Contacts of the strand formed by residues 18 - 23 (chain C) in PDB entry 5J7C
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 18 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA* 4.6 0.7 - - - -
15C THR* 2.9 46.6 + - - +
17C THR* 1.3 82.2 - - - +
19C LEU* 1.3 71.5 + - - +
59C THR* 3.5 19.2 - - - +
60C ILE 3.2 12.3 + - - -
61C SER* 4.2 8.4 - - - -
63C LEU* 4.6 1.9 - - - +
95C THR* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 4.2 6.1 - - + -
13C ALA 3.8 2.0 - - - -
14C ALA* 3.7 11.2 - - + -
15C THR 4.5 0.7 - - - +
18C SER* 1.3 88.1 + - - +
20C LEU* 1.3 59.2 + - - +
21C ILE* 3.8 11.7 + - + -
58C ALA 3.8 0.3 - - - +
59C THR* 3.3 4.5 - - - +
60C ILE* 2.6 46.6 + - + +
63C LEU* 3.6 24.9 - - + -
69C TYR* 5.2 3.1 - - + -
71C ILE* 3.7 27.4 - - + -
93C TYR* 3.6 45.3 - - + +
95C THR* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 3.5 2.4 - - - +
12C VAL* 2.9 44.6 + - + +
13C ALA* 2.8 37.9 + - + +
19C LEU* 1.3 71.0 - - - +
21C ILE* 1.3 62.0 + - - +
57C ARG* 4.5 17.9 - - + +
58C ALA 3.4 24.7 - - - +
59C THR* 3.6 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.4 6.3 - - + -
10C GLU 3.3 8.5 - - - +
11C VAL* 4.0 11.9 - - + -
19C LEU* 4.5 6.3 - - + +
20C LEU* 1.3 77.3 - - - +
22C SER* 1.3 60.8 + - - +
23C TRP* 4.0 15.7 - - + -
34C ILE* 3.8 28.3 - - + -
57C ARG* 3.4 6.1 - - - +
58C ALA* 2.9 43.5 + - + +
60C ILE* 4.0 11.2 - - + -
71C ILE* 3.8 38.8 - - + -
73C VAL* 4.0 16.6 - - + -
91C ILE* 5.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ARG 5.1 0.2 - - - +
9C LEU* 3.3 3.5 + - - +
10C GLU* 2.7 44.2 + - - +
12C VAL* 4.0 24.0 - - - -
21C ILE* 1.3 75.0 - - - +
23C TRP* 1.3 67.5 + - - +
56C HIS* 3.5 12.9 + - - +
57C ARG* 3.9 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ARG 5.6 0.7 - - - -
8C ASP 3.1 14.8 - - - +
9C LEU* 3.8 12.1 - - + -
21C ILE* 4.0 16.4 - - + -
22C SER* 1.3 81.3 + - - +
24C ARG* 1.3 75.8 + - - +
25C GLY 3.8 0.8 + - - -
32C TYR* 3.6 46.0 - + + -
34C ILE* 4.0 9.9 - - + -
49C THR* 3.9 18.4 - - + -
53C ASP* 6.0 1.1 - - - -
56C HIS* 3.2 45.3 + - - +
57C ARG* 3.6 35.4 - - - -
58C ALA* 3.7 17.9 - - + -
73C VAL* 3.8 22.2 - - + -
89C ILE* 5.7 1.3 - - + -
----------------------------------------------------------
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