Contacts of the helix formed by residues 4 - 16 (chain E) in PDB entry 2W5J
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 4 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ASN* 4.2 17.5 - - + +
5D ILE* 3.3 45.8 - - + +
6D ALA 4.5 0.2 + - - -
2E ASN 3.0 2.7 - - - +
3E PRO* 1.3 85.4 - - - +
5E ILE* 1.3 71.4 + - + +
7E ALA* 4.0 0.2 - - - +
8E ALA* 3.3 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 5 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE* 5.3 0.7 - - - -
2E ASN* 2.8 40.1 + - - +
4E LEU* 1.3 79.7 - - + +
6E ALA* 1.3 56.9 + - - +
7E ALA 3.0 1.8 + - - -
8E ALA* 3.2 3.4 + - - +
9E SER* 2.6 37.0 + - - -
4F LEU* 3.4 24.5 - - + +
5F ILE* 5.2 1.6 - - - -
8F ALA* 3.0 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 6 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ASN* 2.4 30.4 + - + +
3E PRO* 5.1 0.7 - - + -
5E ILE* 1.3 72.0 - - - +
7E ALA* 1.3 55.9 + - - +
9E SER* 3.8 8.3 - - - -
10E VAL* 2.9 33.1 + - + +
3F PRO 4.4 3.1 - - - +
7F ALA* 3.8 27.6 - - + -
8F ALA* 3.9 5.2 - - - +
11F ILE* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 7 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ALA* 3.9 16.6 - - + -
2E ASN 3.5 2.6 + - - -
3E PRO* 2.6 29.0 - - + +
5E ILE 3.0 1.6 + - - -
6E ALA* 1.3 72.6 - - - +
8E ALA* 1.3 68.5 + - - +
9E SER 2.8 1.9 + - - -
10E VAL* 2.7 31.6 + - - +
11E ILE* 3.2 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 8 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE* 3.0 38.6 - - + -
6D ALA* 4.3 2.7 - - - +
9D SER* 2.8 37.2 + - - -
4E LEU 3.3 5.3 + - - +
5E ILE* 3.2 3.3 + - - +
7E ALA* 1.3 78.3 - - - +
9E SER* 1.3 61.3 + - - +
11E ILE* 3.2 1.9 - - - +
12E ALA* 2.9 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 9 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ILE* 2.6 23.3 + - - -
6E ALA 3.7 3.6 - - - -
7E ALA 2.8 1.6 + - - -
8E ALA* 1.3 72.5 - - - +
10E VAL* 1.3 54.8 + - - -
11E ILE 3.0 0.7 + - - -
12E ALA* 3.7 3.9 - - - +
13E ALA* 2.8 32.2 + - - +
8F ALA* 2.6 46.5 + - - -
11F ILE* 2.7 15.5 - - - +
12F ALA* 3.8 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ALA* 2.9 19.5 - - + +
7E ALA* 2.7 30.5 + - - +
9E SER* 1.3 76.3 - - - +
11E ILE* 1.3 60.8 + - + +
14E GLY* 2.7 31.4 + - - -
74E LEU* 3.8 26.1 - - - +
75E LEU* 5.4 9.8 + - + +
78E ASN* 4.2 11.7 - - + -
79E PRO* 6.1 0.2 - - + -
11F ILE* 3.0 39.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 11 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ALA* 4.9 1.3 - - + +
9D SER* 2.7 36.6 - - - +
10D VAL* 3.2 33.0 - - + -
13D ALA* 3.0 27.2 - - + +
74D LEU* 3.9 15.7 - - + -
79D PRO* 5.5 2.7 - - + -
7E ALA 3.2 7.4 + - - +
8E ALA* 3.2 2.5 - - - +
9E SER 2.9 0.8 - - - -
10E VAL* 1.3 83.2 - - + +
12E ALA* 1.3 66.4 + - - +
14E GLY* 2.8 9.9 + - - -
15E LEU 3.1 9.9 + - - -
75E LEU* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D SER* 5.0 2.0 - - - +
13D ALA* 3.3 14.9 - - + +
8E ALA 2.9 14.8 + - - +
9E SER* 3.7 7.0 - - - +
11E ILE* 1.3 78.0 - - - +
13E ALA* 1.3 64.2 + - - +
14E GLY 2.9 0.2 + - - -
15E LEU* 3.1 10.7 + - - +
16E ALA* 3.3 11.8 + - - +
12F ALA* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E SER 2.8 8.8 + - - +
12E ALA* 1.3 73.2 - - - +
14E GLY* 1.3 57.0 + - - +
16E ALA* 3.5 11.4 + - - +
74E LEU* 6.0 0.9 - - + -
11F ILE* 3.2 31.2 - - + +
12F ALA* 3.1 39.6 - - - +
15F LEU* 2.4 30.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 14 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D VAL* 5.7 3.6 - - - -
10E VAL 2.7 26.2 + - - -
11E ILE 2.8 4.2 + - - -
13E ALA* 1.3 77.6 - - - +
15E LEU* 1.3 56.7 + - - -
17E VAL* 3.0 25.5 + - - +
71E ALA* 4.4 24.3 - - - +
74E LEU* 5.1 5.6 - - - +
75E LEU* 6.2 1.1 - - - -
15F LEU* 4.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ALA* 2.5 41.7 - - + +
14D GLY* 4.9 0.4 - - - -
16D ALA* 3.0 21.7 - - + +
17D VAL* 3.1 22.4 - - + +
19D LEU* 5.0 0.7 - - - +
70D VAL* 5.6 6.6 - - + +
11E ILE 3.1 3.8 + - - +
12E ALA 3.1 3.2 + - - +
14E GLY* 1.3 68.9 - - - +
16E ALA* 1.3 53.5 + - - +
17E VAL 2.8 14.6 + - - -
18E GLY 3.0 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ALA* 5.1 3.3 - - + +
19D LEU* 5.6 1.8 - - - -
12E ALA 3.3 10.9 + - - +
13E ALA* 3.8 15.0 - - - +
14E GLY 3.2 1.2 - - - -
15E LEU* 1.3 72.4 - - - +
17E VAL* 1.3 58.0 + - - +
18E GLY 3.5 2.7 - - - +
19E LEU* 3.6 27.2 - - + +
15F LEU* 3.0 23.0 - - + +
16F ALA* 5.5 2.7 - - + +
18F GLY* 5.0 0.2 - - - -
----------------------------------------------------------
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