GLY* 4.0 5.4 - - - -
93C SER* 3.4 8.0 - - - -
95C ILE* 3.8 19.0 - - + +
228C THR* 4.4 0.2 - - - +
270C THR* 2.9 28.6 + - - +
501C GOL 2.7 48.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 5.0 5.5 - - - +
64A SER* 5.0 4.3 + - - -
65A ASN* 5.9 0.3 - - - -
11C VAL* 4.8 9.4 - - + +
12C ASP* 1.3 75.1 - - - +
14C THR* 1.3 62.5 + - - +
15C TRP* 3.7 18.2 + - - +
31C LYS* 3.4 29.3 + - + -
33C SER 3.3 6.3 - - - +
34C GLN* 2.3 40.1 + - + +
92C THR* 5.9 4.7 - - + -
93C SER 2.9 14.3 + - - +
94C ILE* 3.6 14.7 - - + +
95C ILE* 2.8 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP* 5.2 1.6 + - - +
13C GLU* 1.3 73.9 - - - +
15C TRP* 1.3 64.4 + - - +
31C LYS* 3.6 4.5 - - - +
32C VAL* 2.8 39.1 + - + -
33C SER* 2.8 31.9 + - - +
95C ILE* 3.5 31.7 - - + +
97C ASN* 4.2 21.3 - - + +
226C ASP* 5.0 11.4 + - - +
228C THR* 5.2 1.4 + - - +
269C GLY* 5.9 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 5.5 4.3 - - - -
91A ASP* 3.0 32.1 - - - -
93A SER* 3.3 27.1 - - - -
106A ILE* 3.5 37.5 - - + -
108A THR* 3.2 27.4 - - + -
13C GLU* 3.7 31.3 + - + +
14C THR* 1.3 82.1 - - - +
16C SER* 1.3 61.1 + - - +
17C ILE* 3.6 4.9 + - + +
29C GLY* 4.8 3.6 - - - -
30C VAL 3.5 4.7 - - - +
31C LYS* 3.4 24.0 - - + +
94C ILE* 4.0 21.2 - - + +
95C ILE 2.8 11.3 + - - +
96C LEU* 3.7 15.8 - - + -
97C ASN* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TRP* 1.3 71.6 - - - +
17C ILE* 1.3 60.7 + - - +
18C PRO* 4.7 0.3 - - - +
29C GLY* 3.4 5.5 - - - -
30C VAL* 2.7 40.8 + - - +
32C VAL* 3.6 23.6 - - - +
97C ASN* 3.4 18.9 + - - +
99C ALA 5.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 3.9 28.3 - - + -
15C TRP* 4.6 9.9 - - + +
16C SER* 1.3 81.7 + - - +
18C PRO* 1.3 74.6 - - + +
19C ASP 3.5 25.6 - - - +
20C ILE* 3.8 12.8 - - + +
21C PRO* 4.0 9.4 - - + -
27C ILE* 4.1 5.4 - - + -
28C HIS 4.0 6.7 - - - +
29C GLY* 4.1 1.3 - - - -
96C LEU* 3.9 26.2 - - + -
97C ASN 2.8 21.4 + - - +
98C SER* 2.9 21.6 - - - -
99C ALA* 3.1 5.7 + - - +
----------------------------------------------------------
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