Contacts of the strand formed by residues 50 - 63 (chain B) 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 THR 50 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 3.4 7.8 - - - -
55A SER* 4.1 14.6 - - - +
56A GLU 4.4 0.3 + - - -
57A SER* 2.6 36.5 - - - +
87A CYS* 5.8 0.9 - - - -
90A HIS* 4.5 10.3 - - + +
32B CYS* 3.8 5.6 - - - -
49B LYS* 1.3 75.8 - - - +
51B CYS* 1.3 74.5 + - - +
52B THR* 3.5 13.8 + - + +
83B HIS 3.4 0.2 - - - +
84B CYS* 3.2 1.9 - - - -
85B GLY 2.6 36.7 + - - +
87B CYS* 4.2 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 3.0 32.6 + - - +
35A ARG 4.1 16.1 + - - +
36A ALA* 4.4 0.5 - - - +
55A SER* 4.7 1.0 + - - -
3B CYS* 2.1 49.1 - - + -
28B CYS* 3.9 6.5 - - - -
29B ALA 3.6 31.6 - - - -
30B GLY 4.4 1.3 - - - +
32B CYS* 3.6 7.6 - - - -
50B THR* 1.3 78.3 + - - +
52B THR* 1.3 63.3 + - - +
83B HIS 3.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 4.1 11.6 - - - +
55A SER* 5.2 2.5 - - - -
28B CYS* 3.4 13.9 - - - -
50B THR* 3.8 21.5 - - + +
51B CYS* 1.3 81.1 - - - +
53B PHE* 1.3 92.5 + - - +
82B CYS* 3.3 2.1 - - - -
83B HIS* 2.9 38.6 + - + +
85B GLY 4.6 0.9 - - - +
86B LYS 4.0 19.3 - - - +
87B CYS* 4.3 8.8 - - - +
88B ASP 5.4 0.8 + - - +
92B THR* 4.8 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 4.7 0.6 - - - +
53A VAL* 4.3 10.1 - - + -
27B TRP* 4.0 26.7 - + + -
28B CYS* 3.5 8.7 - - - -
52B THR* 1.3 92.7 + - - +
54B LYS* 1.3 62.5 + - - +
55B GLU* 4.0 15.0 - - - +
56B LEU* 3.6 43.1 - - + -
79B ALA* 4.5 4.0 - - + -
81B GLN 3.4 9.4 - - - +
83B HIS* 3.1 13.6 - - - -
88B ASP* 5.1 9.2 - - + -
91B SER* 3.6 21.5 - - - -
92B THR* 3.5 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 1.3 78.6 - - - +
55B GLU* 1.3 81.7 + - + +
81B GLN* 2.6 45.3 + - + +
82B CYS 4.4 1.1 - - - +
83B HIS* 3.7 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 4.0 5.9 - - - +
54B LYS* 1.3 96.6 - - + +
56B LEU* 1.3 58.6 + - - +
57B VAL* 6.5 0.2 - - + -
79B ALA* 3.9 1.4 - - - -
80B THR* 2.8 41.0 + - + -
81B GLN* 3.3 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 3.8 26.9 - - + -
27B TRP* 3.9 8.7 - - + -
53B PHE* 3.6 33.2 - - + -
55B GLU* 1.3 78.5 + - - +
57B VAL* 1.3 70.1 + - - +
58B TYR* 4.5 19.0 - - + +
77B PRO* 4.0 13.5 - - + -
78B VAL 3.3 16.2 - - - +
79B ALA* 4.2 2.7 - - - -
80B THR* 3.9 1.6 - - - -
91B SER* 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 1.3 79.3 - - - +
58B TYR* 1.3 69.8 + - - +
59B GLU* 4.2 20.9 - - + +
77B PRO* 3.6 2.8 - - - +
78B VAL* 2.8 44.6 + - + +
80B THR* 3.4 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASN* 2.8 41.7 + - - +
53A VAL* 5.5 0.7 - - - +
93A NAG 3.2 29.2 + - - +
56B LEU* 4.5 23.2 - - + +
57B VAL* 1.3 83.3 - - - +
59B GLU* 1.3 68.3 + - - +
75B THR* 4.3 21.5 - - + -
76B TYR* 3.4 22.9 - - - -
77B PRO* 4.2 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 5.0 0.3 + - - -
57B VAL* 4.2 12.4 - - + +
58B TYR* 1.3 80.2 - - - +
60B THR* 1.3 66.0 + - - +
75B THR* 3.5 3.0 - - - -
76B TYR* 3.1 55.6 + - + +
78B VAL* 3.4 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 1.3 76.4 - - - +
61B VAL* 1.3 75.8 + - - +
73B LEU* 3.9 32.8 - - + -
74B TYR 3.3 13.2 - - - +
75B THR* 3.4 20.8 - - + +
76B TYR* 4.3 3.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 3.7 13.5 - - + -
21B ILE* 4.9 3.1 - - + -
23B ILE* 3.4 38.1 - - + -
60B THR* 1.3 81.7 - - - +
62B ARG* 1.3 72.0 + - - +
63B VAL* 3.6 6.3 - - + +
73B LEU* 3.4 4.9 - - - -
74B TYR* 3.0 41.6 + - + +
76B TYR* 4.1 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 4.0 8.3 - - - +
61B VAL* 1.3 85.6 - - - +
63B VAL* 1.3 62.1 + - - +
64B PRO* 4.1 2.4 - - - +
71B ASP* 4.5 27.1 + - + +
72B SER* 3.5 10.3 + - - +
73B LEU* 3.6 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.3 13.0 - - + +
14B LYS* 3.8 18.6 + - + -
19B PHE* 5.2 1.3 - - + -
21B ILE* 4.0 18.8 - - + -
61B VAL* 3.6 15.0 - - + +
62B ARG* 1.3 77.2 - - - +
64B PRO* 1.3 81.7 - - + +
71B ASP* 3.2 5.6 - - - +
72B SER* 2.8 50.5 + - - +
73B LEU 4.1 0.2 - - - -
74B TYR* 3.8 23.3 - - + +
----------------------------------------------------------
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