Contacts of the helix formed by residues 51 - 68 (chain B) in PDB entry 4WNB
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 51 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE 5.8 0.4 + - - -
23B THR* 5.7 0.4 + - - -
24B ALA* 4.1 9.7 - - + +
27B THR* 2.9 24.4 + - - -
29B ASP* 2.8 25.0 + - - +
34B HIS* 3.3 36.0 + - + +
49B PHE* 3.6 1.8 + - - -
50B VAL* 1.3 80.3 - - - +
52B ILE* 1.3 64.6 + - - +
53B LEU* 3.8 12.2 - - - +
54B THR* 2.5 32.6 + - - -
55B ASP* 3.2 17.8 + - - -
201B CD 4.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 3.8 17.3 - - + -
107A CYS* 4.4 20.4 - - + -
162A TRP* 5.9 3.6 - - + -
203A 4BN 3.9 31.0 - - + -
29B ASP* 5.1 0.4 + - - -
50B VAL 5.7 0.4 - - - +
51B ASN* 1.3 76.2 - - - +
53B LEU* 1.3 59.4 + - + +
55B ASP* 3.1 12.1 + - - +
56B THR* 3.0 30.6 + - - +
78B LEU* 4.3 16.4 - - + -
80B LEU* 3.7 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TRP* 5.0 1.7 + - - -
67A ALA 4.1 18.8 - - - +
70A GLN* 3.4 52.7 - - + +
71A VAL* 4.1 8.1 - - + +
74A MET* 4.1 14.6 - - + -
109A GLN* 4.5 5.8 - - - +
27B THR* 3.7 45.6 - - + +
29B ASP* 5.5 0.7 - - + +
51B ASN* 3.3 8.9 - - - +
52B ILE* 1.3 79.5 - - + +
54B THR* 1.3 58.1 + - - +
56B THR* 3.4 10.9 + - - +
57B GLY* 3.0 22.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
41A ILE* 3.9 15.0 - - + +
19B PHE* 4.2 3.1 - - + -
23B THR* 3.2 45.6 + - + +
27B THR* 4.0 2.5 - - - +
50B VAL* 3.7 19.7 - - + -
51B ASN* 2.5 28.0 + - - -
53B LEU* 1.3 76.3 - - - +
55B ASP* 1.3 64.7 + - - +
57B GLY* 3.1 0.9 + - - -
58B LEU* 2.8 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 4.1 10.3 - - - +
51B ASN 3.2 16.1 + - - +
52B ILE* 3.1 16.8 + - - +
54B THR* 1.3 76.6 - - - +
56B THR* 1.3 63.0 + - - +
58B LEU* 3.3 6.2 + - - +
59B VAL* 3.0 30.2 + - - +
78B LEU* 3.9 13.7 - - + -
80B LEU* 4.4 12.8 - - - +
84B TRP* 4.4 4.0 - - - -
92B PHE* 5.6 2.5 - - - -
117B HIS* 2.6 42.0 + - - +
118B VAL* 4.6 13.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
67A ALA* 3.8 16.4 - - + +
107A CYS* 4.9 6.4 - - - -
109A GLN* 3.7 26.0 - - + +
111A TYR* 3.8 6.7 - - - +
52B ILE* 3.0 17.4 + - - +
53B LEU* 3.6 15.9 - - + +
54B THR 3.2 0.2 - - - -
55B ASP* 1.3 75.7 - - - +
57B GLY* 1.3 62.2 + - - +
59B VAL* 3.7 5.0 - - - +
60B GLN* 3.0 23.9 + - - +
76B ILE* 3.8 16.9 - - + +
78B LEU* 3.4 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TRP* 3.6 32.8 - - - -
41A ILE* 3.9 11.3 - - - +
67A ALA* 3.9 5.1 - - - +
53B LEU 3.0 12.3 + - - -
54B THR 3.1 3.1 + - - -
56B THR* 1.3 78.3 - - - +
58B LEU* 1.3 55.6 + - - +
60B GLN* 3.5 2.9 - - - +
61B ARG* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 3.6 32.3 - - + +
11B LEU* 5.5 2.2 - - + +
13B LEU* 3.6 26.2 - - + -
19B PHE* 3.9 10.3 - - + -
54B THR* 2.8 36.5 + - + +
55B ASP* 3.9 5.4 - - - +
57B GLY* 1.3 74.3 - - - +
59B VAL* 1.3 60.4 + - - +
61B ARG* 3.3 8.6 + - - +
62B TYR* 2.8 32.1 + - - +
84B TRP* 3.6 31.4 - - + -
92B PHE* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP 3.0 21.7 + - - +
56B THR 3.7 4.3 - - - +
58B LEU* 1.3 76.0 - - - +
60B GLN* 1.3 63.7 + - - +
62B TYR* 3.3 6.0 + - - +
63B VAL* 3.1 25.3 + - - +
76B ILE* 4.0 11.2 - - + -
78B LEU* 4.0 8.7 - - + -
92B PHE* 4.2 19.3 - - + -
108B VAL* 4.5 9.9 - - + -
118B VAL* 4.9 6.5 - - + -
