Contacts of the helix formed by residues 39 - 58 (chain B) in PDB entry 3V9M
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 ASP 39 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 2.7 30.1 + - - -
37B PRO 3.4 1.4 + - - -
38B VAL* 1.3 79.9 - - - +
40B GLU* 1.3 65.0 + - - +
41B LEU 3.3 3.9 + - - -
42B ASP* 3.0 23.6 + - - +
43B ARG* 3.0 36.8 + - - +
103B PRO 4.3 3.2 - - - +
105B LYS* 3.6 24.9 - - + +
108B ASN* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASP* 1.3 77.2 - - - +
41B LEU* 1.3 63.3 + - - +
43B ARG* 3.1 38.6 + - - +
44B CYS* 3.2 15.3 + - - -
98B CYS* 5.2 1.5 - - - +
101B LYS* 4.1 8.1 - - - +
102B ALA* 3.6 30.6 + - + +
103B PRO* 3.5 20.3 - - + +
105B LYS* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 3.6 30.7 - - + -
25B TYR* 3.6 42.6 - - + +
29B CYS* 4.6 1.3 - - - -
39B ASP* 3.3 3.3 + - - +
40B GLU* 1.3 78.4 - - - +
42B ASP* 1.3 60.7 + - - +
44B CYS* 3.0 22.1 + - + +
45B CYS* 3.2 7.2 + - - -
99B PHE* 3.4 45.8 - - + +
102B ALA* 3.9 14.9 - - + +
103B PRO 4.3 6.8 + - - +
104B TYR* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.7 7.4 - - + +
26B GLY* 3.5 7.9 - - - -
27B CYS* 2.7 24.6 + - - +
28B TYR* 2.8 27.2 + - - +
29B CYS* 3.7 7.4 + - - -
37B PRO* 3.2 11.4 - - - +
38B VAL* 2.9 29.4 + - + +
39B ASP* 3.0 21.8 + - - +
41B LEU* 1.3 77.0 - - - +
43B ARG* 1.3 57.9 + - - +
45B CYS* 3.1 2.1 + - - +
46B GLN* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PRO* 3.6 27.8 + - + -
38B VAL 5.0 0.4 - - - -
39B ASP* 3.0 27.4 + - - +
40B GLU* 3.1 42.0 + - + +
42B ASP* 1.3 75.1 - - - +
44B CYS* 1.3 65.4 + - - +
46B GLN* 3.2 7.2 + - - +
47B VAL* 3.1 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLU* 3.2 18.8 + - - -
41B LEU* 3.0 17.2 + - - +
43B ARG* 1.3 76.5 - - - +
45B CYS* 1.3 55.0 + - - +
47B VAL* 3.3 7.8 + - - +
48B HIS* 3.0 26.5 + - - +
95B ALA* 5.0 3.3 - - - +
98B CYS* 2.0 67.0 - - + +
99B PHE* 3.5 20.7 - - + -
102B ALA* 4.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.7 4.5 - - - +
29B CYS* 2.0 64.2 - - - +
41B LEU 3.8 2.9 - - - -
42B ASP 3.1 7.6 + - - +
44B CYS* 1.3 77.8 - - - +
46B GLN* 1.3 55.5 + - - +
48B HIS* 3.6 7.4 - - - +
49B ASP* 2.7 39.6 + - - +
99B PHE* 3.5 28.7 - - - -
203B PEG 5.1 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.4 46.2 + - + +
35B GLY 4.3 1.0 + - - -
37B PRO* 3.3 26.7 - - + +
42B ASP 2.9 13.1 + - - +
43B ARG* 3.2 12.4 + - - +
45B CYS* 1.3 75.7 - - - +
47B VAL* 1.3 65.4 + - + +
49B ASP* 3.3 3.5 + - - +
50B ASN* 3.0 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 3.1 16.7 + - + +
44B CYS* 3.5 9.9 - - - +
46B GLN* 1.3 79.2 - - + +
48B HIS* 1.3 60.4 + - - +
50B ASN* 3.2 8.5 + - - +
51B CYS* 3.0 28.4 + - + +
94B ALA* 6.2 3.6 - - + -
98B CYS* 6.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.7 21.7 - + - -
44B CYS 3.0 14.3 + - - +
45B CYS* 3.2 11.9 + - - +
47B VAL* 1.3 75.4 - - - +
49B ASP* 1.3 63.1 + - - +
