Contacts of the helix formed by residues 57 - 71 (chain D) in PDB entry 3ZXT
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 57 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D VAL* 1.3 75.6 - - - +
58D ARG* 1.3 58.7 + - - +
59D GLU* 3.1 21.5 + - - +
60D ASP* 3.1 27.2 + - - +
61D ILE* 2.9 27.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
56D VAL 3.4 4.6 + - - -
57D SER* 1.3 71.6 + - - +
59D GLU* 1.3 50.0 + - - +
61D ILE* 3.5 12.3 + - + +
62D GLU* 2.8 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D SER* 3.1 12.4 + - - +
58D ARG* 1.3 77.7 - - - +
60D ASP* 1.3 65.4 + - - +
62D GLU* 3.2 11.3 + - - +
63D ARG* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D VAL* 5.2 5.4 - - + -
57D SER* 3.1 24.7 + - - +
59D GLU* 1.3 78.7 - - - +
61D ILE* 1.3 61.6 + - - +
63D ARG* 3.4 8.3 + - - +
64D GLU* 3.1 29.2 + - - +
164D LEU* 5.8 4.0 - - - +
166D HIS* 5.2 11.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 4.1 34.8 - - + +
56D VAL* 4.4 24.0 - - + +
57D SER 2.9 12.0 + - - +
58D ARG* 3.7 15.0 - - - +
60D ASP* 1.3 76.5 - - - +
62D GLU* 1.3 68.5 + - - +
64D GLU* 3.5 9.4 + - - +
65D VAL* 3.0 41.0 + - + +
89D VAL* 4.2 24.9 - - + +
91D LEU* 6.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ARG* 2.8 31.3 + - - +
59D GLU* 3.2 10.5 + - - +
61D ILE* 1.3 77.7 - - - +
63D ARG* 1.3 56.8 + - - +
65D VAL* 3.4 4.6 + - - +
66D SER* 2.6 39.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLU 3.1 9.4 + - - +
60D ASP* 3.7 12.1 - - - +
62D GLU* 1.3 74.7 - - - +
64D GLU* 1.3 61.7 + - - +
66D SER* 3.3 5.4 + - - -
67D ILE* 2.8 41.9 + - + +
165D ALA 4.6 12.6 - - - +
166D HIS* 5.6 8.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
42D LYS* 2.7 35.1 + - - +
60D ASP 3.1 14.3 + - - +
61D ILE* 3.8 10.8 - - - +
63D ARG* 1.3 80.3 - - - +
65D VAL* 1.3 67.3 + - + +
67D ILE* 3.6 4.4 - - - +
68D LEU* 2.8 46.2 + - + +
91D LEU* 4.3 9.1 - - + +
93D LEU* 5.8 1.0 - - - +
162D PHE* 3.9 21.9 + - - +
163D GLY* 3.4 26.7 + - - -
165D ALA 5.4 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ILE* 3.0 28.7 + - + +
62D GLU* 4.0 4.9 - - - +
64D GLU* 1.3 74.0 - - + +
66D SER* 1.3 51.6 + - - +
68D LEU* 3.4 8.3 + - - +
69D LYS* 2.7 52.9 + - - +
79D LEU* 4.2 8.2 - - + +
82D VAL* 3.5 33.4 - - + -
89D VAL* 6.3 0.2 - - + -
91D LEU* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D GLU* 2.6 24.6 + - - -
63D ARG* 3.6 5.4 - - - -
65D VAL* 1.3 72.5 - - - +
67D ILE* 1.3 66.2 + - - +
69D LYS* 3.2 15.9 + - - +
70D GLU* 3.1 22.1 + - - +
167D LYS* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ARG* 2.8 27.6 + - + +
64D GLU* 3.8 3.8 - - - +
66D SER* 1.3 74.2 - - - +
68D LEU* 1.3 55.6 + - - +
70D GLU* 2.7 30.0 + - - +
71D ILE* 3.2 15.6 + - + +
135D ILE* 3.6 33.4 - - + -
162D PHE* 3.9 27.6 - - + -
165D ALA* 3.4 37.5 - - + +
166D HIS* 3.9 14.8 - - - -
167D LYS* 4.4 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLU* 2.8 37.2 + - + +
65D VAL* 3.5 4.5 - - - +
67D ILE* 1.3 73.2 - - - +
69D LYS* 1.3 62.3 + - - +
70D GLU 3.2 0.5 + - - -
71D ILE* 3.4 33.7 + - + +
77D ILE* 4.0 31.0 - - + +
79D LEU* 4.0 26.5 + - + +
91D LEU* 3.6 30.7 - - + -
93D LEU* 3.9 16.2 - - + -
162D PHE* 4.3 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D VAL* 2.7 37.7 + - - +
66D SER* 3.4 14.1 - - - +
68D LEU* 1.3 74.2 - - - +
70D GLU* 1.3 60.8 + - - +
71D ILE 3.6 1.4 + - - +
72D GLN* 5.9 1.4 - - - +
79D LEU* 4.1 17.9 - - + +
82D VAL* 5.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D SER* 3.1 10.9 + - - +
67D ILE* 2.7 13.0 + - - +
69D LYS* 1.3 80.5 - - - +
71D ILE* 1.3 60.7 + - + +
72D GLN* 3.7 2.0 + - - +
129D TYR* 3.7 7.8 + - - -
133D LEU* 4.0 25.3 - - - +
135D ILE* 4.5 3.1 - - - +
167D LYS* 2.7 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ILE* 3.6 14.8 - - + +
68D LEU* 3.4 35.5 + - + +
69D LYS 3.4 0.9 - - - +
70D GLU* 1.3 78.8 - - - +
72D GLN* 1.3 69.0 + - - +
73D HIS 4.1 0.4 - - - -
76D VAL* 4.0 16.5 - - + +
77D ILE 4.3 10.5 - - - +
78D THR* 5.1 5.0 - - - -
79D LEU 5.5 0.5 + - - -
129D TYR* 3.5 22.4 - - + +
130D LEU* 4.0 6.7 - - + -
133D LEU* 4.6 3.4 - - + -
135D ILE* 4.0 23.3 - - + -
162D PHE* 3.8 34.3 - - + -
----------------------------------------------------------
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