120B ALA* 3.8 26.5 - - + -
122B VAL* 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TRP* 3.7 14.3 - - - -
43A ASP* 4.0 7.2 + - - +
48A TYR* 3.4 24.6 + - - +
65A PRO* 3.5 20.0 - - - +
66A PRO* 3.4 14.3 - - - +
67A ALA* 2.8 31.1 + - + +
56B THR 3.0 17.5 + - - +
57B GLY 3.5 3.6 - - - +
59B VAL* 1.3 79.5 - - - +
61B ARG* 1.3 62.1 + - - +
63B VAL* 3.4 3.4 + - - +
64B THR* 3.0 31.8 + - + +
73B ILE* 4.3 18.3 - - + +
76B ILE* 3.6 16.0 - - + +
122B VAL* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 2.9 25.8 + - + -
42A GLY* 3.2 26.9 + - - -
43A ASP* 3.6 36.7 + - + +
44A ARG* 5.0 9.1 - - - +
11B LEU* 3.9 31.1 - - - +
13B LEU* 3.9 19.6 - - - +
19B PHE* 5.8 1.0 - - - -
57B GLY 2.9 18.0 + - - +
58B LEU* 3.3 13.5 + - - +
60B GLN* 1.3 76.0 - - - +
62B TYR* 1.3 54.5 + - - +
64B THR* 3.2 2.3 + - - -
65B ASP* 2.7 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.6 30.4 + - + +
9B PRO* 2.9 31.8 + - + -
11B LEU* 3.6 30.7 - - + -
58B LEU 2.8 21.1 + - - +
59B VAL* 3.6 7.0 - - - +
61B ARG* 1.3 75.7 - - - +
63B VAL* 1.3 61.1 + - - +
65B ASP* 3.6 10.3 - - + +
66B TRP* 3.6 17.5 + - - +
92B PHE* 3.3 33.2 + - + -
93B SER* 3.4 6.3 - - - -
94B GLY* 3.0 30.0 + - - -
108B VAL* 3.9 23.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
8B LEU* 4.4 10.8 - - + -
59B VAL 3.1 17.4 + - - +
60B GLN* 4.0 3.4 - - - +
62B TYR* 1.3 76.1 - - + +
64B THR* 1.3 62.0 + - - +
66B TRP* 3.3 14.9 + - + -
67B ALA* 2.8 25.5 + - - +
73B ILE* 4.6 6.5 - - + -
106B VAL* 4.6 6.1 - - + -
108B VAL* 4.0 24.9 - - + -
122B VAL* 4.0 24.2 - - + -
124B LEU* 4.1 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASP* 4.1 9.0 + - - -
45A ASN* 3.8 27.8 + - - +
48A TYR* 4.8 2.7 - - - +
114A TYR* 5.8 0.4 - - - +
60B GLN* 3.0 22.9 + - + +
61B ARG* 3.2 9.4 + - - -
63B VAL* 1.3 72.9 - - - +
65B ASP* 1.3 62.7 + - - +
67B ALA* 4.4 2.0 - - - -
68B GLY* 2.7 40.2 + - - +
71B ALA* 4.8 8.1 - - + +
73B ILE* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASP* 4.3 6.6 - - - +
44A ARG 5.2 2.9 + - - -
45A ASN 5.7 0.3 + - - -
9B PRO* 5.8 3.6 - - + -
11B LEU* 4.4 10.2 - - - +
61B ARG* 2.7 61.5 + - - +
62B TYR* 3.6 8.9 - - + +
64B THR* 1.3 75.7 - - - +
66B TRP* 1.3 58.8 + - - +
68B GLY* 4.4 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B THR* 3.7 39.9 + - + -
6B ALA* 5.5 2.4 - - + +
7B VAL 5.2 3.1 + - - -
8B LEU* 3.4 34.8 - - + +
9B PRO* 3.8 35.0 - - + +
62B TYR 3.6 8.2 + - - +
63B VAL* 3.3 15.1 + - + +
64B THR 3.1 0.2 - - - -
65B ASP* 1.3 81.9 - - - +
67B ALA* 1.3 94.8 + - + +
68B GLY* 3.3 0.9 + - - -
96B VAL* 4.2 11.0 - - + -
104B ILE* 4.5 7.4 - - + -
106B VAL* 4.3 13.5 - - + -
124B LEU* 4.6 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL 2.8 20.7 + - - +
64B THR* 4.4 0.2 - - - -
66B TRP* 1.3 99.1 - - + +
68B GLY* 1.3 61.7 + - - +
70B SER* 4.8 2.9 + - - -
71B ALA* 3.7 24.0 - - + -
124B LEU* 3.8 9.4 - - + -
126B MET 4.5 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASN* 4.7 1.2 + - - -
64B THR* 2.7 32.4 + - - +
65B ASP 4.8 2.7 - - - -
66B TRP 3.3 2.5 - - - -
67B ALA* 1.3 75.2 - - - +
69B PRO* 1.3 75.2 - - - +
70B SER* 3.2 4.3 + - - -
71B ALA* 3.3 16.3 + - - +
----------------------------------------------------------
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