Contacts of the strand formed by residues 53 - 66 (chain B) in PDB entry 3E5Q
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 MET 53 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 3.0 29.8 - - + -
131A LEU* 3.0 37.9 - - + -
52B SER* 1.3 70.8 - - - +
54B ILE* 1.3 59.1 + - - +
55B PHE 3.6 2.0 + - - -
83B LEU* 3.9 26.2 - - + -
84B ILE 3.8 2.5 - - - +
85B GLY 3.5 10.8 - - - +
86B LYS* 3.6 21.8 - - - -
87B LEU* 4.1 5.4 - - - +
106B TRP* 3.4 0.8 - - - -
107B PHE* 2.5 55.4 + - + +
112B LEU* 3.7 13.7 - - + -
126B ILE* 5.5 0.9 - - + -
130B TYR* 3.2 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.0 10.8 - - + -
44B ILE* 4.0 25.4 - - + -
50B ILE* 5.0 1.1 - - + -
52B SER 3.3 7.4 + - - +
53B MET* 1.3 70.5 - - - +
55B PHE* 1.3 57.7 + - - +
56B LEU* 3.5 3.4 + - + +
61B ILE* 5.1 0.7 - - + -
83B LEU* 4.7 0.4 - - - -
84B ILE* 3.1 47.8 + - + +
85B GLY* 4.5 3.6 - - - -
104B THR* 3.8 32.5 - - + -
105B CYS 4.0 3.8 - - - -
106B TRP* 3.4 49.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 4.4 13.7 - - + -
23B GLU 4.6 0.7 - - - -
25B LEU* 4.4 10.3 - - + -
26B ARG* 3.5 35.7 - - + -
29B THR* 3.7 27.6 - - + -
53B MET 3.6 3.0 + - - -
54B ILE* 1.3 69.2 - - - +
56B LEU* 1.3 63.4 + - - +
57B VAL* 3.7 22.2 + - + -
81B ASN* 3.5 36.1 - - - -
82B SER 3.7 9.0 - - - -
83B LEU* 3.6 25.5 - - + +
104B THR* 3.4 1.6 - - - -
105B CYS* 2.7 37.9 + - + -
107B PHE* 3.8 17.9 - + + -
----------------------------------------------------------
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
----------------------------------------------------------
54B ILE* 4.3 5.4 - - + +
55B PHE* 1.3 74.0 - - - +
57B VAL* 1.3 52.5 + - - +
58B GLU 3.9 2.7 - - - +
59B GLY 3.2 34.3 - - - +
61B ILE* 3.7 24.9 - - + -
78B ALA* 3.3 31.9 - - + +
79B GLY 3.2 21.8 - - - +
80B GLY* 3.6 3.1 - - - -
81B ASN* 2.5 36.8 + - - -
82B SER* 3.2 15.9 + - - +
84B ILE* 4.6 4.3 - - + -
102B THR* 3.8 12.1 - - + -
103B ARG 3.9 3.8 - - - -
104B THR* 4.2 6.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
26B ARG* 2.2 47.8 + - + +
29B THR* 4.9 6.5 - - + +
34B ILE* 5.9 2.2 - - + -
55B PHE* 3.7 19.3 - - + +
56B LEU* 1.3 72.1 - - - +
58B GLU* 1.3 62.4 + - + +
80B GLY* 4.7 5.1 - - - -
81B ASN* 4.5 3.2 - - - +
103B ARG* 2.9 46.6 + - + +
104B THR* 3.8 12.8 - - - +
105B CYS* 4.2 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG* 4.5 6.7 - - - +
56B LEU* 3.9 2.6 - - - +
57B VAL* 1.3 86.8 - - + +
59B GLY* 1.3 58.5 + - - +
80B GLY* 4.8 1.6 - - - -
101B PRO 5.5 0.4 - - - -
102B THR* 3.2 2.6 - - - +
103B ARG* 2.8 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.2 18.5 - - - +
