Contacts of the helix formed by residues 89 - 112 (chain B) 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 PRO 89 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA 3.2 8.7 - - - +
88B VAL* 1.3 86.5 - - - +
90B ILE* 1.3 66.6 + - - +
91B SER* 3.8 17.5 - - - +
92B GLU* 3.0 38.5 + - + +
93B ARG* 3.3 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.7 7.0 - - + -
24B GLU* 5.2 2.2 - - + +
25B GLY 5.7 1.1 - - - +
31B HIS* 3.5 54.3 - - + +
42B VAL* 5.1 0.4 - - + -
43B TYR* 3.8 41.1 - - + +
46B VAL* 4.8 5.8 - - + -
88B VAL 3.4 1.6 + - - -
89B PRO* 1.3 71.6 - - - +
91B SER* 1.3 58.9 + - - +
93B ARG* 3.0 11.9 + - + +
94B PHE* 3.0 60.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.3 33.6 - - - +
89B PRO* 3.8 13.1 - - - +
90B ILE* 1.3 80.5 - - - +
92B GLU* 1.3 67.2 + - - +
94B PHE* 3.6 3.4 + - - +
95B LYS* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 3.7 15.9 - - + -
89B PRO* 3.0 34.2 + - + +
91B SER* 1.3 86.4 + - - +
93B ARG* 1.3 65.4 + - - +
95B LYS* 3.4 12.2 + - + +
96B GLU* 3.1 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 2.9 25.0 + - + +
46B VAL* 4.2 13.7 - - + -
47B VAL* 3.9 28.4 - - + +
50B ILE* 3.4 30.7 - - + +
54B LYS* 5.8 1.8 - - - +
85B SER* 2.9 34.4 + - - +
88B VAL* 3.8 22.8 - - - +
89B PRO 3.3 9.4 + - - +
90B ILE* 3.0 15.7 + - + +
92B GLU* 1.3 78.2 - - - +
94B PHE* 1.3 56.6 + - - +
96B GLU* 3.1 20.4 + - - -
97B PHE* 2.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 5.1 4.5 - - - +
19B LEU* 3.9 19.3 - - + -
20B GLU* 4.1 34.2 - - + +
23B LEU* 3.6 32.3 - - + -
24B GLU* 2.8 42.8 - - + +
46B VAL* 4.3 16.4 - - + -
90B ILE* 3.0 49.3 + - + -
91B SER 3.8 4.5 - - - +
92B GLU 3.4 0.2 - - - -
93B ARG* 1.3 75.4 - - - +
95B LYS* 1.3 62.8 + - - +
97B PHE* 3.4 8.1 + + - +
98B GLN* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU* 6.0 0.4 - - - -
91B SER 3.3 11.7 + - - +
92B GLU* 3.5 13.7 - - + +
94B PHE* 1.3 77.4 - - - +
96B GLU* 1.3 63.2 + - - +
98B GLN* 3.9 4.4 - - - +
99B GLN* 3.1 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 3.7 18.3 - - + +
54B LYS* 2.8 31.6 + - - -
88B VAL* 6.1 0.2 - - - +
92B GLU 3.1 12.5 + - - +
93B ARG* 3.1 32.5 + - - +
95B LYS* 1.3 77.6 - - - +
97B PHE* 1.3 56.2 + - - +
99B GLN* 3.3 5.6 + - - +
100B LEU* 2.9 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 3.9 20.2 - - + -
16B PRO* 3.8 33.4 - - + -
19B LEU* 4.2 16.8 - - + -
46B VAL* 5.2 7.4 - - + -
49B LEU* 3.9 26.7 - - + -
50B ILE* 3.8 21.5 - - + +
53B GLU* 3.7 28.5 - - + -
93B ARG 2.9 15.9 + - - +
94B PHE* 3.9 7.9 - + - +
96B GLU* 1.3 77.0 - - - +
98B GLN* 1.3 57.5 + - - +
100B LEU* 4.7 2.5 - - - -
101B ARG* 2.9 58.5 + - - +
143B ASP* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU 4.7 7.9 + - - +
16B PRO* 3.8 30.0 - - + +
17B LYS* 3.9 24.4 + - - +
20B GLU* 5.4 7.9 - - - +
94B PHE 3.0 19.0 + - - +
95B LYS* 3.9 5.4 - - - +
97B PHE* 1.3 75.5 - - - +
99B GLN* 1.3 64.5 + - - +
101B ARG* 4.5 1.8 - - - +
102B LYS* 3.0 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LYS* 3.1 19.0 + - + +
96B GLU* 3.3 5.8 + - - +
98B GLN* 1.3 77.6 - - - +
100B LEU* 1.3 65.6 + - + +
102B LYS* 3.6 23.7 + - - +
103B GLU* 2.6 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 3.8 34.5 - - + +
53B GLU* 3.8 20.6 - - + +
54B LYS* 3.9 29.8 - - + -
96B GLU* 2.9 32.0 + - + +
97B PHE* 4.1 2.7 - - - +
99B GLN* 1.3 73.9 - - + +
101B ARG* 1.3 58.0 + - - +
103B GLU* 3.4 18.3 + - - +
104B ASN* 2.8 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 2.7 48.6 + - - +
13B GLU* 4.8 1.1 - - - -
