Contacts of the strand formed by residues 48 - 65 (chain B) in PDB entry 5DPQ
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 ASN 48 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE 3.7 3.1 - - - +
65A THR* 2.7 34.5 + - - +
43B ASP 3.9 0.9 - - - +
44B GLN* 3.4 4.7 - - - +
45B ASP* 2.9 54.4 + - + +
47B ASP* 1.3 80.3 - - - +
49B PHE* 1.3 59.5 + - - +
50B LYS* 4.6 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP* 3.3 3.9 - - - +
64A PHE* 2.8 73.4 + + + +
66A VAL* 3.7 20.6 - - + -
88A TRP* 4.0 10.8 - + - -
93A LEU* 3.6 24.7 - - + -
108A GLN* 5.2 1.6 - - - -
4B GLN* 4.1 9.4 - - + -
42B ILE* 4.0 22.0 - - + -
43B ASP 3.8 1.6 - - - -
44B GLN* 3.3 44.9 - - + -
46B GLY 4.2 1.6 - - - -
47B ASP 3.7 7.6 - - - -
48B ASN* 1.3 78.5 - - - +
50B LYS* 1.3 65.9 + - - +
51B THR* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP* 3.2 28.7 - - + +
41B VAL 3.8 1.7 - - - +
42B ILE* 3.8 0.5 - - - -
43B ASP* 2.9 59.7 + - + +
45B ASP* 5.6 5.7 - - - +
48B ASN* 4.6 19.6 + - - +
49B PHE* 1.3 75.9 - - - +
51B THR* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 3.4 8.5 - - - +
62A VAL* 2.8 60.0 + - - +
63A ASP* 3.5 0.4 + - - -
64A PHE* 4.4 9.4 - - + -
108A GLN* 5.7 0.7 - - - +
201A ACT 3.8 25.9 - - + +
40B LYS* 5.1 5.4 - - - -
41B VAL 3.4 6.3 - - - -
42B ILE* 4.2 19.5 - - + -
49B PHE* 4.6 10.5 - - + -
50B LYS* 1.3 79.3 - - - +
52B LYS* 1.3 62.3 + - - +
53B THR* 4.2 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 3.2 49.2 - - - +
61A ASP* 3.8 10.5 - - - +
39B THR 3.7 1.6 - - - +
40B LYS* 3.6 0.7 - - - -
41B VAL* 2.9 60.6 + - + +
51B THR* 1.3 74.2 - - - +
53B THR* 1.3 59.7 + - - +
54B THR* 4.1 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 3.8 1.7 - - - -
59A ASN* 2.9 59.6 + - - +
60A TYR 5.4 2.6 + - - -
62A VAL* 6.1 1.4 - - - +
201A ACT 5.6 0.3 - - - -
38B GLN* 3.4 31.6 - - + +
39B THR 3.4 10.1 - - - +
40B LYS* 3.3 29.0 + - + +
51B THR* 4.2 5.5 + - - -
52B LYS* 1.3 76.5 + - - +
54B THR* 1.3 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 4.4 10.3 - - + +
57A PHE 4.0 12.6 - - - +
58A ARG* 3.9 18.2 + - + +
37B THR 3.8 0.3 - - - +
38B GLN* 3.3 4.8 - - - -
39B THR* 2.8 44.0 + - - -
52B LYS* 4.1 5.6 + - - +
53B THR* 1.3 76.8 + - - +
55B SER* 1.3 70.1 + - - +
56B THR* 4.1 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 3.4 3.1 - - - -
57A PHE* 3.0 60.6 + - - +
59A ASN* 3.5 22.1 + - - -
36B LEU* 3.9 17.2 - - - +
37B THR 3.4 7.2 - - - -
38B GLN* 3.6 16.9 + - - +
53B THR 4.4 0.4 + - - -
54B THR* 1.3 72.1 - - - +
56B THR* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 3.4 21.8 - - + -
55A SER 3.4 3.1 - - - -
56A THR* 3.1 17.9 - - + +
35B ARG 4.3 0.7 - - - +
36B LEU* 3.5 7.0 - - - +
37B THR* 2.8 49.0 + - + +
54B THR* 4.1 9.2 + - - +
55B SER* 1.3 76.1 + - - +
