Contacts of the strand formed by residues 75 - 81 (chain A) in PDB entry 4APC
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 SER 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 3.0 28.6 + - - +
35A ILE 3.4 10.8 + - - -
36A ASN* 4.0 10.2 + - - +
37A ILE* 3.8 6.4 - - - +
71A GLU* 3.3 6.8 - - - +
72A GLU 3.0 27.5 + - - +
73A ASN 3.2 3.5 + - - -
74A GLY* 1.3 81.9 + - - +
76A LEU* 1.3 60.0 + - - +
77A TYR* 3.6 25.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS 3.7 1.3 - - - +
34A GLU* 3.5 3.8 - - - +
35A ILE* 2.8 56.2 + - + +
37A ILE* 4.3 13.8 - - + +
48A SER* 3.9 15.9 - - - +
52A VAL* 3.5 32.8 - - + -
69A SER* 4.4 14.6 - - - +
70A PHE 3.7 3.6 - - - +
71A GLU* 3.5 30.3 - - + +
75A SER* 1.3 74.9 - - - +
77A TYR* 1.3 70.3 + - - +
78A ILE* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 5.0 14.4 + - - -
19A ILE* 5.4 3.4 - - + -
32A ILE* 3.7 17.7 - - + -
33A LYS 3.4 2.5 - - - -
34A GLU* 3.4 44.5 + - + -
69A SER* 3.1 7.3 - - - -
70A PHE* 2.8 79.7 + + + +
72A GLU* 3.8 29.3 + - + +
73A ASN* 5.0 7.3 + - - +
75A SER* 3.6 24.6 - - - -
76A LEU* 1.3 76.0 - - - +
78A ILE* 1.3 60.7 + - - +
79A VAL 4.1 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL 3.5 1.9 - - - +
32A ILE* 3.2 5.3 - - - -
33A LYS* 3.0 35.6 + - + +
35A ILE* 3.6 26.9 - - + -
52A VAL* 4.3 17.3 - - + -
55A LEU* 3.8 26.9 - - + -
66A TYR* 3.8 28.7 - - + -
68A GLU 3.8 2.7 - - - -
69A SER* 4.4 8.7 - - - -
76A LEU* 4.4 6.7 - - + -
77A TYR* 1.3 75.9 - - - +
79A VAL* 1.3 61.9 + - - +
80A MET* 3.8 19.0 + - + +
147A PHE* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.8 25.8 - - + +
30A TYR* 3.9 21.5 - - + -
31A VAL 3.5 2.5 - - - -
32A ILE* 3.9 14.4 - - + -
66A TYR* 3.8 1.7 - - - -
67A ARG* 2.8 40.4 + - + -
68A GLU* 2.7 36.3 + - + +
70A PHE* 3.8 30.3 - - + -
78A ILE* 1.3 75.4 - - - +
80A MET* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 3.3 9.5 - - - +
31A VAL* 2.8 40.7 + - + +
33A LYS* 4.9 11.9 - - + -
55A LEU* 5.6 2.2 - - - -
64A VAL* 3.3 25.6 - - + +
65A GLN 3.6 3.1 - - - -
66A TYR* 3.7 22.7 - - - +
67A ARG* 5.0 0.4 - - - -
78A ILE* 4.0 22.9 - - + +
79A VAL* 1.3 77.6 - - - +
81A ASP* 1.3 69.1 + - - +
146A ASP* 3.2 34.1 - - + +
147A PHE* 5.5 2.9 - - + -
1285A CL 3.4 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 3.5 25.3 - - - -
31A VAL* 4.2 5.8 - - - +
64A VAL* 3.5 18.4 - - + +
65A GLN* 2.9 57.8 + - + +
67A ARG* 4.4 9.4 + - - +
80A MET* 1.3 80.2 - - - +
82A TYR* 1.3 62.7 + - - +
83A CYS* 3.9 3.6 + - - -
143A GLN* 5.9 1.1 - - - +
----------------------------------------------------------
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