Contacts of the helix formed by residues 54 - 66 (chain D) in PDB entry 4A12
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 GLU 54 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ARG* 3.5 10.6 - - - +
53D PRO* 1.3 76.2 - - - +
55D LEU* 1.3 64.7 + - - +
56D ARG* 3.8 31.4 + - - +
57D LYS* 2.9 44.8 + - + +
58D ARG* 2.9 11.2 + - - +
28G G 4.2 2.9 - - - +
29G T 3.2 57.9 + - - +
30G A 3.8 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D PRO 3.6 7.9 - - - +
26D PHE 3.3 22.7 - - - +
27D ILE 3.3 20.2 - - - +
28D THR* 3.8 17.5 - - + -
54D GLU* 1.3 68.5 - - - +
56D ARG* 1.3 61.0 + - + +
58D ARG* 3.0 19.3 + - - +
59D ILE* 2.8 55.6 + - + +
28G G 3.7 35.0 - - - +
29G T 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ARG* 3.4 55.6 - - + +
59C ILE* 5.4 1.2 - - - +
54D GLU* 3.3 21.6 + - - +
55D LEU* 1.3 83.5 - - + +
57D LYS* 1.3 59.2 + - + +
59D ILE* 4.1 8.9 - - + +
60D LYS* 3.1 26.9 + - - +
27G A 3.2 29.3 + - - -
28G G 3.2 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PRO* 3.7 22.0 - - + -
54D GLU* 2.9 34.7 + - + +
56D ARG* 1.3 77.2 - - + +
58D ARG* 1.4 62.0 + - - +
60D LYS* 3.5 8.9 + - + +
61D LEU* 3.2 31.9 + - + +
30G A 6.2 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ILE* 3.6 31.0 - - - +
25D PRO* 3.0 33.8 + - + +
27D ILE* 2.6 35.8 + - - +
28D THR 5.1 0.4 - - - -
29D ASP* 4.6 4.2 + - - -
32D LEU* 5.3 0.6 - - - +
47D ARG* 3.5 21.0 - - - +
52D ILE* 3.8 6.4 - - - +
53D PRO* 2.8 45.6 + - + +
54D GLU 2.9 13.2 + - - +
55D LEU* 3.3 28.2 - - - +
57D LYS* 1.4 74.4 - - - +
59D ILE* 1.4 64.0 + - - +
61D LEU* 3.3 12.0 + - - +
62D VAL* 3.2 27.3 + - - +
29G T 4.6 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ARG 5.4 0.7 - - - +
59C ILE* 4.0 5.4 - - + +
60C LYS* 3.6 46.2 - - + +
63C ALA* 3.4 15.0 - - + +
25D PRO* 4.8 2.9 - - + +
26D PHE* 3.7 28.5 - - + +
55D LEU* 2.8 51.2 + - + +
56D ARG* 4.1 8.3 - - + +
58D ARG* 1.4 70.9 - - - +
60D LYS* 1.4 61.8 + - - +
62D VAL* 3.3 6.7 + - - -
63D ALA* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 4.2 17.0 - - + -
59C ILE* 3.6 30.5 - - + +
56D ARG 3.1 18.4 + - - +
57D LYS* 3.6 9.6 - - + +
58D ARG 3.3 0.4 - - - -
59D ILE* 1.4 75.7 - - - +
61D LEU* 1.3 51.8 + - + +
63D ALA* 3.2 3.6 + - - +
64D GLU* 2.8 68.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PRO* 4.3 18.2 - - + -
57D LYS* 3.2 22.7 + - + +
58D ARG* 3.3 8.7 + - - +
60D LYS* 1.3 77.0 - - + +
62D VAL* 1.4 62.4 + - + +
64D GLU* 4.0 17.2 - - + +
65D LYS* 3.2 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ALA* 3.5 29.4 - - + +
66C ASN* 3.3 19.1 + - + +
67C TYR* 4.5 14.4 - - + +
25D PRO* 4.4 24.0 - - + -
26D PHE* 4.5 4.7 - - + -
58D ARG 3.2 17.0 + - - +
59D ILE* 3.6 9.0 - - - +
60D LYS 3.3 0.2 - - - -
61D LEU* 1.4 77.6 - - + +
63D ALA* 1.3 61.6 + - - +
65D LYS* 3.5 17.2 + - + +
66D ASN 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.7 18.8 - - + -
59C ILE* 3.5 28.7 - - + +
62C VAL* 3.8 9.1 - - + +
63C ALA* 3.7 10.2 - - - +
66C ASN* 3.5 18.4 + - - +
59D ILE 3.0 10.4 + - - +
60D LYS 3.4 7.2 - - - +
62D VAL* 1.3 76.3 - - - +
64D GLU* 1.3 61.1 + - - +
65D LYS 3.5 0.5 + - - -
66D ASN 3.5 9.2 - - - +
67D TYR* 3.5 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.9 18.5 - - + -
60D LYS* 2.8 54.3 + - - +
61D LEU* 4.0 22.1 + - + +
62D VAL 3.4 0.2 - - - -
63D ALA* 1.3 69.6 - - - +
65D LYS* 1.4 65.5 + - - +
67D TYR* 3.4 22.7 + - + +
68D ASP* 4.7 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LEU* 3.2 34.0 + - + +
62D VAL* 3.8 9.0 - - + +
63D ALA 3.3 0.6 - - - -
64D GLU* 1.4 76.5 - - - +
66D ASN* 1.3 66.9 + - - +
67D TYR 3.2 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 4.6 2.9 - - - +
66C ASN* 3.2 54.2 + - - +
76C GLN* 5.1 15.9 + - - +
63D ALA 3.5 1.8 - - - +
64D GLU 3.6 0.2 - - - -
65D LYS* 1.3 82.2 - - - +
67D TYR* 1.3 60.9 + - - +
69D GLN* 5.8 2.7 - - - -
----------------------------------------------------------
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