Contacts of the helix formed by residues 16 - 29 (chain E) in PDB entry 2WP9
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 16 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E GLY 3.6 3.0 + - - -
15E ALA* 1.3 79.4 - - - +
17E GLY* 1.3 68.1 + - - -
18E ALA* 3.3 3.6 - - - -
19E GLY 4.5 1.6 - - - +
20E MET* 3.0 22.2 + - - +
44E SER* 3.7 19.9 + - - -
46E THR* 3.9 6.1 - - - -
146E LEU* 3.8 7.0 - - - -
201E ALA 4.9 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 17 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E GLY* 1.3 70.9 - - - +
18E ALA* 1.3 63.2 + - - +
21E ARG* 3.0 26.3 + - - +
46E THR* 3.2 26.9 + - - -
145E LEU* 5.0 5.4 - - - -
146E LEU* 3.8 4.3 - - - +
149E LEU* 3.8 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E GLY* 3.3 1.2 - - - -
17E GLY* 1.3 76.0 - - - +
19E GLY* 1.3 62.8 + - - +
21E ARG* 3.8 4.4 - - - +
22E ALA* 3.1 23.2 + - - +
201E ALA* 4.5 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 3.7 15.0 - - - +
14E GLY 3.4 24.2 - - - -
16E GLY 3.4 5.0 + - - +
17E GLY 3.3 0.4 - - - -
18E ALA* 1.3 77.2 - - - +
20E MET* 1.3 60.6 + - - +
22E ALA* 3.3 3.8 + - - +
23E ALA* 2.8 30.0 + - - +
35E LEU* 4.3 1.8 - - - -
199E VAL* 6.4 0.2 - - - -
201E ALA* 3.9 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E GLY 4.4 0.2 + - - -
15E ALA* 3.2 24.7 - - + +
16E GLY 3.0 15.3 + - - +
17E GLY 4.2 0.9 - - - +
19E GLY* 1.3 73.4 - - - +
21E ARG* 1.3 66.2 + - - +
23E ALA* 4.5 2.9 - - - +
24E LEU* 3.0 21.5 + - - +
35E LEU* 4.3 6.1 - - + -
41E PRO* 4.1 17.0 - - + +
146E LEU* 2.8 56.1 - - + +
149E LEU* 4.0 12.6 - - + -
150E TYR* 3.7 31.4 - - + +
153E ASN* 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E GLY 3.0 18.7 + - - +
18E ALA* 3.8 4.9 - - - +
20E MET* 1.3 78.4 - - - +
22E ALA* 1.3 63.0 + - - +
24E LEU* 3.4 13.0 - - - +
25E GLN* 3.1 42.8 + - + +
28E GLN* 5.2 4.4 + - - -
95E ALA* 5.6 3.8 + - - +
98E GLU* 3.4 35.0 + - - +
99E LEU* 4.8 8.2 - - - +
102E MET* 4.1 14.9 - - - +
149E LEU* 4.1 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 4.8 6.1 - - + -
18E ALA 3.1 15.9 + - - +
19E GLY* 3.6 6.7 - - - +
21E ARG* 1.3 77.4 - - - +
23E ALA* 1.3 62.9 + - - +
25E GLN* 3.0 6.6 + - - +
26E ILE* 2.7 46.0 + - + +
199E VAL* 5.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 4.5 3.5 - - + +
19E GLY 2.8 20.7 + - - +
20E MET 3.9 3.1 - - - +
22E ALA* 1.3 72.3 - - - +
24E LEU* 1.3 65.6 + - - +
26E ILE* 3.8 1.3 - - - +
27E SER* 2.9 28.0 + - - -
33E CYS* 4.0 26.1 - - - -
35E LEU* 4.1 22.2 - - + -
153E ASN* 4.0 11.7 - - - +
158E THR* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E MET 3.0 18.7 + - - +
21E ARG* 3.4 12.3 - - - +
23E ALA* 1.3 77.3 - - - +
25E GLN* 1.3 57.9 + - - +
27E SER* 3.3 4.3 - - - -
28E GLN* 3.0 40.9 + - - +
102E MET* 4.1 22.0 - - + -
149E LEU* 4.2 12.1 - - + -
152E GLN* 3.5 35.4 - - + +
153E ASN* 3.6 20.7 + - - +
156E ASN* 2.7 35.6 - - + +
158E THR* 4.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ARG* 3.1 36.1 + - + +
22E ALA* 3.0 9.5 + - - +
24E LEU* 1.3 75.7 - - - +
26E ILE* 1.3 67.6 + - + +
28E GLN* 3.3 14.2 + - - +
29E SER* 2.9 52.2 + - - +
98E GLU* 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ALA* 4.2 21.1 - - + -
12E VAL* 4.0 26.7 - - + -
22E ALA* 2.7 31.5 + - + +
23E ALA 3.8 3.1 - - - +
25E GLN* 1.3 73.3 - - + +
27E SER* 1.3 64.2 + - - +
29E SER* 3.2 15.0 + - - -
30E GLY 3.5 0.5 + - - -
31E GLN* 3.4 35.6 + - + +
33E CYS* 4.0 20.0 - - + -
199E VAL* 4.7 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ALA 2.9 18.4 + - - -
24E LEU* 3.3 6.5 - - - -
26E ILE* 1.3 79.0 - - - +
28E GLN* 1.3 59.0 + - - +
30E GLY* 2.8 23.0 + - - -
31E GLN 3.7 14.0 + - - +
33E CYS* 5.1 6.7 - - - -
156E ASN* 4.7 14.9 + - - +
158E THR* 4.9 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ARG* 5.2 4.0 + - - -
24E LEU* 3.0 30.4 + - - +
25E GLN* 3.3 18.3 + - - +
27E SER* 1.3 77.1 - - - +
29E SER* 1.3 57.4 + - - +
30E GLY* 3.1 5.2 + - - -
152E GLN* 5.5 3.0 - - - +
156E ASN* 3.3 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E GLN* 2.9 37.0 + - - +
26E ILE* 3.7 6.1 - - - -
27E SER 3.1 1.0 - - - -
28E GLN* 1.3 75.3 - - - +
30E GLY* 1.3 58.8 + - - +
31E GLN* 3.5 15.7 + - - +
----------------------------------------------------------
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