Contacts of the strand formed by residues 92 - 98 (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 92 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TRP* 3.9 18.0 - - - -
31A LYS* 4.8 11.4 + - - +
10C THR* 4.0 3.4 - - - -
11C VAL* 3.3 20.0 - - + +
13C GLU* 5.9 4.3 - - + -
65C ASN* 3.8 24.5 - - + +
90C SER 3.6 9.9 + - - +
91C ASP* 1.3 80.0 - - - +
93C SER* 1.3 64.3 + - - +
94C ILE* 6.1 1.1 - - - -
106C ILE 4.0 0.5 - - - +
107C THR* 3.4 2.3 - - - +
108C THR* 2.9 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TRP* 5.3 0.2 - - - -
10C THR* 4.2 1.0 + - - -
11C VAL 3.1 5.8 + - - +
12C ASP* 3.4 19.0 + - - -
13C GLU* 2.9 31.2 + - - +
92C THR* 1.3 74.6 - - - +
94C ILE* 1.3 64.7 + - - +
95C ILE* 3.9 1.8 - - - -
105C ILE* 4.1 5.6 - - - -
106C ILE 3.2 4.9 - - - -
107C THR* 2.6 34.0 + - - +
501C GOL 2.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 5.1 3.1 - - - +
15A TRP* 3.6 44.2 - - + +
93A SER* 5.0 10.3 - - - +
13C GLU* 3.6 24.0 - - + +
15C TRP* 4.0 22.9 - - + +
92C THR* 5.8 1.8 - - - +
93C SER* 1.3 75.1 - - - +
95C ILE* 1.3 61.0 + - - +
96C LEU* 3.7 29.0 + - + +
104C ALA 3.7 1.4 - - - +
105C ILE* 3.3 5.8 - - - +
106C ILE* 2.8 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP* 3.8 36.8 - - + +
13C GLU 2.8 15.4 + - - +
14C THR* 3.5 22.3 - - + +
15C TRP* 2.8 29.6 + - - +
93C SER* 4.7 2.0 - - - +
94C ILE* 1.3 75.7 - - - +
96C LEU* 1.3 60.5 + - - +
97C ASN 3.4 0.5 + - - -
103C ASN* 3.8 32.1 - - + +
104C ALA 3.6 2.7 - - - -
105C ILE* 4.2 22.9 - - + -
228C THR* 3.9 28.0 - - + +
270C THR* 4.6 1.1 - - - +
501C GOL 5.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 6.1 3.1 - - + -
21A PRO* 5.1 5.4 - - + -
93A SER* 6.6 0.2 - - - -
95A ILE* 6.0 3.4 - - + -
106A ILE* 5.0 15.5 - - + -
15C TRP* 3.7 19.7 - - + -
17C ILE* 3.9 29.1 - - + +
20C ILE* 5.1 6.8 - - + +
21C PRO* 5.0 10.1 - - + -
94C ILE* 3.7 26.5 - - + +
95C ILE* 1.3 70.0 - - - +
97C ASN* 1.3 61.3 + - - +
98C SER* 3.8 2.7 + - - -
102C ASP 4.5 1.0 - - - +
103C ASN* 3.2 5.1 - - - -
104C ALA* 2.7 53.0 + - + +
106C ILE* 5.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C THR* 4.2 19.1 - - + +
15C TRP 2.8 15.9 + - - +
16C SER* 3.4 15.1 + - - +
17C ILE* 2.8 26.5 + - - +
32C VAL* 5.9 0.8 - - - +
95C ILE 3.4 0.8 + - - -
96C LEU* 1.3 70.3 - - - +
98C SER* 1.3 70.7 + - - +
99C ALA* 5.5 1.2 - - - +
101C GLY 5.0 3.1 - - - +
103C ASN* 2.8 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 3.4 28.1 + - - +
16C SER* 6.0 0.2 - - - -
17C ILE* 2.9 14.6 - - - -
18C PRO 3.7 10.5 - - - -
19C ASP* 3.8 15.0 - - - -
20C ILE* 4.5 2.7 - - - -
96C LEU 3.8 4.2 + - - -
97C ASN* 1.3 87.0 + - - +
99C ALA* 1.3 67.1 + - - +
100C ASP 3.0 4.1 + - - +
101C GLY 3.8 19.1 + - - +
102C ASP 4.0 5.4 + - - -
103C ASN* 4.7 0.6 + - - -
----------------------------------------------------------
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