Contacts of the strand formed by residues 60 - 67 (chain A) in PDB entry 3WJG
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 ILE 60 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.7 28.9 - - + -
23A LEU* 3.9 39.7 - - + +
26A LEU* 4.4 10.1 - - + -
27A LEU* 4.1 9.2 - - + -
52A PHE* 3.8 28.0 - - + -
53A SER 3.4 14.6 - - - +
54A HIS* 4.7 0.4 - - + -
59A VAL* 1.3 77.9 - - - +
61A ALA* 1.3 68.7 + - - +
62A TYR 3.7 0.2 + - - -
81A TYR* 3.3 3.3 - - - -
82A PHE* 2.8 46.4 + - + +
84A PRO* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG 3.5 1.3 - - - +
52A PHE* 3.2 7.8 - - - -
53A SER* 2.8 49.4 + - - +
54A HIS* 4.8 1.7 - - - +
59A VAL* 4.1 1.8 + - - +
60A ILE* 1.3 74.1 - - - +
62A TYR* 1.3 59.5 + - - +
63A THR* 5.5 4.5 - - + -
80A GLY 3.6 5.6 - - - +
81A TYR* 3.9 21.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU* 4.7 1.2 + - - -
50A ILE* 3.7 30.4 - - + +
51A ARG 3.4 3.1 - - - -
52A PHE* 3.6 23.1 - + + -
60A ILE 3.7 0.2 + - - -
61A ALA* 1.3 73.5 - - - +
63A THR* 1.3 69.9 + - - +
64A GLN* 3.4 24.8 + - + +
78A GLU* 2.6 40.0 + - + -
79A SER* 3.1 5.2 - - - -
80A GLY* 2.8 47.2 + - - +
82A PHE* 3.7 30.3 - + + -
94A ILE* 4.2 18.8 - - + -
133A ARG* 3.9 6.6 + - - -
135A PHE* 5.3 6.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU 4.0 0.2 - - - +
50A ILE* 3.3 3.8 - - - +
51A ARG* 2.8 54.9 + - - +
61A ALA* 5.5 4.9 - - + -
62A TYR* 1.3 83.2 - - - +
64A GLN* 1.3 62.3 + - - +
78A GLU 3.6 5.6 - - - -
79A SER* 3.9 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR* 5.6 0.2 - - - -
48A GLU* 2.9 33.7 - - + +
49A GLU 3.2 12.6 - - - +
50A ILE* 3.7 3.6 - - + -
62A TYR* 3.4 26.0 - - + +
63A THR* 1.3 77.9 - - - +
65A LYS* 1.3 76.9 + - - +
66A THR* 3.5 12.2 - - - +
76A LEU* 4.3 1.4 + - - +
77A ALA* 3.3 11.6 - - - +
78A GLU* 2.9 58.1 + - + +
144A TYR* 4.7 1.6 + - - -
159A LEU* 6.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU* 3.3 3.8 - - - +
49A GLU* 2.9 68.2 + - + +
64A GLN* 1.3 77.4 - - - +
66A THR* 1.3 67.8 + - - +
67A TRP* 3.8 15.9 - - + -
76A LEU 3.4 11.4 - - - +
77A ALA* 4.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR* 3.6 27.8 - - + -
47A GLY 3.0 14.4 - - - +
48A GLU* 4.0 3.1 - - + -
64A GLN* 3.5 21.3 - - - +
65A LYS* 1.3 81.7 - - - +
67A TRP* 1.3 67.5 + - - +
74A PRO* 3.8 3.6 - - - +
75A LEU* 2.9 26.5 + - - +
76A LEU* 2.9 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 3.8 20.0 - - + -
46A TYR* 3.4 7.8 - - - -
47A GLY* 2.8 36.2 + - - -
48A GLU 3.3 27.6 - - - -
49A GLU* 3.4 31.2 - - + -
65A LYS* 3.8 17.5 - - + -
66A THR* 1.3 83.2 - - - +
68A LYS* 1.3 80.4 + - - +
69A LEU* 4.5 0.9 - - - -
72A GLY* 3.6 22.9 - - - +
73A ALA 3.2 15.0 - - - +
74A PRO* 4.3 1.6 - - + -
75A LEU* 3.4 9.6 - - - +
401A GOL 2.9 40.0 + - - -
----------------------------------------------------------
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