Contacts of the helix formed by residues 56 - 65 (chain D) in PDB entry 3LUE
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 ASP 56 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL 3.4 2.3 + - - +
55D GLY* 1.3 68.2 - - - -
57D GLU* 1.3 64.1 + - - +
58D ALA 2.9 5.4 - - - -
59D GLN* 2.9 25.8 + - + +
60D SER* 3.1 19.6 + - - +
292F ASP* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LYS* 3.6 1.4 + - - -
53D TYR* 3.8 0.3 - - - -
54D VAL 3.3 21.2 + - - +
56D ASP* 1.3 80.8 + - - +
58D ALA* 1.3 47.6 - - - +
60D SER* 4.4 2.7 - - - +
61D LYS* 4.4 0.7 + - - -
149F THR* 5.2 7.6 + - + +
166F TYR* 2.1 37.0 + - - -
167F GLU* 2.7 24.5 - - - +
289F ILE* 5.5 0.2 - - - -
292F ASP* 4.7 17.7 - - - +
127O GLU* 5.2 2.5 - - - +
128O GLU* 2.7 35.8 - - - +
136O MET* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 4.9 2.7 - - + +
36D GLY 4.5 0.7 - - - +
53D TYR* 3.6 32.5 - - + +
54D VAL 4.0 1.6 - - - +
55D GLY 3.5 11.6 + - - +
56D ASP 2.9 0.8 - - - -
57D GLU* 1.3 68.4 - - - +
59D GLN* 1.3 65.8 + - - +
62D ARG* 3.3 17.0 + - - +
65D LEU* 4.5 1.8 - - + -
67D LEU* 3.7 22.0 - - + +
166F TYR* 1.5 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D SER 5.1 6.8 - - - +
34D ILE* 4.4 12.3 - - + +
55D GLY 3.5 4.1 + - - +
56D ASP* 2.9 23.4 + - + +
58D ALA* 1.3 79.4 - - - +
60D SER* 1.3 56.4 + - - +
61D LYS 2.9 0.6 + - - -
62D ARG* 2.8 70.0 + - - +
67D LEU* 5.4 0.4 - - - +
70D PRO* 5.8 2.9 - - - +
203D THR* 3.4 9.5 - - - +
207D GLU* 4.9 13.8 - - + +
288F ASP* 3.8 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ASP 3.1 15.1 + - - -
57D GLU 5.1 0.2 - - - -
58D ALA 3.3 0.4 - - - +
59D GLN* 1.3 73.2 - - - +
61D LYS* 1.3 45.5 - - - +
204D ALA* 3.6 2.1 - - - +
166F TYR* 4.2 0.2 - - - -
286F ASP* 3.8 5.2 - - - -
288F ASP* 1.6 62.6 + - - +
289F ILE* 1.2 100.0 - - - +
292F ASP* 4.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLN 2.9 0.4 + - - -
60D SER* 1.3 73.7 - - - +
62D ARG* 1.4 56.3 + - - +
63D GLY 3.2 2.7 - - - -
64D ILE* 2.8 24.1 + - - -
65D LEU 2.9 8.3 + - - -
149F THR* 1.5 46.4 - - - +
165F ILE 3.1 2.0 - - - -
166F TYR* 0.8 330.7 - - + +
286F ASP* 3.8 4.0 + - - -
289F ILE* 2.9 28.7 - - + +
293F LEU* 5.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 4.8 4.2 - - - +
58D ALA 3.3 13.8 + - - +
59D GLN* 2.8 52.9 + - - +
61D LYS* 1.4 73.6 - - - +
63D GLY* 1.3 63.4 + - - +
65D LEU* 2.9 27.2 - - - +
67D LEU* 3.9 29.3 - - + +
69D TYR* 3.9 15.3 + - - -
70D PRO* 4.9 13.5 - - - +
77D THR* 5.7 1.8 + - - -
78D ASN* 4.4 26.0 - - - +
203D THR* 4.2 13.9 - - + -
166F TYR* 4.5 0.2 - - - -
286F ASP* 3.5 0.8 + - - +
288F ASP* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LYS 3.2 0.4 - - - -
62D ARG* 1.3 84.3 - - - +
64D ILE* 1.3 59.7 + - - +
65D LEU 3.6 1.0 + - - +
286F ASP* 3.2 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D PRO 4.1 9.0 - - - +
61D LYS* 2.8 26.8 + - + +
63D GLY* 1.3 73.2 - - - -
65D LEU* 1.4 59.6 + - + +
166F TYR* 3.0 27.4 - - + +
169F TYR* 4.4 2.3 - - - +
171F LEU* 1.5 91.9 - - + +
172F PRO* 5.9 0.9 - - + -
173F HIS* 3.5 27.8 - - + +
286F ASP* 4.8 4.2 + - + +
289F ILE* 4.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLY* 3.9 16.2 - - - +
37D ARG 4.2 2.9 - - - +
38D PRO* 3.6 38.4 - - + -
39D ARG* 5.7 0.4 - - - -
53D TYR* 3.8 12.3 - - + -
58D ALA* 4.4 2.5 - - + +
61D LYS 2.9 5.5 + - - +
62D ARG* 2.9 19.2 + - - +
63D GLY 3.4 1.1 - - - +
64D ILE* 1.4 84.0 - - + +
66D THR* 1.3 65.6 + - - +
67D LEU* 3.8 5.1 + - + +
166F TYR* 2.3 65.1 - - + +
169F TYR* 3.8 5.6 - - + -
----------------------------------------------------------
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