Contacts of the strand formed by residues 18 - 25 (chain C) in PDB entry 5JMO
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 LEU 18 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY 3.4 23.6 - - - +
9C GLY 4.9 0.2 - - - -
10C GLY* 4.0 14.1 - - - +
11C LEU 5.4 0.2 - - - +
12C VAL* 3.6 44.6 - - + -
17C SER* 1.3 74.1 - - - +
19C THR* 1.3 60.5 + - - +
20C LEU* 4.2 3.1 - - + -
81C LEU 3.8 0.2 - - - +
82C GLN* 4.4 0.9 - - - +
83C MET* 2.7 45.7 + - - +
86C LEU* 4.0 11.5 - - + +
113C VAL* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY* 3.9 17.7 - - - +
18C LEU* 1.3 78.5 + - - +
20C LEU* 1.3 73.2 + - - +
21C SER* 4.1 4.8 + - - +
80C TYR* 4.6 16.2 - - + -
81C LEU 3.5 8.5 - - - +
82C GLN* 3.9 18.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
7C SER 3.6 5.2 - - - +
8C GLY 3.6 28.5 - - - +
9C GLY* 3.9 4.0 - - - +
18C LEU* 4.8 4.5 - - + -
19C THR* 1.3 76.1 - - - +
21C SER* 1.3 62.3 + - - +
36C TRP* 3.8 21.5 - - + -
80C TYR* 3.2 11.7 - - - +
81C LEU* 2.8 37.2 + - + +
83C MET* 3.6 30.7 - - - -
94C TYR* 3.9 33.7 - - + -
111C THR* 4.4 4.0 - - + -
113C VAL* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLU* 3.4 3.6 - - - -
7C SER* 2.9 48.2 + - - +
8C GLY* 5.6 0.9 - - - -
19C THR* 4.5 6.4 + - - +
20C LEU* 1.3 77.0 + - - +
22C CYS* 1.3 62.9 + - - +
23C ALA 5.4 0.2 - - - -
36C TRP* 3.9 5.4 - - - -
78C THR* 4.3 7.9 - - - -
79C LEU 3.4 5.4 - - - -
80C TYR* 3.7 18.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 4.2 19.3 - - - -
5C GLN 3.3 10.5 - - - -
6C GLU* 4.3 3.4 - - + -
21C SER* 1.3 76.6 - - - +
23C ALA* 1.3 63.8 + - - +
24C ALA* 3.9 1.6 + - - +
29C PHE* 5.2 0.9 - - - -
36C TRP* 3.9 8.5 - - + -
77C ASN 3.8 0.2 - - - +
78C THR* 3.2 7.0 - - - +
79C LEU* 2.8 41.6 + - + +
96C CYS* 2.0 55.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLN 3.7 1.4 - - - +
4C LEU* 3.6 3.3 - - - -
5C GLN* 3.0 44.1 + - + +
21C SER* 4.3 0.8 - - - -
22C CYS* 1.3 73.6 - - - +
24C ALA* 1.3 60.9 - - - +
76C LYS 5.8 0.2 - - - +
77C ASN* 3.6 7.2 - - + +
78C THR* 4.3 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLN 3.4 3.8 - - - -
4C LEU* 3.6 18.8 - - + -
22C CYS 5.0 0.4 - - - +
23C ALA* 1.3 75.9 - - - +
25C SER* 1.3 63.6 + - - +
27C PHE* 3.9 9.7 - - + +
29C PHE* 3.5 37.2 - - + -
77C ASN* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C GLN 3.9 3.0 + - - -
2C VAL* 3.5 1.0 - - - -
3C GLN* 2.7 60.4 + - - +
5C GLN* 4.8 1.7 + - - -
24C ALA* 1.3 76.0 - - - +
26C GLY* 1.3 60.2 + - - +
27C PHE* 3.3 11.1 - - - +
----------------------------------------------------------
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