15B THR* 3.8 8.1 - - - -
16B PRO* 3.7 18.6 - - + +
49B LEU* 5.6 0.4 - - - +
53B GLU* 2.9 43.1 + - - +
97B PHE* 2.9 32.2 + - + +
98B GLN* 3.9 4.5 - - - +
100B LEU* 1.3 78.0 - - - +
102B LYS* 1.3 57.1 + - - +
104B ASN* 3.7 0.3 - - - -
105B LEU* 2.9 54.1 + - + +
139B TRP* 3.5 16.7 - - - +
143B ASP* 2.7 43.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLN* 3.0 30.9 + - + +
99B GLN* 3.6 24.8 + - - +
100B LEU 3.3 0.2 - - - -
101B ARG* 1.3 76.6 - - - +
103B GLU* 1.3 62.5 + - - +
105B LEU* 3.4 7.3 + - - +
106B ASN* 3.2 35.5 + - - +
109B ARG* 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLN* 2.6 50.0 + - - +
100B LEU* 3.6 21.5 - - - +
102B LYS* 1.3 79.0 - - + +
104B ASN* 1.3 60.6 + - - +
106B ASN* 3.2 12.3 + - - +
107B THR* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 2.6 60.3 + - - +
57B TRP* 6.3 0.4 - - - +
58B ILE* 3.5 35.6 - - + +
100B LEU* 2.8 22.9 + - - +
101B ARG 3.3 2.7 + - - +
103B GLU* 1.3 74.4 - - - +
105B LEU* 1.3 59.6 - - - +
107B THR* 3.4 4.1 + - - -
108B LEU* 2.8 28.1 + - - +
139B TRP* 4.1 9.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.6 10.0 - - + +
12B LEU* 3.9 22.0 - - + -
13B GLU* 3.5 43.1 - - + +
101B ARG* 2.9 31.3 + - + +
102B LYS* 3.4 7.2 + - - +
104B ASN* 1.3 76.1 - - - +
106B ASN* 1.3 62.3 + - - +
108B LEU* 3.5 26.7 - - + +
109B ARG* 3.1 47.8 + - - +
139B TRP* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS* 3.2 29.1 + - - +
103B GLU* 3.2 12.5 + - - +
105B LEU* 1.3 75.1 - - - +
107B THR* 1.3 64.3 + - - +
109B ARG* 3.0 25.9 + - - +
110B SER* 3.1 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 3.8 12.3 - - + +
62B ARG* 3.6 31.4 + - - +
103B GLU* 3.0 15.6 + - - +
104B ASN* 3.7 11.5 + - - -
105B LEU 3.4 0.2 - - - -
106B ASN* 1.3 73.3 - - - +
108B LEU* 1.3 66.9 + - - +
110B SER* 2.9 9.8 + - - -
111B LEU* 2.9 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B MSE 3.8 17.7 - - + -
8B ALA* 6.4 0.7 - - + -
9B ILE* 4.1 19.3 - - + -
12B LEU* 4.4 7.4 - - + -
58B ILE* 4.1 8.8 - - + +
61B LEU* 3.7 17.3 - - + -
104B ASN 2.8 20.3 + - - +
105B LEU* 3.5 27.8 - - + +
107B THR* 1.3 72.0 - - - +
109B ARG* 1.3 58.8 + - - +
111B LEU* 3.0 0.5 + - - +
112B VAL* 2.9 31.4 + - + +
136B LEU* 3.6 39.0 - - + -
139B TRP* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B MSE 4.8 2.7 - - + -
9B ILE* 3.8 43.8 - - + +
13B GLU* 4.3 8.1 + - - -
102B LYS 5.2 0.2 + - - -
105B LEU* 3.1 38.1 + - - +
106B ASN* 3.0 33.9 + - - +
107B THR 3.2 0.2 - - - -
108B LEU* 1.3 79.2 - - - +
110B SER* 1.3 59.6 + - - +
112B VAL 3.6 9.4 - - - +
113B GLN* 3.5 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASN 3.1 13.7 + - - -
107B THR* 2.9 14.8 + - - -
109B ARG* 1.3 77.2 - - - +
111B LEU* 1.3 64.3 + - - +
113B GLN* 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 4.9 1.1 - - + +
61B LEU* 3.9 25.8 - - + -
62B ARG* 3.9 36.1 - - + +
65B LEU* 3.3 33.1 - - + +
107B THR* 2.9 39.2 + - + +
108B LEU 3.9 1.6 - - - +
110B SER* 1.3 82.8 - - - +
112B VAL* 1.3 61.3 + - - +
113B GLN* 3.8 4.8 + - - +
117B ASP* 4.0 6.8 - - - +
120B ARG* 5.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B MSE 3.6 28.0 - - + +
61B LEU* 3.9 30.1 - - + -
65B LEU* 4.4 3.6 - - + -
108B LEU* 2.9 21.8 + - + +
109B ARG* 3.6 9.1 - - - +
111B LEU* 1.3 80.0 - - - +
113B GLN* 1.3 60.6 + - - +
114B SER 3.9 17.2 + - - +
117B ASP* 4.0 12.1 - - + -
118B LEU* 4.0 24.7 - - + -
132B VAL* 4.1 8.7 - - + -
136B LEU* 4.6 0.4 - - + -
----------------------------------------------------------
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