Contacts of the strand formed by residues 50 - 60 (chain A) in PDB entry 2WJ7
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 PHE 50 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 3.4 30.1 - - + +
44A ARG* 3.5 5.8 - - - -
45A GLN* 3.6 47.3 - - + -
49A GLY* 1.3 74.4 - - - -
51A ILE* 1.3 64.4 + - - +
56B HIS 3.9 1.2 - - - +
57B ARG* 3.2 3.7 + - - +
58B LYS* 2.8 45.4 + - + +
60B ARG* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A HIS* 3.0 17.3 + - - +
43A GLU* 4.2 1.7 - - - +
44A ARG* 3.1 31.3 + - - +
46A ASP* 3.0 33.9 - - + +
50A PHE* 1.3 75.5 - - - +
52A SER* 1.4 82.0 + - - +
53A ARG* 3.5 39.0 - - + +
55B PHE* 4.4 12.3 - - + -
56B HIS 3.4 12.3 - - - +
57B ARG* 3.3 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A HIS* 3.3 16.6 - - - -
42A GLU* 4.1 2.0 - - - -
43A GLU* 3.6 23.3 - - - +
51A ILE* 1.4 81.0 - - - +
53A ARG* 1.4 63.0 - - - +
55B PHE* 3.5 1.3 - - - -
56B HIS* 2.9 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 3.4 51.1 + - - +
21A PHE* 3.9 15.5 - - + -
40A LYS* 3.5 2.1 - - - +
41A HIS* 2.7 81.2 + - + +
44A ARG* 4.5 4.2 - - - +
46A ASP* 4.3 11.3 + - - +
51A ILE* 3.5 31.2 - - + +
52A SER* 1.4 77.0 - - - +
54A GLU* 1.3 61.5 + - - +
54B GLU 3.7 7.0 - - - +
55B PHE* 4.7 6.3 - - + -
57B ARG* 5.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 5.1 0.2 - - - -
38A HIS* 2.8 29.7 + - + -
39A GLY 3.3 13.5 - - - +
40A LYS* 3.9 21.1 - - + +
53A ARG* 1.3 75.3 - - - +
55A PHE* 1.3 70.2 + - - +
53B ARG* 3.6 1.4 - - - +
54B GLU* 2.9 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.4 7.9 - - + -
17A ASP 6.0 0.4 - - - -
18A VAL* 4.3 16.2 - - + -
21A PHE* 3.7 40.4 - + - -
26A LEU* 4.5 3.6 - - + -
37A VAL* 3.8 39.0 - - + -
38A HIS* 3.1 8.9 + - - -
39A GLY* 2.9 46.5 + - - -
54A GLU* 1.3 77.4 - - - +
56A HIS* 1.3 68.0 - - - +
57A ARG* 4.2 10.3 - - + -
51B ILE* 4.2 13.5 - - + -
52B SER 3.4 12.1 - - - +
53B ARG* 4.4 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 3.5 33.4 + - + -
37A VAL 3.2 9.8 + - - -
38A HIS* 3.8 22.6 - + + +
55A PHE* 1.3 76.6 - - - +
57A ARG* 1.3 68.5 + - - +
58A LYS* 2.7 34.3 + - - +
50B PHE 3.9 0.3 - - - +
51B ILE* 3.2 6.7 - - - -
52B SER* 3.0 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 5.1 4.3 - - + -
35A ILE 3.5 0.2 - - - +
36A GLU* 3.3 5.4 - - - -
37A VAL* 2.9 41.6 + - + +
55A PHE* 4.2 14.1 - - + -
56A HIS* 1.3 74.8 + - - +
58A LYS* 1.3 70.4 + - - +
59A TYR* 3.5 40.9 - - + +
46B ASP* 2.7 41.4 + - - -
48B HIS* 3.7 14.4 + - - +
49B GLY 3.3 23.2 - - - +
50B PHE 3.4 11.6 + - - +
51B ILE* 3.6 24.8 - - + +
53B ARG* 5.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.8 17.7 - - + -
35A ILE 3.1 4.3 - - - -
36A GLU* 3.8 20.0 + - + +
56A HIS* 2.7 41.7 + - - +
57A ARG* 1.3 83.6 + - - +
59A TYR* 1.3 63.3 + - - +
48B HIS 3.8 0.2 - - - +
49B GLY* 3.5 6.1 - - - -
50B PHE* 2.9 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MET 6.0 0.3 + - - -
14A VAL* 3.5 30.6 - - + +
15A ASN 5.0 0.2 + - - -
16A LEU* 3.2 30.1 - - + +
34A VAL* 3.2 9.8 - - - +
35A ILE* 2.9 62.2 + - + +
37A VAL* 4.3 13.5 - - + -
57A ARG* 3.5 29.0 + - + -
58A LYS* 1.3 75.3 - - - +
60A ARG* 1.3 67.8 + - - +
82A VAL* 5.9 3.1 - - + -
48B HIS* 3.4 48.7 + - + +
49B GLY* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP 3.6 7.6 - - - +
34A VAL* 4.8 5.8 - - + +
35A ILE* 5.4 1.1 - - - +
59A TYR* 1.3 80.1 - - - +
61A ILE* 1.3 68.5 + - - +
62A PRO* 3.5 8.0 - - - +
48B HIS 4.9 2.8 + - - -
49B GLY* 5.5 1.2 - - - -
50B PHE* 5.3 13.5 - - + -
----------------------------------------------------------
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