Contacts of the strand formed by residues 47 - 53 (chain A) in PDB entry 2N8A
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 LYS 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.0 7.3 - - - +
4A SER 5.5 0.2 + - - -
5A SER* 3.9 34.3 + - - +
38A MET* 3.4 48.2 - - + -
39A VAL 3.0 15.9 - - - +
40A GLN* 4.3 2.2 - - + +
44A PHE* 5.3 1.0 - - - -
46A GLY* 1.3 77.6 - - - -
48A VAL* 1.3 63.8 + - - +
49A PRO* 3.8 5.9 - - - +
22B C 5.3 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MET* 4.8 0.7 - - - -
39A VAL* 2.7 52.2 + - + +
41A SER* 3.7 13.9 - - - +
44A PHE* 3.4 33.7 - - + -
47A LYS* 1.3 73.9 - - - +
49A PRO* 1.3 75.4 - - + +
50A HIS* 3.8 6.3 + - + -
22B C 4.0 25.8 - - + +
23B T 3.3 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 3.9 7.9 - - + -
37A ILE 4.2 4.5 - - - +
38A MET* 4.7 13.7 - - - -
47A LYS 3.8 5.8 - - - +
48A VAL* 1.3 93.2 - - + +
50A HIS* 1.3 63.8 + - - +
51A TRP* 3.2 48.5 + - + +
21B G 6.3 1.6 - - + -
22B C 4.3 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 4.3 21.4 + - + -
36A ALA* 3.1 13.0 - - - +
37A ILE* 3.4 25.2 + - + -
39A VAL* 2.9 51.4 - - + +
48A VAL* 4.5 10.9 - - + +
49A PRO* 1.3 73.1 + - - +
51A TRP* 1.3 59.2 + - - +
52A TYR* 2.8 36.2 - - + +
149A PRO* 5.1 2.8 - - - +
150A GLN* 5.1 14.1 - - + +
22B C 6.1 1.4 - - + +
23B T 4.7 28.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 3.3 34.5 - - + -
12A GLU* 3.6 18.8 - - + -
19A ALA* 4.6 7.6 - - + -
20A SER 3.7 3.9 + - - +
21A CYS* 3.5 2.1 - - - -
22A LYS* 3.0 26.8 + - - +
28A ILE* 3.7 18.8 - - + -
34A ARG* 3.0 51.6 - - + +
35A MET* 3.1 20.9 - - - -
36A ALA* 2.9 35.4 - - + -
49A PRO* 3.2 40.6 + - + +
50A HIS* 1.3 70.4 - - - +
52A TYR* 1.3 67.4 + - - +
21B G 5.0 6.8 + - + -
22B C 4.0 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A CYS* 3.7 7.0 - - - -
22A LYS* 3.0 38.3 - - + +
23A LYS* 3.6 26.5 - - + -
28A ILE* 4.0 7.6 - - - -
34A ARG* 3.6 4.3 - - - +
35A MET 2.9 31.7 + - - +
37A ILE* 4.2 4.5 - - + +
50A HIS* 2.8 44.5 - - + +
51A TRP* 1.3 78.4 - - - +
53A HIS* 1.3 71.6 + - - +
54A PHE 3.5 0.2 + - - -
56A CYS 4.7 0.7 - - - -
57A PHE* 3.7 30.3 - + - +
60A VAL* 4.8 12.5 - - + +
62A HIS* 3.8 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A CYS* 3.2 20.7 - - + +
24A CYS* 3.5 6.9 - - - -
26A GLU* 3.3 16.8 - - + -
27A SER 2.8 25.7 + - - -
28A ILE* 3.4 20.6 - - + -
29A PRO* 4.1 7.8 - - + +
32A SER* 5.5 0.9 - - - -
33A LEU 4.6 3.1 - - - -
34A ARG* 4.8 1.6 - - - +
52A TYR* 1.3 76.9 - - - +
54A PHE* 1.3 68.6 + - - +
55A SER* 3.1 5.6 + - - +
56A CYS* 3.2 16.7 + - - +
57A PHE* 3.2 6.6 + - - +
1000A ZN 2.0 38.1 - - - -
----------------------------------------------------------
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