Contacts of the helix formed by residues 4 - 24 (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 GLN 4 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ARG* 5.5 0.7 - - - +
158A TYR* 3.8 3.6 + - - -
2B ASN 3.3 6.0 + - - +
3B PHE* 1.3 88.9 + - - +
5B MSE 1.3 66.4 + - - +
6B ASN* 3.3 19.7 - - - +
7B GLU* 3.2 26.4 + - + +
8B ALA* 2.9 23.9 + - - +
115B GLU* 4.9 16.0 + - - +
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Residues in contact with MSE 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.5 18.0 - - + -
4B GLN* 1.3 73.9 + - - +
6B ASN* 1.3 63.7 + - - +
8B ALA* 3.3 2.4 + - - +
9B ILE* 3.0 43.5 + - + +
108B LEU* 3.8 31.4 - - + +
109B ARG* 4.8 3.6 - - + -
112B VAL* 3.6 38.6 - - + +
115B GLU* 6.5 0.4 - - + -
118B LEU* 4.6 10.2 - - + +
136B LEU* 4.2 21.5 - - - -
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Residues in contact with ASN 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 5.5 1.8 - - - -
4B GLN* 3.3 25.1 - - - +
5B MSE 1.3 77.8 - - - +
7B GLU* 1.3 81.3 + - - +
9B ILE* 3.4 9.1 + - - +
10B GLN* 3.1 41.4 + - - +
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 3.3 30.3 + - - -
29A SER* 3.4 10.3 + - - -
30A TRP* 3.0 31.1 + - + +
157A ARG* 2.9 33.8 + - - -
158A TYR* 4.4 1.7 + - - +
2B ASN 4.2 1.6 - - - +
4B GLN* 3.2 27.3 + - + +
6B ASN* 1.3 97.7 + - - +
8B ALA* 1.3 64.0 + - - +
10B GLN* 3.3 18.3 + - - +
11B LEU 3.4 3.3 + - - -
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Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 4.6 2.2 - - - -
158A TYR* 3.8 8.6 + - - +
3B PHE* 3.5 33.7 - - + -
4B GLN 2.9 11.4 + - - +
5B MSE 3.6 5.4 - - - +
7B GLU* 1.3 72.7 - - - +
9B ILE* 1.3 60.6 + - + +
11B LEU* 3.2 5.2 + - - +
12B LEU* 2.9 36.4 + - + +
108B LEU* 6.4 0.7 - - + -
136B LEU* 5.8 0.7 - - + -
140B VAL* 3.6 19.2 - - + +
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Residues in contact with ILE 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B MSE 3.0 46.5 + - + +
6B ASN* 3.7 7.6 - - - +
8B ALA* 1.3 74.7 - - + +
10B GLN* 1.3 64.7 + - - +
12B LEU* 4.4 6.5 - - - +
13B GLU* 2.9 42.7 + - + +
105B LEU* 4.6 6.7 - - + +
108B LEU* 4.1 20.4 - - + -
109B ARG* 3.8 39.3 - - + +
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Residues in contact with GLN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY 4.3 6.7 + - - +
26A LEU* 3.6 16.7 - - + -
27A SER* 2.8 43.7 + - - +
30A TRP* 3.6 8.8 + - - -
6B ASN* 3.1 33.3 + - - +
7B GLU* 3.4 9.4 - - - +
8B ALA 3.2 0.6 - - - -
9B ILE* 1.3 77.3 - - - +
11B LEU* 1.3 64.4 + - - +
13B GLU* 3.5 17.7 - - - +
14B ARG* 3.1 30.4 + - - +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.7 24.9 - - + +
26A LEU* 4.4 8.3 - - + -
30A TRP* 3.4 40.6 - - + +
154A MSE 3.3 33.9 - - + -
7B GLU 3.4 3.2 + - - +
8B ALA 3.2 9.2 + - - +
10B GLN* 1.3 76.7 - - - +
12B LEU* 1.3 67.5 + - + +
14B ARG* 2.9 15.8 + - + +
15B THR* 3.3 17.4 + - - +
140B VAL* 3.6 20.6 - - + -
143B ASP* 5.2 0.9 - - + -
144B LEU* 3.8 15.0 - - + -
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 2.9 25.3 + - + +
9B ILE 4.0 1.6 - - - +
11B LEU* 1.3 78.3 - - + +
13B GLU* 1.3 61.3 + - - +
14B ARG 3.3 0.9 + - - -
16B PRO* 3.8 3.1 - - - +
101B ARG* 2.7 34.8 + - - +
105B LEU* 3.9 27.4 - - + -
108B LEU* 4.4 7.6 - - + -
136B LEU* 5.0 2.5 - - + +
139B TRP* 3.7 61.9 - - + +
140B VAL* 3.8 21.3 - - + -
143B ASP* 3.7 17.7 - - - +
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 2.9 33.8 + - - +
10B GLN* 3.5 17.0 - - - +
12B LEU* 1.3 78.5 - - - +
14B ARG* 1.3 80.0 + - + +
16B PRO* 3.9 6.9 - - - +
17B LYS* 3.9 15.8 - - - +
98B GLN* 4.7 8.5 + - - +
101B ARG* 4.8 1.3 - - - -
105B LEU* 3.5 19.7 - - + -
109B ARG* 4.3 7.3 + - - -
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Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL 3.8 12.4 + - - +
22A PHE* 3.3 27.1 + - + +
24A GLU 3.0 29.0 + - - -
25A GLY* 3.6 17.5 + - - -
26A LEU* 3.6 15.4 - - - +
10B GLN* 3.1 26.2 + - - +
11B LEU* 2.9 11.6 + - - +
13B GLU* 1.3 103.6 + - - +
15B THR* 1.3 63.9 + - - +
16B PRO* 3.2 4.3 - - - -
17B LYS* 3.2 28.0 + - - +
