Contacts of the helix formed by residues 6 - 15 (chain M) in PDB entry 3A0B
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 LEU 6 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045B BCR 5.2 16.5 - - + +
4M ASN* 2.5 42.4 + - - +
5M GLN* 1.3 77.5 - - + +
7M GLY* 1.3 64.1 + - - +
8M PHE 3.0 1.3 - - - -
9M ILE* 3.4 18.8 - - + -
10M ALA* 3.2 24.4 + - + +
5008m PHE* 5.3 5.8 - - + -
5001t MET* 5.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 7 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L PHE* 4.1 20.9 - - - +
36L PHE* 3.6 19.1 - - - -
4M ASN* 2.4 28.1 + - - -
6M LEU* 1.3 65.6 - - - +
8M PHE* 1.3 71.3 + - - +
10M ALA* 3.2 6.6 - - - +
11M THR* 2.7 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 8 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L PHE* 3.3 13.5 - + + -
4M ASN 4.2 0.6 + - - -
5M GLN 4.6 3.8 - - - +
7M GLY* 1.3 74.1 - - - +
9M ILE* 1.3 82.6 + - + +
10M ALA 2.8 0.2 - - - -
11M THR* 2.3 24.4 + - - -
12M ALA* 3.3 20.8 + - + -
1T MET* 3.8 28.9 - - + -
4T ILE* 4.8 7.9 - - + -
5T THR* 2.8 39.7 - - + -
5006m LEU* 6.4 1.1 - - + -
5009m ILE* 4.3 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045B BCR 4.4 12.3 - - + -
5M GLN 3.6 2.2 - - - +
6M LEU* 3.4 32.3 - - + +
8M PHE* 1.3 80.0 - - + +
10M ALA* 1.3 64.5 + - - +
12M ALA* 4.7 5.2 - - - -
13M LEU* 3.1 38.9 + - + +
5005m GLN 4.7 1.3 - - - +
5008m PHE* 2.6 48.7 - - + -
5009m ILE* 2.4 59.4 - - + +
5012m ALA* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045B BCR 3.9 22.3 - - + +
35L PHE* 4.4 24.2 - - + -
6M LEU* 3.2 18.0 + - + +
7M GLY* 3.2 11.9 - - - +
8M PHE 2.4 8.3 + - - -
9M ILE* 1.3 75.5 - - - +
11M THR* 1.3 69.0 + - - +
13M LEU* 3.9 1.0 - - - +
14M PHE* 3.2 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 11 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L ALA* 5.6 0.7 - - + -
32L SER* 4.0 19.3 + - - -
35L PHE* 4.0 17.3 - - - +
36L PHE* 5.0 2.4 - - - -
7M GLY 2.7 14.2 + - - -
8M PHE* 2.3 22.6 + - + -
10M ALA* 1.3 76.4 - - - +
12M ALA* 1.3 70.2 + - + +
13M LEU 2.5 12.5 + - - -
14M PHE* 2.6 18.9 + - - +
15M VAL* 3.4 10.1 + - + -
5T THR* 4.0 17.7 - - + +
9T ILE* 3.9 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M PHE* 3.3 27.3 + - + +
9M ILE* 4.2 4.7 - - - +
11M THR* 1.3 82.9 - - - +
13M LEU* 1.3 62.3 + - + +
15M VAL* 3.2 12.9 + - - +
16M LEU* 3.1 31.1 + - + +
5009m ILE* 6.2 2.7 - - + -
5013m LEU* 5.5 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045B BCR 4.3 31.0 - - + -
9M ILE* 3.1 27.8 + - + +
10M ALA* 3.9 2.2 - - - +
11M THR 2.5 5.3 + - - -
12M ALA* 1.3 71.6 - - + +
14M PHE* 1.3 51.6 + - - +
15M VAL 2.7 5.9 + - - -
16M LEU* 2.5 34.1 + - + -
17M VAL* 2.7 33.3 + - + -
5012m ALA* 5.6 6.5 - - + -
5013m LEU* 4.7 13.2 - - + -
5016m LEU* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 14 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015B CLA 5.2 5.8 - - + -
1021B CLA 3.6 46.9 - - + -
1060B MGE 4.1 9.4 - - + -
24L ILE* 4.0 8.1 - - + +
27L LEU* 3.0 32.5 - - + -
28L ALA* 3.7 28.5 - - + -
31L PHE* 5.2 6.5 - + + -
35L PHE* 4.9 19.1 - + + -
10M ALA 3.2 9.7 + - - +
11M THR* 2.6 15.4 + - - +
13M LEU* 1.3 73.3 - - - +
15M VAL* 1.3 61.0 + - + -
16M LEU 3.4 0.9 - - - -
17M VAL* 5.2 1.3 - - - -
18M PRO* 2.7 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L ILE* 4.2 6.3 - - + -
25L LEU* 4.3 26.9 - - + -
28L ALA* 3.3 34.8 - - + -
11M THR* 3.9 22.9 - - + +
12M ALA* 3.6 9.9 - - - +
13M LEU 2.7 3.2 + - - -
14M PHE* 1.3 81.7 - - + +
16M LEU* 1.3 69.3 + - + +
18M PRO* 4.3 0.2 - - - -
19M SER* 3.1 20.2 + - - -
9T ILE* 4.9 8.5 - - + -
----------------------------------------------------------
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