57B PHE* 1.3 75.3 + - - +
58B ARG* 4.1 1.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 4.3 9.9 - - + -
36A LEU* 3.7 40.6 - - + -
54A THR* 3.1 24.8 - - - +
55A SER* 2.7 24.2 + - - +
57A PHE* 4.5 2.5 - + - -
32B ILE* 3.4 46.0 - - + -
35B ARG* 4.2 22.9 - - + -
36B LEU* 3.5 32.1 - - + -
56B THR* 1.3 75.5 - - - +
58B ARG* 1.3 59.1 + - - +
59B ASN* 3.2 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS* 3.1 42.5 - - - +
53A THR 4.3 0.2 - - - -
54A THR* 3.5 16.9 + - - +
35B ARG 4.9 4.9 + - - -
37B THR* 6.1 0.8 - - + +
56B THR* 4.1 2.5 + - + -
57B PHE* 1.3 72.5 - - - +
59B ASN* 1.3 80.8 + - - +
61B ASP* 3.6 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 5.4 1.2 - - - +
53A THR* 2.9 32.9 + - - +
54A THR 4.0 1.0 - - - -
55A SER* 2.7 37.5 + - - +
57B PHE* 3.2 21.2 + - - +
58B ARG* 1.3 96.7 + - - +
60B TYR* 1.3 76.4 + - + +
61B ASP 3.4 2.0 + - - -
76B SER* 4.3 15.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 4.1 0.9 + - - +
53A THR* 3.3 26.8 + - - -
202A ACT 5.6 1.1 - - - -
59B ASN* 1.3 83.1 - - + +
61B ASP* 1.3 65.3 + - - +
62B VAL* 3.3 32.5 + - + +
72B ALA* 4.6 9.6 - - + +
73B TYR 3.2 28.0 + - - -
74B THR* 3.5 18.2 - - - +
75B LYS* 3.6 18.4 - - + -
76B SER* 3.7 28.6 - - - -
82B VAL* 5.9 0.2 - - - +
97B GLN* 5.4 1.2 + - - -
201B ACT 3.3 32.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR 3.4 4.5 - - - +
52A LYS* 3.2 40.0 - - - +
58B ARG* 3.6 16.1 + - - -
59B ASN 3.4 1.4 + - - -
60B TYR* 1.3 76.3 - - - +
62B VAL* 1.3 65.9 + - - +
63B ASP* 4.3 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE 4.3 0.2 - - - +
50A LYS 3.8 0.2 - - - -
51A THR* 2.7 51.4 + - - +
202A ACT 4.7 8.7 - - + +
60B TYR* 3.3 47.4 + - + +
61B ASP* 1.3 75.0 - - - +
63B ASP* 1.3 66.1 + - - +
64B PHE* 3.8 24.3 - - + -
70B PHE* 4.8 13.0 - - + -
72B ALA* 6.2 2.7 - - + -
106B TRP* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE 3.2 8.7 - - - +
50A LYS* 3.3 31.6 - - + +
51A THR 3.4 4.2 + - - +
61B ASP* 4.6 8.4 - - - +
62B VAL* 1.3 88.7 + - - +
64B PHE* 1.3 65.9 + - - +
70B PHE* 4.6 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 3.8 0.3 - - - +
49A PHE* 2.8 77.4 + + + +
51A THR* 4.5 3.6 - - + -
202A ACT 4.1 23.8 - - + -
62B VAL* 3.8 16.2 - - + -
63B ASP* 1.3 79.4 - - - +
65B THR* 1.3 68.2 + - - +
66B VAL* 4.5 0.7 - - + -
70B PHE* 3.5 33.0 - + + -
86B VAL* 3.8 29.6 - - + -
93B LEU* 4.0 12.6 - - + -
106B TRP* 4.0 13.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 3.3 11.7 - - + +
48A ASN* 3.0 26.6 + - - +
64B PHE* 1.3 80.2 + - - +
66B VAL* 1.3 78.9 + - - +
67B GLY 3.3 0.3 + - - -
68B VAL* 3.1 42.9 + - + +
70B PHE* 5.5 0.5 - - - -
86B VAL* 4.7 1.9 + - - +
----------------------------------------------------------
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