Contacts of the strand formed by residues 56 - 63 (chain A) in PDB entry 4OP0
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 VAL 56 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.9 10.3 - - - +
29A GLN* 3.5 34.5 - - + +
43A LEU* 3.8 15.4 - - + +
46A ARG* 3.2 30.1 - - - +
52A ASP 3.8 9.0 - - - +
53A ILE* 3.1 33.2 + - + +
55A GLY* 1.3 76.5 - - - +
57A VAL* 1.3 65.2 + - - +
86A VAL* 3.1 7.4 - - - +
87A GLY 2.9 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TRP* 3.6 41.5 - - + -
29A GLN 2.9 19.0 + - - +
30A LEU* 3.4 18.4 - - + -
31A ASP* 3.1 24.1 + - - +
46A ARG* 5.5 0.3 + - - -
56A VAL* 1.3 77.4 - - - +
58A LEU* 1.3 63.8 + - - +
59A ILE* 4.1 20.2 - - + -
84A LEU* 4.7 2.5 - - + -
85A SER 3.6 7.4 - - - +
86A VAL* 4.0 8.5 - - + -
191A LEU* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 3.6 13.5 - - + +
33A VAL* 4.0 27.4 - - + -
39A THR* 3.9 26.1 - - + +
42A ASP* 3.4 39.9 - - + +
43A LEU* 4.0 18.2 - - + -
46A ARG* 3.9 22.9 - - - +
56A VAL 4.2 0.2 - - - -
57A VAL* 1.3 73.4 - - - +
59A ILE* 1.3 67.5 + - - +
83A ILE 4.0 0.2 - - - +
84A LEU* 3.2 3.9 - - - +
85A SER 2.9 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.6 27.8 - - + -
16A LEU* 4.1 22.2 - - + -
30A LEU* 4.1 28.7 - - + -
31A ASP 2.9 10.8 + - - +
32A VAL* 3.2 9.4 - - + -
33A VAL* 2.9 27.5 + - - +
57A VAL* 4.1 7.2 - - + -
58A LEU* 1.3 78.0 - - - +
60A ALA* 1.3 66.8 + - - +
82A ILE* 5.2 4.9 - - + -
83A ILE 3.3 16.4 - - - +
84A LEU* 3.7 25.1 - - + -
187A ALA* 5.2 5.4 - - + -
191A LEU* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.3 18.4 - - + -
36A THR* 3.8 6.3 - - + -
39A THR* 3.6 22.6 - - + +
59A ILE* 1.3 79.2 - - - +
61A GLU* 1.3 65.0 + - - +
62A HIS 3.5 20.0 - - - +
63A GLN* 4.9 0.2 - - + -
81A GLN 5.0 1.7 - - - +
83A ILE* 3.0 32.6 + - + +
183A ARG* 5.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 3.3 11.8 - - - +
11A LEU* 2.8 37.6 + - - +
32A VAL* 4.1 11.8 - - + +
33A VAL 2.9 15.7 + - - +
34A ALA* 3.3 17.0 - - - +
60A ALA* 1.3 72.9 - - - +
62A HIS* 1.3 58.4 + - + +
77A THR 4.1 2.6 - - - +
78A ALA* 3.5 2.8 - - + -
79A ARG* 2.9 41.6 + - + +
80A ALA 4.7 0.5 + - - -
81A GLN 4.9 1.4 + - - +
83A ILE* 4.3 5.1 - - - +
183A ARG* 2.8 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA 3.0 14.0 + - - +
35A GLN* 3.2 18.1 + - + +
36A THR 3.1 22.4 + - - -
60A ALA* 3.5 8.8 - - - +
61A GLU* 1.3 79.9 - - - +
63A GLN* 1.3 74.3 + - - +
64A THR* 3.5 30.2 - - + +
76A ALA* 3.3 21.1 + - + -
77A THR* 3.6 9.4 - - - +
78A ALA* 3.6 33.3 - - + +
83A ILE* 4.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 3.1 7.0 - - + +
37A GLY 3.2 23.3 - - - +
38A SER* 3.9 1.1 - - - -
39A THR* 2.9 25.6 + - - +
60A ALA* 4.9 0.9 - - + -
62A HIS* 1.3 88.5 + - - +
64A THR* 1.3 62.3 - - - +
65A ALA 3.8 0.5 + - - -
66A GLY* 3.5 20.5 + - - -
74A TRP* 4.0 12.8 + - - +
75A ALA* 5.5 0.2 - - - -
76A ALA* 3.9 16.5 + - + +
83A ILE* 3.4 33.5 - - + +
301A BT5 3.0 40.8 + - - -
----------------------------------------------------------
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