Contacts of the helix formed by residues 44 - 56 (chain B) in PDB entry 3V9G
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 SER 44 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 2.8 34.4 + - - -
42B GLN 3.2 2.8 + - - -
43B GLY* 1.3 79.8 - - - +
45B PRO* 1.3 74.3 - - - +
46B GLU* 3.3 26.2 - - - -
47B ARG* 3.3 11.3 + - - +
48B ASP* 3.2 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY 3.6 3.3 - - - +
44B SER* 1.3 89.0 - - - +
46B GLU* 1.3 64.8 + - - +
48B ASP* 3.4 6.8 + - + +
49B ALA* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.7 37.2 - - + +
39B ALA* 3.5 10.4 + - - +
40B PHE* 3.0 47.0 + - + -
44B SER* 3.3 19.0 + - - +
45B PRO* 1.3 89.3 - - - +
47B ARG* 1.3 60.8 + - - +
49B ALA* 3.5 7.4 + - - +
50B LEU* 3.0 29.8 + - - +
140B ARG* 5.9 0.9 - - - -
141B ALA* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A TYR* 3.1 27.3 + - - +
40B PHE* 2.9 34.7 + - + +
41B THR 3.3 17.0 - - - +
42B GLN* 3.8 22.9 - - - +
43B GLY 4.5 2.9 - - - +
44B SER* 3.3 18.2 + - - +
46B GLU* 1.3 79.9 - - - +
48B ASP* 1.3 63.4 + - - +
50B LEU* 4.0 2.6 - - - +
51B GLN* 3.1 40.6 + - - +
384B PHE* 3.6 41.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY* 5.7 2.2 - - - +
44B SER 3.2 13.3 + - - +
45B PRO* 3.9 8.5 - - + +
46B GLU 3.3 0.2 - - - -
47B ARG* 1.3 74.2 - - - +
49B ALA* 1.3 65.5 + - - +
51B GLN* 3.2 9.0 + - - +
52B LYS* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PRO 3.0 18.6 + - - +
46B GLU* 3.7 7.9 - - - +
48B ASP* 1.3 75.8 - - - +
50B LEU* 1.3 55.4 + - - +
52B LYS* 3.4 7.0 + - - +
53B ALA* 3.0 22.7 + - - +
141B ALA* 3.5 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.8 25.4 - - + -
46B GLU 3.0 18.8 + - - +
47B ARG 4.0 3.4 - - - +
49B ALA* 1.3 74.9 - - - +
51B GLN* 1.3 60.0 + - - +
53B ALA* 3.3 0.9 + - - +
54B LEU* 2.9 33.6 + - + +
141B ALA* 3.8 28.2 - - + +
144B LEU* 3.9 17.5 - - + -
145B ALA* 3.9 10.1 - - + +
148B MET* 4.0 14.8 - - - -
155B VAL* 3.9 31.9 - - + -
384B PHE* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ARG* 3.1 38.7 + - - +
48B ASP* 3.8 7.0 - - - +
50B LEU* 1.3 75.6 - - - +
52B LYS* 1.3 63.5 + - - +
54B LEU* 3.4 9.8 + - + +
55B LYS* 3.0 24.1 + - - +
381B ALA 5.6 2.2 - - - +
384B PHE* 3.6 33.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
48B ASP 3.1 13.1 + - - +
49B ALA* 3.7 10.1 - - - +
51B GLN* 1.3 77.6 - - - +
53B ALA* 1.3 56.4 + - - +
55B LYS* 3.4 6.5 + - - +
56B ASP* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA 3.0 17.0 + - - +
50B LEU 3.6 5.4 - - - +
51B GLN 3.3 0.2 - - - -
52B LYS* 1.3 73.8 - - - +
54B LEU* 1.3 64.3 + - - +
56B ASP* 3.6 12.6 + - - +
57B LEU* 3.5 20.4 + - - +
141B ALA* 3.7 31.6 - - + +
142B GLU* 4.0 6.5 - - + +
145B ALA* 3.8 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 2.9 32.6 + - + +
51B GLN* 3.7 9.0 - - + +
52B LYS 3.3 0.2 - - - -
53B ALA* 1.3 75.2 - - - +
55B LYS* 1.3 63.6 + - - +
57B LEU* 3.0 14.7 + - - +
58B LYS* 3.3 11.8 + - - +
145B ALA* 3.8 23.3 - - + +
148B MET* 4.2 14.4 - - + -
149B VAL* 3.9 24.4 - - + +
381B ALA* 4.2 23.1 - - + +
384B PHE* 4.0 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLN 3.0 16.9 + - - +
52B LYS* 3.8 6.5 - - - +
54B LEU* 1.3 71.3 - - - +
56B ASP* 1.3 58.8 + - - +
57B LEU 2.8 11.6 + - - -
58B LYS* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LYS 3.0 17.3 + - - +
53B ALA* 3.9 10.3 - - - +
54B LEU 3.3 0.6 - - - -
55B LYS* 1.3 74.7 - - - +
57B LEU* 1.3 60.9 + - - +
58B LYS 5.1 0.9 - - - -
60B ARG* 4.5 10.0 - - - +
----------------------------------------------------------
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