Contacts of the helix formed by residues 56 - 68 (chain D) in PDB entry 2RD9
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 ASN 56 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-10A HIS* 3.0 32.7 + - - +
-9A HIS* 3.5 21.4 + - - -
-6A GLU* 5.1 0.4 + - - -
52D ALA* 3.0 17.0 + - + +
54D LYS 3.8 0.6 - - - -
55D THR* 1.3 78.6 - - - +
57D TRP* 1.3 95.2 + - + +
58D ILE 3.6 1.3 - - - -
59D PRO* 3.7 2.3 - - - +
60D ARG* 3.0 35.7 + - - +
76D PHE* 3.6 23.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-9A HIS* 5.2 2.7 - + - -
165C TRP* 5.3 9.6 - + - -
169C LEU* 5.6 2.5 - - + -
52D ALA* 3.6 31.3 + - - +
53D GLU* 3.8 9.1 + - - -
56D ASN* 1.3 98.2 - - - +
58D ILE* 1.3 61.4 + - - +
60D ARG* 6.2 0.2 - - - -
61D LEU* 3.0 27.7 + - - +
104D ASN* 6.2 0.7 - - - +
135D LEU* 3.5 34.0 - - + +
138D ALA* 3.8 23.6 - - + -
139D TRP* 3.3 75.6 - + + -
142D HIS* 3.4 36.8 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ALA 5.4 0.2 + - - -
53D GLU 5.3 1.0 + - - +
57D TRP* 1.3 74.1 - - - +
59D PRO* 1.3 71.9 - - + +
61D LEU* 3.1 27.3 + - + +
62D ARG* 2.9 49.0 + - + +
104D ASN* 3.5 57.1 - - + +
107D THR* 3.7 22.7 - - + -
108D LEU* 4.1 8.1 - - - +
111D LEU* 4.9 0.4 - - + -
139D TRP* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLU 4.9 3.6 - - - +
54D LYS 3.7 16.4 - - - +
55D THR* 3.6 29.2 - - - +
56D ASN 3.7 9.6 - - - +
58D ILE* 1.3 97.0 - - + +
60D ARG* 1.3 57.4 + - + +
62D ARG* 3.6 12.0 - - + +
63D PHE* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-6A GLU* 3.1 27.3 + - - -
-5A ASN* 5.2 1.8 + - - -
165C TRP* 3.9 9.9 - - - +
55D THR 5.3 0.4 - - - +
56D ASN* 3.0 33.3 + - - +
57D TRP* 3.9 0.4 - - - +
59D PRO* 1.3 74.9 - - + +
61D LEU* 1.3 57.2 + - - +
63D PHE* 3.2 7.1 + - + +
64D ILE* 2.8 38.3 + - - +
73D PHE* 3.2 48.9 - - + +
74D PRO* 4.5 8.8 + - + -
76D PHE* 3.2 39.8 - - + -
124D HIS* 3.8 15.2 + - - -
125D PRO* 4.6 7.1 - - - +
135D LEU* 3.8 21.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
57D TRP 3.0 14.4 + - - +
58D ILE* 3.3 26.2 - - + +
60D ARG* 1.3 75.4 - - - +
62D ARG* 1.3 61.6 + - - +
64D ILE* 3.2 4.9 + - + +
65D LEU* 3.0 34.6 + - + +
108D LEU* 3.8 28.3 - - + -
111D LEU* 4.0 18.8 - - + -
112D VAL* 3.9 10.1 - - + -
132D VAL* 3.5 40.8 - - + -
135D LEU* 3.3 16.0 - - + +
136D LEU* 4.4 6.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
58D ILE* 2.9 32.8 + - - +
59D PRO* 3.6 10.2 - - - +
61D LEU* 1.3 73.2 - - - +
63D PHE* 1.3 57.8 + - - +
65D LEU* 3.3 5.0 + - - +
66D GLN* 2.9 42.5 + - - +
107D THR* 3.8 30.9 + - - +
111D LEU* 3.8 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D PRO 3.0 14.3 + - - +
60D ARG* 3.2 8.7 + - - +
62D ARG* 1.3 77.9 - - - +
64D ILE* 1.3 66.0 + - - +
66D GLN* 4.7 1.3 - - - -
67D GLU* 2.8 58.9 + - + +
68D GLY 3.8 2.1 + - - -
71D LYS* 3.6 30.5 - - + -
72D PRO 3.4 26.5 - - - -
73D PHE* 3.9 18.2 - + + -
74D PRO* 3.7 25.8 - - + -
123D ALA 6.2 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
60D ARG 2.8 17.4 + - - +
61D LEU* 3.2 6.7 + - - +
63D PHE* 1.3 72.4 - - - +
65D LEU* 1.3 62.9 + - + +
68D GLY* 3.0 27.9 + - - +
73D PHE* 3.7 26.0 - - + -
120D ARG* 3.8 18.0 + - + +
121D THR 3.7 21.8 - - - +
122D GLY* 4.1 12.6 - - - +
130D VAL* 4.7 4.7 - - + -
131D LYS 4.2 9.0 - - - +
132D VAL* 3.8 31.9 - - + +
135D LEU* 4.0 27.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
61D LEU* 3.0 32.3 + - + +
62D ARG* 4.0 3.6 - - - +
64D ILE* 1.3 76.7 - - - +
66D GLN* 1.3 60.7 + - - +
68D GLY 4.9 0.3 + - - -
111D LEU* 3.6 51.6 - - + +
112D VAL* 4.4 2.2 - - + -
117D ASP* 4.8 5.6 - - + +
120D ARG* 3.1 58.3 + - + +
132D VAL* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ARG* 2.9 26.7 + - - +
63D PHE* 4.2 1.5 - - - +
65D LEU* 1.3 81.1 - - + +
67D GLU* 1.3 83.2 + - + +
68D GLY 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D PHE* 2.8 60.2 + - + +
66D GLN* 1.3 103.2 - - + +
68D GLY* 1.3 64.5 + - - +
69D GLU 3.5 0.2 + - - -
70D HIS* 3.4 24.3 + - - +
71D LYS* 2.9 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D PHE* 3.8 3.2 + - - +
64D ILE 3.0 15.4 + - - -
65D LEU 4.7 0.6 + - - -
66D GLN 3.7 1.4 - - - -
67D GLU* 1.3 82.5 - - - +
69D GLU* 1.3 60.4 + - - -
70D HIS* 3.3 2.0 + - - -
71D LYS 3.8 10.2 - - - +
120D ARG* 6.3 0.4 - - - -
121D THR 3.4 20.2 - - - -
122D GLY* 3.6 9.9 - - - -
----------------------------------------------------------
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