Contacts of the strand formed by residues 21 - 25 (chain C) in PDB entry 3QBY
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 TRP 21 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 3.3 4.4 - - - -
13C ALA 2.9 41.4 + - - +
18C TYR* 4.1 23.6 - + + -
19C PRO* 3.7 20.4 - - + +
20C HIS* 1.3 72.1 - - - +
22C PRO* 1.4 98.6 - - + +
23C ALA* 3.3 3.5 + - - +
44C PHE* 3.7 23.7 - + + +
45C PHE 3.0 21.0 + - - -
47C THR* 3.7 14.3 - - + +
74C ARG* 3.9 23.1 - - + -
75C LYS 3.3 28.5 - - - -
76C GLY 4.0 0.4 - - - -
77C PHE* 3.6 37.2 - + + +
95C UNX 4.0 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL 3.6 7.2 - - - +
12C PHE* 3.9 13.4 - - + -
20C HIS 4.2 0.4 - - - +
21C TRP* 1.4 102.0 - - + +
23C ALA* 1.3 58.6 + - - +
45C PHE* 3.0 23.9 + - + -
77C PHE* 3.8 24.0 - - + +
80C GLY* 3.5 30.1 - - - +
81C LEU* 3.7 6.7 - - + +
84C ILE* 3.7 31.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
10C LEU* 3.6 1.6 - - - -
11C VAL* 2.8 32.7 + - + +
13C ALA* 3.8 10.5 - - + -
21C TRP 3.7 9.2 - - - +
22C PRO* 1.3 75.2 - - - +
24C ARG* 1.3 63.2 + - - +
42C ILE* 3.6 22.2 - - + -
43C PHE 3.1 15.5 - - - +
44C PHE* 4.1 5.2 - - + -
45C PHE* 3.4 16.0 - - - -
84C ILE* 3.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY* 4.4 5.6 - - - +
9C ASP 3.2 12.1 - - - +
10C LEU* 3.9 13.0 - - + -
11C VAL* 4.3 3.1 - - - -
23C ALA* 1.3 76.5 - - - +
25C ILE* 1.3 71.2 + - - +
26C ASP* 4.1 14.5 + - - -
42C ILE* 3.6 4.3 - - - +
43C PHE* 2.9 68.3 + - + -
45C PHE* 3.7 12.8 - - + -
87C ASN 5.3 0.4 + - - -
88C PRO 2.8 36.4 + - - -
89C HIS* 3.6 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 3.9 16.4 - - + -
6C LYS 3.3 29.6 - - - +
7C PRO* 4.1 2.5 - - + -
8C GLY* 2.7 29.2 + - - -
9C ASP* 2.9 28.1 + - + +
11C VAL* 4.2 11.0 - - + -
24C ARG* 1.3 75.3 + - - +
26C ASP* 1.3 70.8 + - - +
40C TYR* 3.9 20.4 - - + -
41C PRO* 3.6 11.0 - - + +
42C ILE* 3.6 21.1 - - + -
58C LEU* 3.9 18.6 - - + -
----------------------------------------------------------
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