Contacts of the helix formed by residues 7 - 18 (chain B) in PDB entry 1BI8
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 ARG 7 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 1.3 81.5 - - + +
8B ALA* 1.3 62.0 + - + +
9B GLY 2.7 3.1 + - - -
10B ASP* 2.4 35.3 + - - +
11B ARG* 3.0 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 4.5 2.4 - - + +
7B ARG* 1.3 82.8 - - + +
9B GLY* 1.3 62.8 + - - +
10B ASP 3.1 0.2 - - - -
11B ARG* 3.5 26.1 - - - +
12B LEU* 2.9 27.4 + - - +
33B VAL* 3.4 36.1 - - + +
37B ALA* 5.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.4 7.4 + - - +
7B ARG 2.7 4.8 + - - -
8B ALA* 1.3 74.8 - - - +
10B ASP* 1.3 57.1 + - - +
12B LEU* 4.2 1.1 - - - +
13B SER* 2.9 33.4 + - - -
37B ALA* 3.6 20.6 - - - +
38B LEU 3.1 25.1 + - - -
39B ASN* 3.7 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 4.3 19.6 + - + +
6B VAL 3.0 16.6 + - - +
7B ARG* 2.4 18.3 + - - +
9B GLY* 1.3 71.1 - - - -
11B ARG* 1.3 58.5 + - + +
13B SER* 3.2 4.4 + - - -
14B GLY* 3.0 28.2 + - - -
39B ASN* 3.0 23.2 + - - +
40B ARG* 2.4 48.0 + - - +
41B PHE* 4.7 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 5.6 0.9 - - - -
7B ARG* 3.0 17.7 + - - +
8B ALA* 3.2 31.3 + - - +
10B ASP* 1.3 77.8 - - + +
12B LEU* 1.3 61.1 + - - +
14B GLY* 4.4 0.3 - - - -
15B ALA* 3.4 21.3 + - - +
18B ARG* 4.7 3.5 + - - -
23B GLU* 5.3 0.8 - - - +
26B ARG* 4.3 6.5 - - - +
27B LEU* 3.6 31.9 - - + +
31B GLU* 3.3 34.4 + - - +
33B VAL* 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA 2.9 17.7 + - - +
9B GLY* 4.2 2.0 - - - +
11B ARG* 1.3 75.4 - - - +
13B SER* 1.3 69.0 + - - +
15B ALA* 3.4 2.1 + - - +
16B ALA* 3.0 19.2 + - - +
24B VAL* 3.9 30.7 - - + +
27B LEU* 3.7 28.7 - - + +
28B LEU* 4.1 22.0 - - + -
33B VAL* 4.1 17.7 - - + -
34B HIS 4.4 0.4 - - - +
35B PRO* 4.1 23.6 - - + +
37B ALA* 5.5 2.9 - - + +
45B ALA* 4.2 8.1 - - + -
60B LEU* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 4.3 6.1 - - - +
18A GLU* 4.9 2.1 + - - +
9B GLY 2.9 21.4 + - - -
10B ASP* 3.2 10.6 + - - -
12B LEU* 1.3 76.2 - - - +
14B GLY* 1.3 72.7 + - - +
16B ALA* 2.7 15.8 + - - +
17B ALA* 2.8 15.2 + - - +
37B ALA 5.9 0.2 - - - -
39B ASN* 3.8 19.8 + - - +
44B THR 5.1 1.3 - - - -
45B ALA* 3.8 17.9 - - - +
48B VAL* 3.9 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 3.5 25.1 - - - -
19A ILE 3.4 0.9 - - - +
10B ASP 3.0 11.4 + - - -
11B ARG 4.4 0.4 - - - -
13B SER* 1.3 81.8 + - - +
15B ALA* 1.3 61.9 + - - +
17B ALA* 3.3 3.0 + - - +
18B ARG* 2.9 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG 3.4 16.8 + - - +
12B LEU 3.5 6.7 - - - +
13B SER 3.1 0.6 - - - -
14B GLY* 1.3 71.1 - - - +
16B ALA* 1.3 67.9 + - - +
18B ARG* 3.0 17.1 + - - +
19B GLY 2.9 17.7 + - - -
20B ASP* 2.9 12.3 + - - +
23B GLU* 3.8 24.2 - - + -
24B VAL* 3.4 20.9 - - + -
27B LEU* 4.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU 3.0 10.3 + - - +
13B SER* 2.7 13.5 + - - +
15B ALA* 1.3 74.7 - - - +
17B ALA* 1.3 55.1 + - - +
19B GLY* 2.6 29.1 + - - -
24B VAL* 3.4 5.1 - - + +
45B ALA* 3.8 17.0 - - + +
49B MET* 3.8 22.0 - - + +
50B MET 3.3 9.7 + - - -
56B ILE* 3.2 23.4 - - + +
60B LEU* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 5.3 3.6 - - + -
18A GLU 4.9 0.9 - - - +
19A ILE* 4.3 25.3 - - + +
29A LYS* 4.7 9.3 + - + +
100A HIS* 5.7 3.3 + - - -
13B SER 2.8 14.8 + - - +
14B GLY* 3.4 13.7 - - - +
16B ALA* 1.3 74.4 - - - +
18B ARG* 1.3 59.9 + - - +
19B GLY 3.2 0.7 + - - -
48B VAL* 3.7 24.7 - - + +
49B MET* 4.0 0.4 - - - +
50B MET* 3.4 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 5.0 4.4 + - - -
19A ILE* 2.8 59.1 + - + +
20A GLY* 4.1 8.3 - - - -
104A ASP* 4.7 5.0 - - - +
107A THR* 5.6 0.2 - - - +
166A LEU* 4.4 17.7 - - + -
167A ALA 5.6 4.8 + - - -
11B ARG 4.7 3.2 + - - -
14B GLY* 2.9 26.8 + - - +
15B ALA* 3.0 26.6 + - - +
17B ALA* 1.3 74.4 - - - +
19B GLY* 1.3 61.2 + - - +
20B ASP* 3.2 14.7 + - + +
23B GLU* 4.8 10.7 - - - +
50B MET* 3.5 14.3 - - - +
----------------------------------------------------------
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