51B CYS* 3.1 6.0 + - - +
52B TYR* 2.9 65.1 + + - +
91B CYS* 3.5 16.8 - - + -
92B ASP* 2.9 21.2 + - - -
95B ALA* 3.3 30.7 - - + -
99B PHE* 5.5 1.9 - + + -
203B PEG 4.6 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.3 21.8 - - + +
32B GLY 3.0 13.5 - - - +
33B GLY* 3.9 0.3 - - - -
45B CYS* 2.7 22.2 + - - +
46B GLN* 3.4 7.6 - - - +
48B HIS* 1.3 78.7 + - - +
50B ASN* 1.3 57.4 + - - +
52B TYR* 3.3 7.9 + - - +
53B GLU* 3.0 27.3 + - - +
202B CA 2.4 30.4 - - - -
203B PEG 4.4 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN* 3.0 15.1 + - + +
47B VAL* 3.2 10.2 + - - +
49B ASP* 1.3 76.7 - - - +
51B CYS* 1.3 59.8 + - - +
53B GLU* 3.3 13.3 + - - +
54B GLN* 3.0 43.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
47B VAL* 3.0 15.5 + - + +
48B HIS* 3.1 11.4 + - - +
50B ASN* 1.3 76.3 - - - +
52B TYR* 1.3 59.2 + - - +
54B GLN* 3.3 5.7 + - - +
55B ALA* 2.8 23.6 + - - +
87B PHE* 3.4 20.9 - - - -
90B ALA* 6.0 0.7 - - - -
91B CYS* 2.0 55.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ASN 5.3 0.2 + - - -
2B LEU* 3.8 24.7 - - + +
5B PHE* 4.6 0.3 - - - -
48B HIS* 2.9 52.2 + + - +
49B ASP* 3.7 7.2 - - - +
51B CYS* 1.3 73.8 - - - +
53B GLU* 1.3 60.3 + - - +
55B ALA* 3.3 5.3 + - - +
56B GLY* 2.9 24.6 + - - -
62B PRO* 3.6 51.5 + - + +
63B LYS* 4.4 11.9 - - + -
88B VAL* 4.2 3.6 - - + -
91B CYS* 4.0 16.2 - - + -
92B ASP* 2.7 28.0 + - - -
203B PEG 4.6 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ASP 3.0 13.7 + - - +
50B ASN* 3.4 19.1 - - - +
51B CYS 3.2 0.2 - - - -
52B TYR* 1.3 78.2 - - - +
54B GLN* 1.3 60.5 + - + +
56B GLY* 3.1 4.3 + - - -
57B LYS* 2.8 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASN* 3.0 35.5 + - - +
51B CYS* 3.6 7.2 - - - +
53B GLU* 1.3 76.4 - - + +
55B ALA* 1.3 63.6 + - - +
57B LYS* 3.5 22.3 + - - +
58B LYS* 3.2 48.8 + - - +
87B PHE* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B CYS 2.8 13.3 + - - +
52B TYR* 3.6 9.2 - - - +
53B GLU 3.2 0.2 - - - -
54B GLN* 1.3 76.5 - - - +
56B GLY* 1.3 61.5 + - - +
58B LYS* 3.1 8.1 + - - -
60B CYS* 3.0 35.1 + - + +
62B PRO* 4.3 5.8 - - + -
87B PHE* 3.4 29.1 - - + -
88B VAL* 4.0 20.0 - - + -
91B CYS* 4.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR 2.9 14.5 + - - -
53B GLU 3.1 4.6 + - - -
55B ALA* 1.3 76.8 - - - +
57B LYS* 1.3 56.5 + - - +
59B GLY* 3.0 19.2 + - - -
60B CYS 3.5 15.3 + - - +
62B PRO* 4.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 2.8 53.9 + - - +
54B GLN* 3.9 25.1 - - - +
55B ALA 3.3 0.2 - - - -
56B GLY* 1.3 75.2 - - - +
58B LYS* 1.3 60.2 + - + +
59B GLY 3.3 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN* 3.2 42.5 + - - +
55B ALA 3.1 9.8 + - - +
57B LYS* 1.3 77.7 - - + +
59B GLY* 1.3 59.4 + - - +
60B CYS* 3.4 10.8 + - - -
84B CYS* 4.4 3.3 - - - -
87B PHE* 3.5 39.4 - - + -
----------------------------------------------------------
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