Contacts of the helix formed by residues 41 - 54 (chain B) in PDB entry 3NBV
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 GLY 41 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.6 22.2 - - - -
13B VAL* 3.7 13.5 - - - +
15B ASP* 4.7 0.6 + - - -
40B GLY* 1.3 72.0 - - - -
42B ASN* 1.3 59.8 + - - -
43B ALA 3.6 1.8 - - - -
44B SER 3.4 0.3 + - - -
45B ASN* 2.8 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 5.5 0.4 - - - +
41B GLY* 1.3 68.6 - - - -
43B ALA* 1.3 66.6 + - - +
45B ASN* 3.3 3.1 + - - +
46B SER* 3.0 27.0 + - - -
139B GLU* 3.5 29.1 + - + +
171B GLU* 3.7 19.8 + - - +
173B GLU* 3.3 31.3 + - - +
258B ASP* 2.9 33.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B CYS* 3.8 15.9 - - + +
9B VAL 3.7 7.6 - - - +
10B GLY* 3.5 39.3 - - - +
11B LEU 4.1 0.2 + - - -
41B GLY 3.6 0.2 - - - -
42B ASN* 1.3 74.0 - - - +
44B SER* 1.3 62.9 + - - +
46B SER* 3.3 6.8 + - - -
47B CYS* 3.0 26.0 + - - -
59B PHE* 4.1 7.9 - - + -
137B HIS* 5.6 4.0 - - + -
139B GLU* 3.1 12.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU 3.7 10.9 + - - -
12B VAL* 3.9 10.5 - - - -
39B ARG* 2.8 58.1 + - - +
40B GLY 3.3 21.3 + - - -
41B GLY 3.5 1.3 - - - -
42B ASN 3.2 0.4 - - - -
43B ALA* 1.3 78.8 - - - +
45B ASN* 1.3 62.9 + - - +
47B CYS* 3.2 12.0 + - - +
48B THR 3.2 5.0 + - - -
59B PHE* 4.1 3.1 - - - -
76B PHE* 4.0 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 3.9 17.4 + - - +
40B GLY* 4.0 3.8 - - - -
41B GLY 2.8 29.2 + - - +
42B ASN* 3.6 0.6 + - - +
44B SER* 1.3 71.8 + - - +
46B SER* 1.3 63.5 + - - +
48B THR* 3.2 9.0 + - - -
49B VAL* 3.2 23.7 + - - +
254B LEU 5.6 0.2 - - - -
255B GLY* 4.2 10.7 - - - -
258B ASP* 2.9 36.2 + - + +
294B PHE* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B CYS* 4.2 13.9 - - - -
42B ASN 3.0 17.6 + - - -
43B ALA* 3.6 6.5 - - - -
45B ASN* 1.3 77.3 - - - +
47B CYS* 1.3 62.0 + - - +
49B VAL* 3.1 2.5 + - - -
50B LEU* 3.0 28.0 + - - +
137B HIS* 5.2 8.2 + - - -
258B ASP* 3.2 25.2 + - - +
261B ASN* 4.4 6.1 + - - +
262B ALA* 3.5 21.1 + - - +
265B ILE* 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B CYS* 3.7 16.4 - - - -
43B ALA 3.0 17.7 + - - -
44B SER* 3.5 9.9 - - - +
46B SER* 1.3 76.1 - - - +
48B THR* 1.3 63.6 + - - +
50B LEU* 3.3 4.2 + - - -
51B SER* 3.0 20.8 + - - -
57B CYS* 3.4 16.7 - - - -
58B ALA 3.5 28.0 - - - -
59B PHE* 3.8 17.0 - - - -
76B PHE* 4.6 1.8 - - + -
81B VAL* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 2.9 33.6 + - - -
44B SER 3.2 2.8 + - - -
45B ASN* 3.2 10.6 + - - -
47B CYS* 1.3 79.1 - - - +
49B VAL* 1.3 62.9 + - - +
51B SER* 3.3 2.6 + - - -
52B LEU* 3.1 33.2 + - + +
79B ARG* 3.7 33.7 - - + +
81B VAL* 4.1 7.1 - - - +
294B PHE* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASN 3.2 13.0 + - - +
46B SER 3.1 8.3 + - - +
48B THR* 1.3 75.0 - - - +
50B LEU* 1.3 59.0 + - - +
52B LEU* 3.2 7.2 + - - +
53B LEU* 2.9 48.7 + - + +
258B ASP 4.7 0.2 - - - +
259B THR* 3.7 44.0 - - + +
262B ALA* 3.7 17.9 - - + -
263B SER* 4.0 3.1 - - - +
284B VAL* 4.8 0.9 - - + -
294B PHE* 4.0 19.5 - - + -
297B ILE* 4.1 11.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
6B ILE* 3.7 46.7 - - + -
8B CYS* 3.7 23.3 - - - -
46B SER 3.0 17.9 + - - +
47B CYS* 3.7 4.3 - - - +
49B VAL* 1.3 77.4 - - - +
51B SER* 1.3 59.3 + - - +
53B LEU* 3.3 6.0 + - - +
54B GLY 3.2 5.0 + - - -
55B ALA* 3.0 29.1 + - + +
57B CYS* 4.1 15.9 - - + -
262B ALA* 3.4 32.8 - - + +
265B ILE* 4.4 4.0 - - + -
266B PHE* 4.1 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B CYS 3.0 10.4 + - - -
48B THR 3.6 7.4 - - - -
49B VAL 3.3 0.2 - - - -
50B LEU* 1.3 74.2 - - - +
52B LEU* 1.3 65.5 + - - +
54B GLY* 3.1 14.7 + - - -
55B ALA 3.7 10.1 + - - -
57B CYS* 3.4 15.4 - - - -
79B ARG 3.0 29.2 + - - -
80B GLY* 3.3 18.5 + - - -
81B VAL* 4.0 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B THR* 3.1 22.4 + - + +
49B VAL* 3.7 6.3 - - - +
51B SER* 1.3 78.3 - - - +
53B LEU* 1.3 59.1 + - + +
54B GLY* 3.4 0.9 + - - -
79B ARG* 4.4 25.6 - - - +
294B PHE* 3.6 40.4 - - + +
295B ASP* 5.3 0.9 - - - -
296B GLY 5.8 0.4 - - - +
297B ILE* 4.1 12.6 - - + -
298B VAL* 3.4 21.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
49B VAL* 2.9 30.1 + - + +
50B LEU* 3.5 7.9 - - - +
51B SER 3.2 0.2 - - - -
52B LEU* 1.3 78.7 - - + +
54B GLY* 1.3 55.9 + - - +
55B ALA 3.6 0.2 - - - -
262B ALA 4.2 2.0 - - - +
263B SER* 3.8 25.6 - - - +
266B PHE* 3.6 53.9 - - + -
280B PHE* 4.0 23.6 - - + -
284B VAL* 4.6 12.1 - - + -
297B ILE* 6.0 1.3 - - + -
298B VAL* 3.9 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B SER 3.1 13.1 + - - -
52B LEU 3.2 1.3 - - - -
53B LEU* 1.3 79.0 - - - +
55B ALA* 1.3 62.0 + - - +
56B PRO* 3.9 5.5 - - - +
266B PHE* 4.4 6.2 - - - -
----------------------------------------------------------
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