Contacts of the helix formed by residues 42 - 51 (chain B) in PDB entry 4DQ0
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 42 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B CYS* 2.9 17.3 + - - -
40B GLY 3.3 2.2 + - - -
41B ASN* 1.3 77.8 - - - +
43B ARG* 1.3 66.3 + - - +
44B ASN 3.1 2.6 + - - -
45B SER* 3.2 12.2 + - - -
46B LEU* 2.8 34.3 + - - +
68B VAL* 4.0 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASN* 4.7 0.4 + - - -
9B PHE* 5.6 2.5 - - - +
10B THR* 5.3 1.1 - - - +
15B LEU* 4.6 11.2 - - + +
16B THR* 3.1 35.6 + - - +
17B ARG 3.1 28.3 + - - +
18B THR* 4.3 5.0 + - - +
19B HIS* 3.6 27.5 - - - +
39B CYS 5.0 4.0 + - - +
41B ASN* 3.1 17.7 + - - +
42B GLY* 1.3 78.5 - - - +
44B ASN* 1.3 80.7 + - - +
46B LEU* 3.8 3.2 - - - +
47B TYR* 3.1 25.1 + - - +
102B THR* 4.0 11.3 + - - -
103B VAL* 4.3 7.3 - - - +
202B NHE 2.9 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 3.2 10.7 - - - +
19B HIS* 2.9 34.1 + - - +
22B VAL* 3.8 16.4 - - + +
36B ASP* 3.7 14.0 + - - +
39B CYS* 5.3 2.2 + - - +
42B GLY 3.2 0.6 - - - -
43B ARG* 1.3 93.0 - - - +
45B SER* 1.3 60.9 + - - +
47B TYR* 3.4 5.5 + - - +
48B LEU* 2.9 36.4 + - - +
100B LEU* 4.1 13.4 - - + +
102B THR* 3.5 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP* 2.7 36.1 + - - +
39B CYS* 3.8 1.4 - - - +
42B GLY* 3.2 12.0 + - - -
44B ASN* 1.3 74.5 - - - +
46B LEU* 1.3 59.7 + - - +
48B LEU* 4.6 2.9 - - - -
49B ALA* 2.9 32.8 + - - +
55B VAL* 3.5 19.9 - - - +
57B ALA* 3.3 22.6 - - - +
68B VAL* 5.7 0.7 - - - -
80B LEU* 4.0 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.7 22.6 - - + -
15B LEU* 3.4 33.4 - - + -
41B ASN 4.7 1.3 - - - +
42B GLY* 2.8 28.0 + - - +
43B ARG* 3.8 3.1 - - - +
45B SER* 1.3 70.7 - - - +
47B TYR* 1.3 65.4 + - - +
49B ALA* 3.5 2.2 + - - +
50B ALA* 2.9 26.0 + - - +
68B VAL* 4.5 12.1 - - + +
71B ILE* 3.9 30.1 - - + -
77B LEU* 3.6 27.1 - - + +
80B LEU* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU* 4.1 34.4 + - + +
9B PHE* 4.4 12.4 - + + -
18B THR* 3.9 29.8 - - + +
22B VAL* 4.5 2.7 - - + -
23B LEU* 3.6 25.6 - - + +
26B VAL* 4.2 26.2 - - + +
43B ARG 3.1 18.4 + - - +
44B ASN 3.5 4.3 - - - +
46B LEU* 1.3 77.0 - - - +
48B LEU* 1.3 78.4 + - + +
50B ALA* 3.2 2.7 + - + +
51B ASN* 2.9 57.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 4.1 13.2 - - + -
26B VAL* 3.5 32.3 - - + -
34B THR* 4.2 10.5 - - + -
36B ASP* 5.4 0.4 - - - +
44B ASN 2.9 22.8 + - - +
45B SER* 4.8 2.7 - - - +
47B TYR* 1.3 79.7 - - + +
49B ALA* 1.3 66.3 + - - +
51B ASN* 3.1 7.7 + - - -
53B TYR* 3.0 48.8 + - + -
55B VAL* 3.8 13.7 - - + -
98B PHE* 4.3 6.5 - - + -
100B LEU* 4.0 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER 2.9 18.7 + - - +
46B LEU* 4.0 2.9 - - - +
48B LEU* 1.3 76.5 - - - +
50B ALA* 1.3 64.0 + - - +
51B ASN 3.2 0.5 + - - -
52B GLY* 3.2 4.0 + - - -
53B TYR 3.5 13.5 - - - +
55B VAL* 3.7 5.5 - - + +
77B LEU* 4.6 9.6 - - + +
79B ASN* 2.8 32.8 + - - +
80B LEU* 3.9 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.7 18.7 - - - +
2B ILE 5.0 2.8 + - - +
4B ARG* 3.8 24.0 + - + +
9B PHE* 3.7 25.8 - - + -
46B LEU 2.9 19.0 + - - +
47B TYR* 3.5 5.8 - - + +
48B LEU 3.2 0.2 - - - -
49B ALA* 1.3 77.5 - - - +
51B ASN* 1.3 62.8 + - - +
52B GLY 3.3 2.5 + - - -
77B LEU* 4.2 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.1 40.1 - - - +
31B PRO* 3.7 9.4 - - - +
47B TYR* 2.9 57.3 + - + +
48B LEU* 3.1 8.7 + - - +
50B ALA* 1.3 83.7 - - - +
52B GLY* 1.3 56.3 + - - +
53B TYR* 3.4 23.9 - - + -
----------------------------------------------------------
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