Contacts of the helix formed by residues 30 - 42 (chain A) in PDB entry 4DUQ
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 30 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 4.7 9.0 + - - +
28A LYS 3.7 1.4 + - - -
29A LEU* 1.3 75.8 - - - +
31A LYS* 1.3 65.8 + - - +
32A GLY* 3.4 4.9 + - - -
33A GLU* 2.9 37.4 + - - +
34A MET* 2.9 22.3 + - - +
59A MET* 3.8 2.2 - - - -
68A GLN 4.5 0.4 - - - -
69A GLN* 3.8 19.2 + - - -
----------------------------------------------------------
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 SER* 1.3 73.6 - - - +
32A GLY* 1.3 57.6 + - - +
34A MET* 3.4 2.6 + - - +
35A LYS* 2.9 26.9 + - - +
52A GLU* 2.3 36.9 + - - -
55A LEU* 3.7 27.0 - - + +
56A LYS* 4.0 22.7 - - + +
59A MET* 3.6 27.4 - - + +
68A GLN 4.3 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 5.8 4.9 - - - -
30A SER* 3.2 6.2 + - - -
31A LYS* 1.3 81.5 - - - +
33A GLU* 1.3 60.2 + - - +
35A LYS* 3.4 10.3 + - - +
36A GLU* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.1 27.7 - - + +
20A SER* 3.1 3.1 - - - +
22A GLN* 4.8 2.5 - - + -
23A GLU* 2.7 42.5 + - + +
28A LYS 3.0 4.9 - - - +
29A LEU* 3.2 11.4 - - + -
30A SER* 2.9 36.3 + - - +
32A GLY* 1.3 74.1 - - - +
34A MET* 1.3 59.6 + - - +
36A GLU* 3.3 13.9 + - - +
37A LEU* 2.9 27.9 + - - +
101A CA 2.5 30.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.9 28.3 - - + +
30A SER 2.9 17.0 + - - +
31A LYS 3.7 2.0 - - - +
33A GLU* 1.3 73.5 - - - +
35A LYS* 1.3 66.1 + - - +
37A LEU* 3.5 17.0 - - - +
38A LEU* 2.8 43.9 + - + +
55A LEU* 4.0 12.1 - - + -
58A LEU* 4.3 6.5 - - + -
59A MET* 3.7 20.6 - - - -
62A LEU* 3.7 28.7 - - + -
70A VAL* 4.4 11.2 - - + -
75A TYR* 5.1 0.9 - - + -
78A PHE* 4.5 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS 2.9 14.8 + - - +
32A GLY* 3.5 13.0 - - - +
33A GLU 3.3 0.2 - - - -
34A MET* 1.3 75.9 - - - +
36A GLU* 1.3 58.5 + - + +
38A LEU* 3.4 1.3 + - - -
39A HIS* 3.0 29.3 + - + +
50A VAL* 3.6 43.0 + - + +
52A GLU* 4.3 12.3 + - - +
55A LEU* 3.9 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.9 11.3 - - + -
22A GLN* 3.3 29.7 + - - +
23A GLU* 3.9 16.2 - - - +
32A GLY 3.1 17.7 + - - +
33A GLU* 3.6 11.5 - - - +
35A LYS* 1.3 77.5 - - + +
37A LEU* 1.3 66.2 + - - +
39A HIS* 3.3 3.7 + - - -
40A LYS* 2.9 55.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 4.2 12.6 - - + +
16A PHE* 4.8 1.1 - - - -
19A TYR* 3.8 36.0 - - + -
29A LEU* 4.1 28.7 - - + -
33A GLU 2.9 16.6 + - - +
34A MET* 3.2 18.1 + - - +
36A GLU* 1.3 76.2 - - - +
38A LEU* 1.3 61.9 + - + +
41A GLU* 2.7 38.9 + - + +
42A LEU* 4.3 10.8 - - + -
75A TYR* 4.3 12.8 - - + -
78A PHE* 4.5 6.3 - - + -
5B LEU* 4.3 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A MET* 2.8 29.2 + - + +
35A LYS 3.7 3.1 - - - +
37A LEU* 1.3 76.1 - - + +
39A HIS* 1.3 60.1 + - - +
42A LEU* 3.0 46.2 + - + +
45A PHE* 5.9 1.3 - - + -
46A VAL* 3.4 27.5 - - + +
50A VAL* 4.2 16.4 - - + -
55A LEU* 4.0 19.3 - - + -
58A LEU* 3.7 24.2 - - + -
78A PHE* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 3.0 18.3 + - + +
36A GLU* 4.0 3.1 - - - +
38A LEU* 1.3 78.0 - - - +
40A LYS* 1.3 83.8 + - + +
43A PRO* 3.8 18.4 - - + +
46A VAL* 4.1 9.2 - - - -
47A GLY 4.1 6.9 + - - +
48A GLU* 3.6 33.1 + - + +
50A VAL* 3.8 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.5 26.4 - - + +
36A GLU* 2.9 47.8 + - - +
39A HIS* 1.3 96.8 - - + +
41A GLU* 1.3 63.8 + - - +
43A PRO* 3.8 5.8 - - - +
3B SER* 3.6 14.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 4.0 12.9 + - + +
18A LYS* 3.1 21.0 + - - -
19A TYR* 2.6 39.3 + - + +
37A LEU* 2.7 24.6 + - + +
40A LYS* 1.3 75.2 - - - +
42A LEU* 1.3 60.8 + - - +
43A PRO* 3.2 6.7 - - - -
3B SER* 2.5 26.0 + - - -
4B SER* 4.0 7.1 + - - -
5B LEU* 3.4 40.6 + - + +
6B GLU* 3.4 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.6 4.2 + - + -
38A LEU* 3.0 28.9 + - + +
41A GLU* 1.3 89.0 - - + +
43A PRO* 1.3 58.9 - - - +
44A SER 3.1 2.2 - - - -
45A PHE* 2.8 45.3 + - + -
46A VAL* 3.2 8.8 + - - +
78A PHE* 3.8 35.4 - - + -
82A ILE* 4.0 12.1 - - + -
5B LEU* 3.7 21.3 - - + -
6B GLU* 3.3 9.4 - - + -
9B LEU* 3.9 22.9 - - + -
----------------------------------------------------------
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