58B GLU* 1.3 73.0 - - - +
60B LYS* 1.3 64.4 + - - +
80B GLY* 3.4 19.0 + - - -
100B GLU* 3.2 17.0 - - - -
101B PRO 4.8 1.8 - - - -
102B THR* 3.8 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 4.4 21.8 - - - -
56B LEU* 4.5 0.2 - - - -
59B GLY* 1.3 74.7 - - - +
61B ILE* 1.3 63.7 + - - +
77B TYR* 3.5 36.7 - - + +
78B ALA 3.4 7.9 - - - +
79B GLY* 4.9 1.6 - - - -
99B MET* 2.6 53.9 + - + -
100B GLU* 3.2 17.6 + - - +
102B THR* 3.5 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.9 21.5 - - + -
56B LEU* 3.7 22.2 - - + -
60B LYS* 1.3 84.1 - - - +
62B LYS* 1.3 62.5 + - - +
63B LEU* 3.7 10.5 + - + -
77B TYR* 3.4 7.7 - - - +
78B ALA* 3.1 32.8 + - + +
84B ILE* 3.5 23.1 - - + -
96B ALA* 3.7 27.4 - - + -
97B THR 3.3 9.6 - - - +
98B ALA* 4.5 7.2 - - - -
99B MET* 4.3 3.6 - - - -
102B THR* 4.3 7.0 - - + -
104B THR* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 1.3 72.1 - - - +
63B LEU* 1.4 58.0 + - - +
64B ASP* 3.0 38.2 + - - +
72B GLU* 4.7 3.6 + - - +
74B LEU* 4.7 7.2 - - + -
76B TYR 4.5 1.6 - - - -
77B TYR* 3.8 33.4 - - + +
95B TYR 3.6 1.4 - - - +
96B ALA* 2.9 23.5 - - - -
97B THR* 2.9 23.4 + - - +
99B MET* 4.0 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 6.4 0.7 - - + -
61B ILE* 3.9 17.7 - - + +
62B LYS* 1.4 68.4 - - - +
64B ASP* 1.3 62.1 + - - +
74B LEU* 4.7 0.3 - - - +
75B LEU* 2.9 29.3 + - + +
76B TYR* 3.1 60.2 + - + +
78B ALA* 3.9 14.8 - - + -
84B ILE* 4.0 21.3 - - + -
85B GLY 5.3 1.8 - - - +
94B ILE* 4.6 22.9 - - + -
95B TYR 4.6 0.2 - - - -
96B ALA* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS* 3.0 49.0 + - - +
63B LEU* 1.3 76.0 - - - +
65B ILE* 1.3 60.2 - - - +
72B GLU* 2.7 33.0 - - - +
73B LYS 3.4 16.4 - - - +
74B LEU* 3.4 14.6 - - - +
75B LEU* 4.2 1.8 - - - +
94B ILE* 3.4 8.6 - - - +
95B TYR* 2.8 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 4.0 24.9 - - + +
64B ASP* 1.3 73.5 - - - +
66B ILE* 1.3 68.6 + - - +
67B PHE* 3.6 32.5 + - + +
72B GLU* 2.4 29.5 - - - +
73B LYS* 3.3 8.8 + - + +
74B LEU 4.8 2.2 - - - +
75B LEU* 3.5 24.4 - - + +
92B ASN* 3.2 43.7 - - + +
93B ASN 3.2 18.2 - - - +
94B ILE* 3.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 3.8 7.2 - - + -
64B ASP 4.7 0.2 - - - +
65B ILE* 1.3 75.9 - - - +
67B PHE* 1.3 73.5 + - - +
68B GLU* 3.8 0.7 + - - -
70B GLY* 4.1 13.5 - - - +
71B SER 3.2 8.7 - - - +
72B GLU* 3.4 19.5 - - - +
93B ASN* 2.8 51.9 + - + +
95B TYR* 2.8 42.4 - - + +
----------------------------------------------------------
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