Contacts of the helix formed by residues 18 - 34 (chain E) in PDB entry 4PEI
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 LYS 18 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 3.0 20.3 + - - +
16E HIS* 3.7 13.4 + - - +
17E GLY* 1.3 77.1 - - - +
19E TYR* 1.3 64.1 + - - +
20E ARG 3.4 2.0 - - - -
21E GLU* 4.1 22.2 - - + +
22E MET* 3.1 21.7 + - - +
69E ASP* 3.9 4.5 - - - +
249E LYS* 4.3 18.0 - - - +
250E ILE* 3.4 36.3 + - + +
251E GLY* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 4.0 13.5 - - + -
17E GLY* 3.3 15.8 + - - -
18E LYS* 1.3 73.8 - - - +
20E ARG* 1.3 67.1 + - - +
21E GLU 3.2 0.2 + - - -
22E MET* 3.3 21.2 + - + +
23E TYR* 3.2 28.3 + + + -
46E MET* 2.5 60.0 + - + +
48E THR* 3.6 8.8 - - - +
69E ASP* 3.4 10.8 + - + -
70E PHE* 3.9 24.9 - + + -
73E TYR* 3.3 27.8 - + + -
84E THR* 5.9 0.9 - - + -
86E PHE* 5.8 0.2 - - - -
110E MET* 3.6 35.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E TYR* 1.3 73.5 - - - +
21E GLU* 1.3 55.3 + - - +
23E TYR* 3.7 1.6 + - - +
24E ARG* 3.0 44.1 + - - +
69E ASP* 2.5 39.9 + - - +
72E LEU* 3.5 26.6 - - - +
73E TYR* 3.4 19.3 - - + +
78E GLU* 3.9 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E LYS* 3.5 31.4 + - + +
19E TYR 3.2 0.6 - - - -
20E ARG* 1.3 77.0 - - - +
22E MET* 1.3 65.5 + - - +
24E ARG* 3.1 27.5 - - - +
25E GLN* 3.0 43.4 + - + +
69E ASP* 4.4 0.6 + - - -
250E ILE* 4.3 5.4 - - + -
251E GLY* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 3.9 20.6 - - + -
15E VAL* 3.9 11.2 - - + -
18E LYS 3.1 16.7 + - - +
19E TYR* 3.3 26.0 + - + +
21E GLU* 1.3 76.7 - - - +
23E TYR* 1.3 91.3 + - + +
25E GLN* 3.1 7.1 + - - +
26E LEU* 2.9 46.2 + - + +
40E VAL* 5.0 0.4 - - - -
42E CYS* 3.8 28.9 - - - -
84E THR* 4.8 0.4 - - + -
250E ILE* 3.6 24.8 - - + +
256E ILE* 4.4 0.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E TYR* 3.2 23.2 + + - +
20E ARG 4.4 2.0 - - - +
22E MET* 1.3 98.9 - - + +
24E ARG* 1.3 66.8 + - - +
26E LEU* 3.3 14.8 + - + +
27E SER* 2.9 28.0 + - - -
40E VAL* 5.0 0.9 - - + -
73E TYR* 3.6 20.2 - + - +
80E ALA* 3.6 13.8 - - + +
81E PRO* 3.7 22.9 - - + -
82E TYR* 3.8 26.8 - + - -
84E THR* 2.7 37.5 + - + +
110E MET* 3.4 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ARG* 3.0 34.5 + - - +
21E GLU* 3.1 45.2 - - - +
23E TYR* 1.3 78.8 - - - +
25E GLN* 1.3 64.3 + - - +
27E SER* 3.1 14.0 + - - -
28E GLU* 3.2 23.0 + - + +
----------------------------------------------------------
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 GLU* 3.0 41.4 + - + +
22E MET 3.3 7.4 - - - +
24E ARG* 1.3 78.6 - - + +
26E LEU* 1.3 63.3 + - - +
28E GLU* 3.1 26.7 + - - +
29E TYR* 3.2 7.4 + - - +
250E ILE* 4.7 4.4 - - - +
251E GLY* 4.3 15.4 - - - +
252E TYR 5.1 7.4 + - - +
253E LYS* 5.9 3.1 - - - +
255E ALA* 5.7 0.3 - - - +
256E ILE* 3.3 28.7 - - + +
258E TYR* 4.6 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ALA* 3.3 31.6 - - + -
12E VAL* 4.9 0.9 - - + -
22E MET* 2.9 38.4 + - + +
23E TYR* 3.3 22.0 + - + +
25E GLN* 1.3 75.9 - - - +
27E SER* 1.3 60.9 + - - +
29E TYR* 3.4 3.6 - - - +
30E GLU 3.2 15.9 + - - -
37E ILE* 3.4 17.4 - - + +
40E VAL* 4.0 25.1 - - + -
82E TYR* 3.9 15.4 + - + -
256E ILE* 4.1 16.2 - - + -
258E TYR* 3.6 17.9 - - - +
----------------------------------------------------------
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 TYR 2.9 14.4 + - - -
24E ARG* 3.1 12.0 + - - -
26E LEU* 1.3 73.4 - - - +
28E GLU* 1.3 70.7 + - - +
30E GLU* 3.1 6.1 + - - +
31E LYS* 3.0 38.5 + - - +
81E PRO* 4.9 5.7 - - - +
82E TYR* 3.3 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ARG* 3.2 20.5 + - + +
25E GLN* 3.1 14.3 + - - +
27E SER* 1.3 75.5 - - - +
29E TYR* 1.3 65.0 + - - +
31E LYS* 2.8 26.2 + - - +
32E SER* 2.7 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E HIS* 3.8 16.6 + - + +
25E GLN 3.2 4.8 + - - +
26E LEU 3.4 5.6 - - - +
28E GLU* 1.3 77.1 - - - +
30E GLU* 1.3 61.9 + - - +
32E SER* 3.1 7.7 + - - -
33E THR* 2.7 66.1 + - + -
35E LYS* 3.6 32.4 + - + +
37E ILE* 3.9 18.6 - - + -
258E TYR* 3.2 71.5 - + + +
260E ASP* 4.4 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LEU 3.2 3.1 + - - +
27E SER* 3.1 11.0 + - - +
29E TYR* 1.3 81.6 - - + +
31E LYS* 1.3 58.9 + - + +
34E GLY* 3.0 32.2 + - - -
35E LYS 3.0 20.4 - - - +
36E GLU* 3.4 8.7 - - - +
37E ILE* 2.7 40.8 + - + +
82E TYR* 2.7 38.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E SER* 3.0 27.1 - - - +
28E GLU* 2.8 32.1 + - - +
30E GLU* 1.3 73.5 - - + +
32E SER* 1.3 66.9 + - - +
34E GLY* 3.5 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E GLU* 2.7 19.0 + - - -
29E TYR* 3.1 10.6 + - - -
31E LYS* 1.3 75.1 - - - +
33E THR* 1.3 82.6 + - - +
34E GLY 3.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E TYR* 2.7 50.6 + - + +
32E SER* 1.3 88.7 + - - +
34E GLY* 1.3 56.4 + - - +
35E LYS* 2.9 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E GLU 3.0 14.6 + - - -
31E LYS 3.5 5.6 + - - -
32E SER 3.2 4.0 + - - -
33E THR* 1.3 75.2 - - - +
35E LYS* 1.3 63.2 + - - +
36E GLU* 3.8 1.7 + - - +
----------------------------------------------------------
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