Contacts of the strand formed by residues 52 - 61 (chain A) in PDB entry 1PU5
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 52 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PRO 4.0 1.5 + - - +
51A LEU* 1.3 72.7 - - - +
53A VAL* 1.3 68.1 + - - +
54A ASP* 3.4 24.5 + - + +
78A THR* 3.7 12.6 - - + -
79A PHE 3.4 11.7 - - - +
80A GLU* 3.8 19.3 + - + +
144A VAL 3.5 0.9 - - - +
145A LEU* 3.4 8.0 - - - +
146A SER* 2.8 55.3 + - - +
147A SER* 5.4 0.7 - - - -
148A SER 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU 4.1 0.2 + - - -
52A LYS* 1.3 78.4 - - - +
54A ASP* 1.3 63.3 + - - +
55A LEU* 3.9 28.5 - - + -
77A CYS 3.8 0.7 - - - +
78A THR* 3.3 2.9 - - - +
79A PHE* 2.7 57.1 + - + +
82A PHE* 3.8 32.1 - - + -
143A SER* 4.1 8.7 - - - +
144A VAL 3.4 3.6 - - - +
145A LEU* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS* 3.4 18.2 + - + -
53A VAL* 1.3 72.7 - - - +
55A LEU* 1.3 66.1 + - - +
56A VAL* 5.0 8.1 - - + +
77A CYS 3.7 1.6 - - - -
78A THR* 2.9 38.2 + - - +
142A GLU 3.6 1.2 - - - +
143A SER* 3.4 2.3 - - - -
144A VAL* 2.9 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 3.9 12.6 - - + -
54A ASP* 1.3 77.9 - - - +
56A VAL* 1.3 66.5 - - - +
73A TYR 5.7 2.2 - - - +
75A GLY 4.1 13.5 - - - +
76A SER* 3.1 22.9 - - - +
77A CYS* 2.7 27.8 + - + +
78A THR* 5.2 0.3 + - - -
79A PHE* 4.2 21.5 - - + -
141A ILE* 4.2 20.6 - - + -
142A GLU 3.3 3.1 - - - +
143A SER* 3.1 37.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASP* 5.0 9.0 - - + +
55A LEU* 1.3 80.1 - - - +
57A LEU* 1.3 58.7 + - - +
58A GLU* 4.1 28.7 - - + +
67A LYS* 4.3 24.9 - - + +
76A SER* 3.6 8.1 - - - +
140A ARG 3.8 0.7 - - - +
141A ILE* 3.2 6.6 - - - -
142A GLU* 2.8 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 1.3 73.0 - - - +
58A GLU* 1.3 64.5 + - - +
67A LYS* 3.4 2.9 - - - -
68A ILE* 2.7 55.9 + - + -
74A ILE* 5.2 6.1 - - + -
75A GLY* 4.0 36.6 - - - +
76A SER* 2.9 10.1 + - - +
139A TYR* 4.5 15.5 - - + -
140A ARG 3.5 15.9 - - - +
141A ILE* 4.2 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 4.1 21.8 - - + +
57A LEU* 1.3 79.2 - - - +
59A LYS* 1.3 60.2 + - - +
65A TRP* 3.9 17.9 - - + +
66A ILE 3.1 10.5 - - - +
67A LYS* 3.8 17.2 + - + +
68A ILE* 4.5 2.2 - - - +
139A TYR* 3.2 10.7 - - - +
140A ARG* 2.9 82.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 1.3 74.3 - - - +
60A GLU* 1.3 72.6 + - - +
61A VAL* 3.5 18.8 + - + +
64A LEU 3.4 0.7 - - - +
65A TRP* 3.8 2.9 - - - -
66A ILE* 2.9 36.7 + - + +
68A ILE* 3.8 14.8 - - + +
134A LEU* 3.2 27.5 + - - +
136A THR 3.2 18.4 + - - -
137A GLY* 4.3 4.0 - - - -
138A ASN 3.7 4.9 - - - +
139A TYR* 3.2 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HIS 4.9 3.5 + - - +
59A LYS* 1.3 80.8 + - - +
61A VAL* 1.3 65.7 + - - +
62A ALA 5.1 0.4 - - - +
63A GLY* 4.3 24.8 - - - +
64A LEU 3.2 7.6 - - - +
65A TRP* 3.5 40.1 + - + -
137A GLY* 5.6 0.9 - - - -
138A ASN* 3.0 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LYS* 3.9 29.4 - - + +
60A GLU* 1.3 80.5 - - - +
62A ALA* 1.3 69.1 + - + +
63A GLY 3.2 0.4 - - - -
64A LEU* 2.5 48.4 + - + +
66A ILE* 4.2 19.5 - - + -
----------------------------------------------------------
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