18B THR* 2.9 33.1 + - - +
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Residues in contact with THR 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 5.3 2.1 - - - -
11B LEU* 3.3 17.2 + - - +
14B ARG* 1.3 76.3 - - - +
16B PRO* 1.4 63.7 - - - +
18B THR* 3.3 5.8 + - - -
19B LEU* 2.9 38.0 + - + +
49B LEU* 4.9 2.9 - - + -
97B PHE* 3.9 15.5 - - + -
101B ARG* 3.8 2.9 - - - -
143B ASP* 2.7 39.6 + - + +
144B LEU* 6.1 0.2 - - - +
147B ILE* 4.0 26.4 - - + +
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Residues in contact with PRO 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU 3.8 10.8 - - - +
13B GLU 3.9 6.3 - - - +
14B ARG 3.4 4.9 - - - -
15B THR* 1.4 93.2 - - - +
17B LYS* 1.3 57.3 + - - +
19B LEU* 3.4 2.8 + - + +
20B GLU* 3.0 29.0 + - - +
94B PHE* 5.1 4.8 - - - +
97B PHE* 3.8 27.4 - - + +
98B GLN* 3.8 34.5 - - + +
101B ARG* 3.7 29.8 - - + -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.2 29.7 + - + +
13B GLU* 3.9 19.5 - - - +
14B ARG* 3.3 43.4 - - + +
16B PRO* 1.3 76.5 - - - +
18B THR* 1.3 60.3 + - - +
20B GLU* 3.4 11.4 + - - +
21B VAL* 2.9 35.9 + - + +
98B GLN* 3.9 15.8 + - - +
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Residues in contact with THR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 4.0 17.3 - - + +
21A VAL* 3.5 12.4 - - - +
22A PHE* 3.4 54.2 - - + -
14B ARG 2.9 18.5 + - - -
15B THR* 3.5 6.7 - - - -
17B LYS* 1.3 76.8 - - - +
19B LEU* 1.3 66.3 + - + +
21B VAL* 3.4 1.9 + - - +
22B PHE* 3.0 27.0 + - + +
147B ILE* 5.3 9.9 - - + -
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 2.9 26.8 + - + +
16B PRO* 3.9 4.0 - - + +
18B THR* 1.3 74.6 - - + +
20B GLU* 1.3 57.1 + - - +
22B PHE* 4.3 11.4 - - + -
23B LEU* 2.9 42.3 + - + +
46B VAL* 4.4 11.0 - - + -
49B LEU* 3.7 30.3 - - + -
94B PHE* 3.9 11.8 - - + -
97B PHE* 4.2 15.5 - - + -
147B ILE* 4.0 27.4 - - + -
150B ILE* 4.1 24.7 - - + -
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PRO 3.0 18.3 + - - +
17B LYS* 3.7 10.2 - - - +
18B THR 3.3 0.4 - - - -
19B LEU* 1.3 76.2 - - - +
21B VAL* 1.3 60.2 + - + +
24B GLU* 2.8 63.1 + - + +
94B PHE* 4.1 31.7 - - + +
95B LYS* 6.0 0.2 - - - -
98B GLN* 5.4 7.4 - - - +
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 3.8 21.2 + - + +
17A LYS* 3.8 33.0 - - + +
18A THR* 3.8 19.5 - - - +
21A VAL* 4.3 21.3 - - + -
17B LYS* 2.9 25.7 + - + +
18B THR 3.4 3.1 + - - +
20B GLU* 1.3 74.7 - - + +
22B PHE* 1.3 61.4 + - - +
24B GLU* 4.5 2.0 + - - +
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Residues in contact with PHE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.5 12.5 - - + +
14A ARG* 3.3 26.2 - - + +
15A THR* 5.3 4.7 - - - -
18A THR* 3.5 29.4 - - + -
144A LEU* 3.6 28.0 - - + -
147A ILE* 4.1 20.2 - - + -
18B THR* 3.0 20.2 + - + +
19B LEU* 3.8 11.0 - - + +
20B GLU 3.2 0.2 - - - -
21B VAL* 1.3 78.7 - - - +
23B LEU* 1.3 73.9 + - + +
26B LEU* 3.5 10.4 - - - +
147B ILE* 6.0 2.5 - - + -
150B ILE* 4.4 5.6 - - + -
151B VAL* 3.8 24.9 - - + -
154B MSE 3.8 20.0 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 2.9 24.3 + - + +
22B PHE* 1.3 90.1 - - + +
24B GLU* 1.3 65.9 + - - +
25B GLY 3.2 0.2 + - - -
26B LEU* 3.0 22.7 + - + +
30B TRP 5.7 0.4 - - - +
31B HIS* 2.8 30.6 + - + +
42B VAL* 3.6 28.5 - - + -
46B VAL* 4.3 14.6 - - + -
90B ILE* 4.7 1.8 - - + -
94B PHE* 3.6 20.4 - - + -
150B ILE* 4.2 10.5 - - + -
154B MSE 3.8 30.3 - - - -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.0 23.7 + - - -
20B GLU* 2.8 39.8 + - + +
21B VAL 4.7 1.4 - - - +
22B PHE 3.7 0.4 - - - -
23B LEU* 1.3 75.5 - - - +
25B GLY* 1.3 62.4 - - - +
26B LEU 3.2 0.7 + - - -
31B HIS* 5.3 0.7 - - - -
90B ILE* 5.2 1.6 - - + +
91B SER* 3.3 26.4 - - - +
94B PHE* 2.8 38.7 - - + +
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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
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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) + - + + + + + -
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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