Contacts of the helix formed by residues 29 - 42 (chain A) in PDB entry 4O8H
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 VAL 29 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 2.9 20.7 + - + +
28A VAL* 1.3 79.9 - - + +
30A PRO* 1.3 66.4 - - - +
31A LYS 3.3 0.2 + - - -
32A THR* 3.3 4.0 + - - -
33A ALA* 2.9 21.4 + - + +
86A GLU* 3.2 20.0 - - + +
87A ASN* 3.4 34.1 - - - +
90A LEU* 4.7 0.2 - - + -
127A VAL* 4.0 18.4 - - + -
128A VAL 3.8 5.4 - - - +
129A PHE* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.3 28.3 - - + +
27A ASP 4.6 2.2 - - - +
28A VAL 3.5 7.4 - - - +
29A VAL* 1.3 89.4 - - - +
31A LYS* 1.3 66.0 + - + +
33A ALA* 3.9 0.7 - - - +
34A GLU* 2.9 31.4 + - - +
86A GLU* 3.1 12.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
30A PRO* 1.3 81.3 - - + +
32A THR* 1.3 63.3 + - - +
34A GLU* 4.6 0.4 - - - -
35A ASN* 3.1 10.2 + - - +
79A TYR* 2.7 42.8 + - + +
83A PHE* 4.6 7.0 - - + -
86A GLU* 2.9 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.9 9.0 - - - -
31A LYS* 1.3 75.0 - - - +
33A ALA* 1.3 65.4 + - - +
35A ASN* 3.4 4.3 + - - +
36A PHE* 3.2 21.7 + - - +
83A PHE* 3.7 21.3 - - + -
86A GLU* 2.7 32.9 + - - +
100A MET* 3.7 26.5 - - + +
108A ASN* 6.0 0.6 - - - -
127A VAL* 4.1 10.4 - - + +
129A PHE* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 5.3 2.5 - - + -
24A LEU* 3.5 23.5 - - + +
25A LYS 4.3 2.5 - - - +
26A ALA* 3.7 33.0 - - + +
29A VAL* 2.9 19.2 + - + +
30A PRO 3.9 0.7 - - - +
32A THR* 1.3 77.8 - - - +
34A GLU* 1.3 56.9 + - - +
36A PHE* 3.2 1.6 + - - -
37A ARG* 2.9 30.4 + - - +
129A PHE* 4.5 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO 2.9 19.8 + - - +
31A LYS* 4.6 0.4 - - - -
33A ALA* 1.3 73.5 - - - +
35A ASN* 1.3 67.5 + - - +
37A ARG* 2.8 45.4 + - - -
38A ALA* 3.0 27.4 + - - +
44A LYS* 4.8 6.2 + - - -
78A ILE* 3.9 10.7 - - + +
79A TYR* 3.7 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS 3.1 17.4 + - - +
32A THR 3.6 5.3 + - - +
33A ALA 3.3 0.2 - - - -
34A GLU* 1.3 79.2 - - - +
36A PHE* 1.3 64.9 + - - +
38A ALA* 3.8 1.4 - - - +
39A LEU* 3.0 39.4 + - - +
48A TYR* 5.0 0.8 + - - -
77A SER* 3.3 11.1 - - - -
78A ILE* 2.8 41.3 + - - +
79A TYR* 3.8 10.0 + - + -
83A PHE* 3.5 13.6 - - + -
100A MET* 4.4 8.3 - - - +
109A GLY 3.0 24.2 + - - -
110A SER* 4.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 3.8 12.3 - - + -
8A LEU* 4.6 2.7 - - + -
22A LEU* 3.8 24.5 - - + -
24A LEU* 3.7 21.5 - - + -
32A THR 3.2 5.9 + - - +
33A ALA 3.8 6.3 - - - +
35A ASN* 1.3 81.6 - - - +
37A ARG* 1.3 63.3 + - - +
39A LEU* 3.2 2.8 + - - +
40A CYS* 2.9 44.2 + - - -
48A TYR* 3.3 31.1 - + - -
98A LEU* 4.5 2.0 - - + -
100A MET* 5.3 2.5 - - - -
112A PHE* 3.5 43.1 - + + -
129A PHE* 3.5 33.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 4.2 14.1 - - + -
6A VAL* 4.3 13.9 - - + +
24A LEU* 3.8 12.7 - - + +
33A ALA 2.9 16.8 + - - +
34A GLU* 2.8 44.5 + - - +
36A PHE* 1.3 76.5 - - - +
38A ALA* 1.3 69.2 + - - +
40A CYS* 3.1 6.2 + - - +
41A THR* 3.0 27.3 + - - +
43A GLU* 3.0 42.8 + - - -
163A GLN* 2.9 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 3.0 18.3 + - - +
37A ARG* 1.3 93.1 - - - +
39A LEU* 1.3 60.0 + - - +
41A THR* 3.2 10.2 + - - -
42A GLY* 2.9 26.3 + - - -
43A GLU* 3.6 7.6 + - + -
44A LYS* 4.2 13.3 + - + +
46A PHE 4.4 1.2 - - - +
78A ILE* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASN* 3.0 41.4 + - - +
36A PHE 3.2 0.6 + - - +
38A ALA* 1.3 77.2 - - - +
40A CYS* 1.3 61.2 + - - +
42A GLY* 3.6 3.8 + - - -
44A LYS* 6.2 0.2 - - + -
46A PHE* 3.7 38.4 - - + +
47A GLY* 3.3 11.4 - - - -
48A TYR* 3.0 61.1 + - + +
67A PHE* 3.9 11.9 - - + -
76A LYS 4.0 2.9 - - - +
78A ILE* 4.0 9.2 - - + -
110A SER* 3.6 22.0 - - - -
161A CYS* 4.5 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.0 14.6 - - + -
7A TYR 4.5 1.3 - - - -
8A LEU* 4.1 14.6 - - - -
36A PHE* 2.9 44.9 + - - -
37A ARG 3.1 8.3 + - - +
39A LEU* 1.3 77.7 - - - +
41A THR* 1.3 62.3 + - - +
42A GLY 3.5 0.2 + - - -
48A TYR* 4.0 11.0 - - - -
49A LYS* 5.8 0.2 - - - +
161A CYS* 3.1 35.4 - - - +
162A GLY* 3.8 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 3.0 18.2 + - - +
38A ALA* 3.2 6.6 + - - -
40A CYS* 1.3 76.7 - - - +
42A GLY* 1.3 62.3 + - - +
43A GLU* 2.7 39.8 + - - +
161A CYS 4.8 1.1 - - - +
162A GLY* 4.3 4.7 - - - -
163A GLN* 3.8 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 2.9 7.7 + - - -
39A LEU 3.6 4.4 + - - -
40A CYS 3.3 3.8 - - - -
41A THR* 1.3 75.9 - - - +
43A GLU* 1.3 58.3 + - - +
44A LYS 3.2 3.1 - - - -
45A GLY* 2.9 24.5 + - - -
46A PHE 3.5 21.8 + - - -
47A GLY* 4.9 0.4 - - - -
----------------------------------------------------------
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