Contacts of the helix formed by residues 18 - 34 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.0 24.0 + - - +
16A HIS* 3.9 10.9 + - + +
17A GLY* 1.3 81.6 + - - +
19A TYR* 1.3 56.4 - - - +
20A ARG 3.5 2.2 - - - -
21A GLU* 3.7 19.5 + - + +
22A MET* 3.0 26.2 + - - +
66A GLN* 5.0 8.9 + - - -
69A ASP* 4.1 6.3 + - - +
250A ILE* 3.6 26.6 - - + +
403A GOL 5.9 0.8 + - - -
501V A 5.7 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 4.0 9.2 - - + -
17A GLY* 3.3 16.7 + - - -
18A LYS* 1.3 72.3 - - - +
20A ARG* 1.3 66.7 + - - +
22A MET* 3.3 21.1 + - + +
23A TYR* 3.0 31.3 + + + -
46A MET* 2.7 61.9 + - + +
48A THR* 3.5 9.2 - - - +
69A ASP* 3.5 2.5 + - + -
70A PHE* 3.8 39.5 - + + -
73A TYR* 3.4 25.1 - + + -
84A THR* 6.0 0.9 - - + -
110A MET* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 1.3 74.1 - - - +
21A GLU* 1.3 63.2 + - - +
23A TYR* 3.9 2.2 - - - +
24A ARG* 3.0 57.9 + - - +
69A ASP* 2.8 42.0 + - - +
72A LEU* 3.6 22.7 - - - +
73A TYR* 3.4 24.5 - - + +
78A GLU* 3.8 23.6 + - - -
403A GOL 4.1 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 3.7 25.6 + - + +
19A TYR 3.3 0.2 - - - -
20A ARG* 1.3 80.1 - - - +
22A MET* 1.3 64.4 + - - +
24A ARG* 3.3 19.3 + - - +
25A GLN* 3.0 32.8 + - + +
69A ASP* 4.4 0.8 + - - -
250A ILE* 3.7 10.1 - - + -
251A GLY* 3.3 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.9 12.6 - - - -
15A VAL* 3.8 28.7 - - + -
18A LYS 3.0 16.4 + - - +
19A TYR* 3.3 33.2 + - + +
21A GLU* 1.3 76.5 - - - +
23A TYR* 1.3 81.1 + - + +
25A GLN* 3.1 7.7 + - - +
26A LEU* 2.9 46.1 + - + +
40A VAL* 4.9 1.6 - - - -
42A CYS* 3.8 19.1 - - - -
84A THR* 5.1 0.9 - - + -
250A ILE* 4.0 23.8 - - + -
256A ILE* 4.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.0 24.3 + + - +
20A ARG* 3.9 2.7 - - - +
22A MET* 1.3 93.7 - - + +
24A ARG* 1.3 55.6 + - - +
26A LEU* 3.3 23.3 + - + +
27A SER* 2.7 36.3 + - - -
40A VAL* 5.0 0.7 - - + -
73A TYR* 3.5 26.7 - + - +
80A ALA* 3.5 15.8 - - + +
81A PRO* 3.7 28.8 - - + +
82A TYR* 4.0 13.4 - + + -
84A THR* 2.7 36.0 + - + +
110A MET* 3.6 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 3.0 52.4 + - + +
21A GLU* 3.6 23.0 - - - +
23A TYR* 1.3 75.6 - - - +
25A GLN* 1.3 58.5 + - - +
27A SER* 3.2 8.8 + - - -
28A GLU* 2.9 31.7 + - - +
31A LYS* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.0 28.5 + - + +
22A MET* 3.4 9.0 - - - +
24A ARG* 1.3 76.7 - - - +
26A LEU* 1.3 61.5 + - - +
28A GLU* 3.2 17.5 + - + +
29A TYR* 3.2 11.6 + - - +
250A ILE* 5.1 3.2 - - - +
251A GLY* 4.9 7.6 + - - -
252A TYR 4.6 12.6 + - - +
253A LYS* 4.8 18.6 - - - +
255A ALA* 5.3 0.6 - - - +
256A ILE* 3.6 35.7 - - + +
258A TYR* 4.4 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 3.6 25.4 - - + -
12A VAL* 5.0 1.6 - - + -
22A MET* 2.9 27.0 + - + +
23A TYR* 3.7 28.9 - - + +
25A GLN* 1.3 71.7 - - - +
27A SER* 1.3 67.0 + - - +
29A TYR* 3.2 16.8 + - - +
30A GLU* 3.3 5.9 + - - +
37A ILE* 3.6 19.2 - - + +
40A VAL* 3.8 29.6 - - + -
82A TYR* 4.0 9.0 - - + -
256A ILE* 3.7 19.5 - - + -
258A TYR* 3.7 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR 2.7 22.5 + - - -
24A ARG* 3.3 9.6 - - - -
26A LEU* 1.3 73.8 - - - +
28A GLU* 1.3 61.8 + - - +
30A GLU* 3.1 6.6 + - - +
31A LYS* 2.3 66.1 + - - +
81A PRO* 6.4 0.9 - - - -
82A TYR* 3.5 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG 2.9 14.6 + - - +
25A GLN* 3.2 14.1 + - + +
27A SER* 1.3 75.2 - - - +
29A TYR* 1.3 52.7 + - - +
31A LYS* 3.2 34.7 - - - +
32A SER* 2.7 47.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A HIS* 3.7 19.1 + - + +
25A GLN 3.2 7.2 + - - +
26A LEU 3.2 9.3 + - - +
28A GLU* 1.3 74.0 - - - +
30A GLU* 1.3 64.5 + - - +
32A SER* 3.5 6.0 + - - -
33A THR* 2.8 49.8 + - + -
35A LYS* 3.1 48.0 + - + +
37A ILE* 3.8 23.1 - - + -
258A TYR* 3.3 65.9 - + + +
260A ASP* 4.2 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU 3.3 9.4 + - - +
27A SER* 3.1 6.9 + - - +
29A TYR* 1.3 78.1 - - + +
31A LYS* 1.3 59.9 + - + +
34A GLY* 2.9 28.4 + - - -
35A LYS 3.3 20.6 - - - +
36A GLU* 3.5 7.3 - - - +
37A ILE* 2.9 37.6 + - + +
82A TYR* 2.6 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG 5.3 0.2 - - - -
27A SER* 2.3 45.3 + - - +
28A GLU* 3.2 30.7 - - - +
30A GLU* 1.3 80.8 - - + +
32A SER* 1.3 62.1 + - - +
33A THR 3.5 0.2 + - - -
34A GLY* 4.0 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 2.7 31.5 + - - -
29A TYR* 3.5 7.8 + - - -
31A LYS* 1.3 74.7 - - - +
33A THR* 1.3 68.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 2.8 37.9 + - + +
32A SER* 1.3 90.9 - - - +
34A GLY* 1.3 58.3 + - - +
35A LYS* 3.1 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU 2.9 16.1 + - - -
31A LYS 4.0 3.9 + - - -
32A SER 3.8 0.8 - - - -
33A THR* 1.3 76.3 - - - +
35A LYS* 1.3 62.7 + - - +
36A GLU 4.0 0.3 + - - -
----------------------------------------------------------
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