Contacts of the strand formed by residues 27 - 33 (chain R) in PDB entry 3K9Q
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 27 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R ALA* 4.2 0.2 - - - -
3R VAL* 3.7 33.9 - - + -
5R VAL* 4.1 10.8 - - + -
21R ILE* 3.7 23.9 - - + +
24R VAL* 3.6 39.3 - - + +
25R GLU* 3.3 3.0 - - - +
26R GLY* 1.3 81.9 + - - +
28R GLU* 1.3 67.1 + - - +
325R VAL* 4.1 17.5 - - + -
328R LEU* 4.3 19.5 - - + -
329R ALA* 4.0 25.8 - - + -
332R ALA* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1R MET* 5.3 7.1 - - - +
2R ALA* 4.1 18.9 + - + +
3R VAL 3.1 13.2 + - - +
4R LYS* 3.8 2.9 - - + -
5R VAL* 2.9 29.2 + - - +
21R ILE* 4.4 0.9 - - - -
27R LEU* 1.3 78.4 - - - +
29R VAL* 1.3 65.8 + - - +
30R VAL* 3.4 18.0 + - + +
70R LYS* 4.4 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R VAL* 3.4 9.6 - - + +
7R ILE* 3.8 14.8 - - + -
18R PHE* 3.7 40.3 - - + -
21R ILE* 3.8 39.5 - - + +
22R GLN* 4.9 2.7 + - - +
28R GLU* 1.3 75.7 - - - +
30R VAL* 1.3 58.9 + - - +
31R ALA 3.4 24.7 - - - +
32R VAL* 4.0 9.0 - - + -
71R GLU 4.7 1.7 - - - +
72R VAL* 3.8 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R LYS* 4.1 29.4 - - + -
5R VAL 2.9 10.3 + - - +
28R GLU* 4.0 26.2 - - + +
29R VAL* 1.3 77.5 - - - +
31R ALA* 1.3 63.2 + - + +
71R GLU 4.3 7.7 - - - +
72R VAL* 3.8 3.8 - - - -
73R LYS* 3.0 28.3 + - - +
88R LEU* 4.7 11.4 - - + +
90R ILE* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R VAL 3.6 1.0 + - - -
6R ALA* 3.3 8.5 - - + -
7R ILE 3.0 21.9 + - - -
29R VAL* 3.4 5.2 - - - +
30R VAL* 1.3 85.8 - - + +
32R VAL* 1.3 68.3 + - - +
72R VAL* 4.2 1.1 - - - -
73R LYS 3.1 9.4 - - - +
75R PHE* 4.3 4.0 - - + -
85R TRP* 3.7 19.3 - - + -
88R LEU* 3.6 27.8 - - + -
90R ILE* 4.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R ILE* 3.4 11.2 - - + +
10R PHE* 3.6 56.5 - - + -
18R PHE* 4.7 0.7 - - + -
29R VAL* 4.0 14.8 - - + -
31R ALA* 1.3 80.5 - - - +
33R ASN* 1.3 66.8 + - - +
41R LEU* 4.1 19.5 - - + -
65R PHE* 4.6 4.9 - - + -
72R VAL* 4.1 13.5 - - + -
73R LYS 2.8 6.4 + - - +
74R SER* 3.2 5.6 - - - -
75R PHE* 2.9 26.9 + - - -
85R TRP* 5.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 33 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0R NAD 3.2 15.4 + - - -
7R ILE 2.9 11.5 + - - +
8R ASN* 2.8 25.9 + - - +
9R GLY* 2.8 29.8 + - - -
10R PHE 3.9 1.2 + - - -
32R VAL* 1.3 77.4 - - - +
34R ASP* 1.3 63.6 + - - +
75R PHE* 3.0 21.6 - - + +
77R GLU 2.8 46.6 + - - -
80R ALA* 5.8 0.2 - - - +
83R LEU* 3.4 24.1 - - + +
85R TRP* 4.4 6.5 - - + -
----------------------------------------------------------
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