Contacts of the strand formed by residues 59 - 70 (chain A) in PDB entry 1XWD
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 CYS 59 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A CYS* 3.6 5.8 - - - -
58A THR* 1.3 71.3 - - - -
60A CYS* 1.3 63.6 + - - +
61A VAL* 3.2 6.8 + - + +
84A CYS* 3.1 2.1 - - - -
85A SER* 2.4 51.3 + - - +
86A THR 4.2 1.8 - - - +
87A CYS* 2.0 47.8 - - - -
90A HIS* 5.3 0.2 - - - -
34B THR* 4.2 11.9 - - - +
48B GLN* 3.4 40.2 - - + +
49B LYS 5.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A CYS* 2.1 50.0 - - + -
28A CYS* 3.9 4.7 - - - -
29A MET* 3.6 32.5 - - - -
30A GLY 4.2 2.5 - - - +
32A CYS* 3.4 8.3 - - - -
59A CYS* 1.3 73.3 - - - +
61A VAL* 1.3 64.7 + - - +
83A HIS 3.7 0.4 - - - -
34B THR* 3.3 28.2 + - - +
35B ARG 4.0 8.7 - - - +
36B ASP* 3.7 11.3 - - - +
48B GLN* 5.4 0.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
28A CYS* 3.7 6.6 - - - -
59A CYS* 3.2 9.8 + - + +
60A CYS* 1.3 80.4 - - - +
62A ALA* 1.3 64.7 + - - +
63A LYS 3.5 0.3 + - - -
82A CYS* 3.4 2.9 - - - +
83A HIS* 3.0 56.6 + - + +
85A SER* 4.1 12.8 - - - -
86A THR 4.5 8.3 - - - +
35B ARG 5.8 0.2 - - - +
36B ASP* 3.7 19.7 - - + +
48B GLN* 4.2 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A CYS* 3.6 3.7 - - - -
61A VAL* 1.3 79.0 - - - +
63A LYS* 1.3 64.6 + - - +
64A SER* 3.5 5.9 + - - +
65A TYR* 4.8 12.9 - - + -
79A HIS* 3.5 36.3 - - + +
81A ALA 3.3 8.1 - - - +
83A HIS* 4.8 0.2 + - - -
36B ASP* 3.0 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL 3.5 3.2 + - - -
62A ALA* 1.3 72.8 - - - +
64A SER* 1.3 59.6 + - - +
81A ALA* 2.5 32.9 + - + +
82A CYS 4.3 4.7 - - - +
83A HIS* 3.1 51.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 3.3 1.6 - - - +
63A LYS* 1.3 83.2 - - - +
65A TYR* 1.3 66.5 + - - +
79A HIS* 3.8 1.9 - - - +
80A THR* 2.8 36.9 + - - -
81A ALA* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 4.8 14.1 - - + -
63A LYS 5.6 0.2 - - - -
64A SER* 1.3 81.8 - - - +
66A ASN* 1.3 71.2 + - - +
67A ARG* 2.9 52.3 + - + +
77A GLU* 3.0 38.7 + - + -
78A ASN 3.5 10.1 - - - +
79A HIS* 3.9 17.3 - + + -
80A THR* 3.5 6.0 + - - -
123C GLN* 4.8 13.8 + - - -
145C GLN* 5.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 1.3 80.5 - - - +
67A ARG* 1.3 60.1 + - - +
68A VAL* 3.5 12.3 + - + -
77A GLU 3.4 0.5 - - - -
78A ASN* 2.5 53.4 + - + +
80A THR* 3.7 26.7 + - - +
94A NAG 5.5 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 2.9 45.4 + - + +
66A ASN* 1.3 72.0 - - - +
68A VAL* 1.3 60.5 + - - +
69A THR* 5.3 0.2 + - - -
75A LYS* 4.4 29.3 - - + +
76A VAL 3.4 11.0 - - - +
77A GLU* 4.4 4.7 - - + +
123C GLN* 5.9 0.2 - - - +
145C GLN* 4.6 15.6 + - - +
171C GLU* 5.8 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 4.2 12.3 - - + -
66A ASN* 3.5 17.1 + - + -
67A ARG* 1.3 76.9 - - - +
69A THR* 1.3 66.9 - - - +
70A VAL* 4.9 0.7 - - + -
75A LYS* 3.9 1.1 - - - -
76A VAL* 2.9 40.3 + - + +
78A ASN* 4.2 12.1 - - + +
94A NAG 3.7 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG 5.3 0.2 + - - -
68A VAL* 1.3 79.3 - - - +
70A VAL* 1.3 74.1 + - - +
73A GLY* 4.4 11.2 - - - +
74A PHE 3.4 18.6 - - - +
75A LYS* 4.0 18.7 + - - +
94A NAG 5.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.9 40.8 - - + +
20A GLN* 4.6 10.5 - - - +
23A ALA 5.9 1.1 - - - +
25A ILE* 4.3 18.2 - - + -
68A VAL* 4.9 0.7 - - + -
69A THR* 1.3 82.1 - - - +
71A MET* 1.3 70.4 + - + +
72A GLY 3.2 2.4 + - - -
73A GLY* 3.2 12.3 + - - -
74A PHE* 3.3 21.7 + - + +
76A VAL* 3.8 19.5 - - + -
94A NAG 4.8 8.5 - - + -
----------------------------------------------------------
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