Contacts of the helix formed by residues 20 - 32 (chain A) in PDB entry 4U0J
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 SER 20 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY 3.7 14.5 + - - -
15A ILE* 4.1 0.7 - - - -
16A ILE* 3.0 23.1 + - - +
17A THR* 3.0 22.3 + - - -
19A SER* 1.3 79.0 - - - +
21A ILE* 1.3 66.2 + - - +
22A ALA 3.9 4.0 - - - -
23A PHE* 2.9 18.0 + - - +
24A HIS* 3.3 10.9 - - - -
196A THR* 4.6 0.9 - - - -
400A NAD 2.6 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER 3.4 1.9 + - - -
20A SER* 1.3 71.0 - - - +
22A ALA* 1.3 59.0 + - - +
24A HIS* 3.1 10.9 + - + +
25A ILE* 2.9 42.4 + - + +
94A SER* 4.3 5.8 - - - +
147A MET* 4.2 13.0 - - + -
191A ALA* 4.9 2.7 - - + -
194A ILE* 4.2 30.1 - - + -
196A THR* 4.7 0.4 - - + -
235A ALA* 4.7 7.4 - - + -
238A VAL* 4.0 21.3 - - + -
239A ALA 5.5 0.7 - - - +
400A NAD 2.9 68.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.8 5.7 - - + +
13A SER 3.2 27.1 - - - +
14A GLY 3.6 22.2 - - - +
15A ILE* 3.6 8.3 - - + +
20A SER* 3.0 1.2 - - - -
21A ILE* 1.3 76.5 - - - +
23A PHE* 1.3 64.5 + - - +
25A ILE* 3.7 12.9 - - + +
26A ALA* 2.9 24.6 + - - +
94A SER* 3.7 13.1 + - - -
400A NAD 4.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.5 20.0 - - + +
17A THR 3.8 12.8 - - - +
18A ASP* 3.9 25.6 - - + +
20A SER* 2.9 13.2 + - - +
22A ALA* 1.3 78.3 - - - +
24A HIS* 1.3 67.9 + + - +
26A ALA* 3.3 3.6 + - - +
27A ARG* 2.9 39.2 + - + +
50A ILE* 3.5 46.2 - - + -
51A THR* 4.9 0.2 - - + -
53A ARG* 4.3 16.4 - - + -
54A LEU* 3.7 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP 3.4 20.7 + - - -
19A SER* 4.2 9.4 + - - -
20A SER 3.3 22.4 - - - -
21A ILE 3.1 6.8 + - - +
23A PHE* 1.3 82.1 - + + +
25A ILE* 1.3 64.8 + - - +
27A ARG* 3.1 35.1 + - - +
28A VAL* 3.0 30.0 + - - +
235A ALA* 3.8 33.8 - - + +
236A THR* 4.6 3.1 + - - -
239A ALA* 3.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 4.5 7.6 - - + -
21A ILE* 2.9 36.2 + - + +
22A ALA* 3.7 13.0 - - - +
24A HIS* 1.3 77.7 - - - +
26A ALA* 1.3 57.8 + - - +
28A VAL* 3.4 1.4 + - - +
29A ALA* 2.9 29.9 + - + +
92A VAL* 3.9 33.7 - - + -
94A SER* 4.6 2.7 - - - +
147A MET* 4.1 6.1 - - - -
239A ALA* 3.7 24.2 - - - +
242A VAL* 3.8 38.1 - - + -
243A CYS* 4.2 4.4 - - - -
246A LEU* 4.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 4.4 8.7 - - + -
15A ILE* 4.0 10.1 - - + -
22A ALA 2.9 18.1 + - - +
23A PHE 3.6 4.5 - - - +
24A HIS 3.3 0.2 - - - -
25A ILE* 1.3 77.2 - - - +
27A ARG* 1.3 63.3 + - - +
29A ALA* 3.3 1.6 + - - -
30A GLN* 3.0 28.2 + - - +
36A LEU* 3.5 23.9 - - + +
38A LEU* 4.4 1.3 - - + -
54A LEU* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 2.9 28.5 + - + +
24A HIS* 3.1 32.7 + - - +
25A ILE 3.3 0.2 - - - -
26A ALA* 1.3 75.9 - - - +
28A VAL* 1.3 73.5 + - - +
30A GLN* 3.3 3.5 + - - +
31A GLU* 2.9 69.3 + - - +
54A LEU* 3.7 14.5 - - + +
55A PRO* 4.0 19.9 - - + +
236A THR* 3.1 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS 3.0 20.7 + - - +
25A ILE 4.0 2.0 - - - +
27A ARG* 1.3 98.5 - - - +
29A ALA* 1.3 63.3 + - - +
31A GLU* 3.2 13.6 + - - +
32A GLN* 3.0 33.0 + - + +
236A THR* 4.5 11.9 - - + -
239A ALA* 3.8 16.2 - - + -
240A LYS* 4.3 21.3 - - + -
243A CYS* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.9 20.0 - - + -
10A ILE* 4.9 2.9 - - + -
12A VAL* 5.7 1.3 - - + -
25A ILE* 2.9 22.5 + - + +
26A ALA* 3.7 4.9 - - - +
28A VAL* 1.3 76.9 - - - +
30A GLN* 1.3 59.5 + - - +
32A GLN* 3.2 9.7 + - - +
33A GLY 3.2 0.9 + - - -
34A ALA* 3.0 34.1 + - + +
36A LEU* 4.2 11.9 - - + -
243A CYS* 3.7 13.1 - - - -
246A LEU* 5.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.0 18.8 + - - +
27A ARG 3.7 3.1 - - - +
29A ALA* 1.3 71.8 - - - +
31A GLU* 1.3 65.5 + - - +
32A GLN 3.0 2.0 - - - -
33A GLY* 3.0 13.3 + - - -
34A ALA 3.9 13.7 + - - +
36A LEU* 3.6 30.8 - - + +
54A LEU* 3.4 9.7 - - - +
55A PRO* 3.1 25.3 - - + +
56A ALA* 2.9 54.1 + - + +
57A LYS 4.0 6.9 + - - -
58A ALA* 4.0 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLY* 5.2 1.6 - - - -
27A ARG* 2.9 57.9 + - - +
28A VAL* 3.2 16.8 + - - +
30A GLN* 1.3 76.7 - - - +
32A GLN* 1.3 69.8 + - - +
33A GLY 3.3 1.8 + - - -
55A PRO* 4.4 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLY* 3.3 20.5 - - - -
4A LEU* 2.9 42.4 + - + +
5A LEU* 2.9 32.1 + - + +
6A ASP 3.3 1.9 + - - -
28A VAL* 3.0 29.9 + - + +
29A ALA* 3.4 6.5 - - - +
30A GLN 3.0 0.4 - - - -
31A GLU* 1.3 89.6 + - - +
33A GLY* 1.3 55.0 + - - +
34A ALA 3.5 0.4 - - - -
243A CYS* 5.5 2.0 - - + -
----------------------------------------------------------
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