Contacts of the strand formed by residues 51 - 60 (chain A) in PDB entry 1CXZ
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 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.6 17.9 - - + -
46A ILE 3.9 0.2 - - - +
47A GLU* 3.2 6.2 - - - +
48A VAL 2.9 29.8 + - - +
49A ASP* 3.6 29.0 + - - +
50A GLY* 1.3 78.8 - - - +
52A GLN* 1.3 60.8 + - - +
53A VAL* 3.7 4.1 + - + +
179A LEU* 3.9 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.9 5.5 - - - +
2A ALA 5.5 0.2 - - - -
3A ALA* 3.4 27.1 - - + +
4A ILE* 3.1 27.0 + - - +
45A ASP* 4.9 1.6 + - - -
46A ILE 3.7 2.9 - - - -
47A GLU* 4.2 7.5 - - + +
50A GLY 4.1 2.2 + - - -
51A LYS* 1.3 71.0 - - - +
53A VAL* 1.3 66.1 + - - +
43B ARG 5.1 2.5 + - - +
46B ILE* 4.2 19.0 - - - +
47B ARG* 2.8 59.4 + - + +
50B LEU* 3.7 31.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
3A ALA* 4.1 4.3 - - - -
4A ILE* 3.3 15.7 - - + +
6A LYS* 4.2 13.5 - - + -
45A ASP* 3.8 2.6 - - - +
46A ILE* 2.7 47.6 + - + +
48A VAL* 4.9 1.1 - - + -
51A LYS* 3.9 11.0 - - + +
52A GLN* 1.3 80.5 - - - +
54A GLU* 1.3 70.4 + - - +
55A LEU* 3.7 14.8 + - + -
175A THR* 3.8 26.5 - - + -
179A LEU* 3.8 22.7 - - + -
50B LEU* 4.7 1.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
3A ALA* 3.7 17.2 - - + +
4A ILE 2.8 11.3 + - - +
5A ARG* 3.2 47.4 + - + +
6A LYS 3.4 21.8 + - - +
43A VAL* 4.7 17.3 - - + +
44A ALA 3.7 9.4 - - - +
45A ASP* 4.2 4.5 - - - +
53A VAL* 1.3 72.3 - - - +
55A LEU* 1.3 61.3 + - - +
56A ALA* 3.7 1.0 + - - +
46B ILE* 5.7 0.2 - - - +
88B HIS* 3.1 35.6 + - + +
91B LEU* 5.7 3.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
6A LYS* 3.5 27.6 - - + +
8A LEU* 4.3 21.8 - - + -
25A PHE* 4.6 6.3 - - + -
43A VAL* 3.5 4.3 - - - +
44A ALA* 2.9 48.8 + - + +
46A ILE* 4.4 10.3 - - + -
53A VAL* 3.7 12.8 + - + -
54A GLU* 1.3 71.8 - - - +
56A ALA* 1.3 63.3 + - - +
57A LEU* 3.6 19.9 + - + -
79A VAL* 5.3 1.3 - - + -
171A PHE* 4.3 13.2 - - + +
175A THR* 3.6 31.0 - - + +
178A ALA* 5.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 6.0 3.8 - - - +
6A LYS 2.9 14.7 + - - +
7A LYS* 3.9 19.7 - - + +
8A LEU* 2.7 35.9 + - - +
42A TYR 3.7 5.2 - - - +
43A VAL* 4.8 7.4 - - + +
54A GLU 3.7 1.8 + - - +
55A LEU* 1.3 71.9 - - - +
57A LEU* 1.3 58.3 + - - +
58A TRP* 3.8 10.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
8A LEU* 3.7 20.6 - - + -
22A LEU* 4.0 26.7 - - + +
25A PHE* 4.4 4.0 - - + -
26A SER* 3.8 31.4 - - - +
41A ASN* 3.1 5.4 - - - -
42A TYR* 2.7 50.5 + - + +
44A ALA* 3.8 9.9 - - + +
55A LEU* 4.1 26.7 - - + +
56A ALA* 1.3 76.7 - - - +
58A TRP* 1.3 64.2 + - - +
59A ASP 3.5 1.0 + - - -
171A PHE* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 3.4 53.7 - - + +
8A LEU* 2.7 16.1 + - - +
9A VAL* 3.6 11.6 - - + +
10A ILE* 3.2 28.0 + - - +
22A LEU* 4.5 0.2 - - - -
39A PHE* 3.8 28.7 - + + -
40A GLU 3.8 2.5 - - - -
41A ASN* 3.8 19.2 - - + +
56A ALA* 4.1 8.6 - - + +
57A LEU* 1.3 80.1 - - - +
59A ASP* 1.3 62.5 - - - +
60A THR* 3.7 1.1 + - - -
72A LEU 4.6 4.3 - - - -
73A SER* 3.5 24.9 - - - -
75A PRO* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.6 15.5 - - - +
18A LYS* 4.2 6.4 - - - +
19A THR* 2.5 32.4 + - - -
22A LEU* 3.7 17.9 - - + -
37A THR* 3.6 10.9 + - - +
39A PHE* 3.3 12.8 - - - -
40A GLU* 2.7 38.6 + - + +
42A TYR* 3.3 22.0 + - + +
57A LEU 3.5 1.6 + - - -
58A TRP* 1.3 70.9 - - - +
60A THR* 1.3 70.3 + - - +
501A MG 4.0 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.0 14.6 - - + -
10A ILE 2.6 27.4 + - - +
11A VAL* 3.7 13.2 - - - +
18A LYS* 3.5 15.8 - - - -
37A THR* 4.0 9.2 - - - +
38A VAL 4.2 5.4 - - - -
39A PHE* 4.6 5.2 - - + -
58A TRP 4.3 2.0 - - - +
59A ASP* 1.3 85.6 + - - +
61A ALA* 1.3 63.1 + - - +
70A ARG* 3.7 22.5 - - + -
73A SER* 3.4 30.5 - - - +
500A GSP 4.3 0.3 + - - -
----------------------------------------------------------
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