Contacts of the helix formed by residues 9 - 28 (chain B) in PDB entry 2W9M
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 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ALA 3.5 3.1 + - - -
8B PRO* 1.3 74.7 - - - +
10B ARG* 1.3 61.8 + - - +
11B HIS* 3.3 16.8 + - - +
12B ARG* 2.8 31.9 + - - +
13B LEU* 3.1 10.9 + - - +
50B GLU* 3.2 16.6 - - - -
51B THR* 3.5 1.6 - - - -
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Residues in contact with ARG 10 (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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9B SER* 1.3 73.8 - - - +
11B HIS* 1.3 110.1 + - - +
13B LEU* 3.1 15.6 + - + +
14B VAL* 3.0 31.2 + - + +
44B LEU* 4.9 4.4 - - + +
47B LEU* 2.9 67.8 - - + +
49B GLU 4.6 4.0 - - - +
50B GLU* 3.0 33.3 + - - +
51B THR* 3.5 5.1 + - - +
54B LEU* 5.5 5.8 - - + -
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Residues in contact with HIS 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 3.0 9.8 - - - +
10B ARG* 1.3 122.6 + - - +
12B ARG* 1.3 61.4 + - - +
14B VAL* 3.9 6.7 - - + +
15B HIS* 3.0 72.2 + + - +
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Residues in contact with ARG 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 3.7 14.4 - - + -
9B SER* 2.8 29.2 + - - +
11B HIS* 1.3 78.2 - - - +
13B LEU* 1.3 62.6 + - - +
15B HIS* 3.5 5.3 + - - +
16B ALA* 3.1 29.4 + - - +
19B ARG* 4.0 24.6 - - - +
76B PHE* 3.9 23.5 - - - -
85B LEU* 5.6 2.8 - - - +
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Residues in contact with LEU 13 (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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8B PRO* 4.1 15.3 - - + +
9B SER 3.1 10.5 + - - +
10B ARG* 3.5 10.5 - - - +
12B ARG* 1.3 76.7 - - - +
14B VAL* 1.3 63.7 + - - +
16B ALA* 3.3 2.6 + - - +
17B LEU* 3.1 29.9 + - - +
44B LEU* 4.1 11.4 - - + -
51B THR* 4.1 14.8 - - + +
54B LEU* 5.1 3.6 - - + -
59B PHE* 3.6 36.6 - - + -
73B LEU* 3.8 20.3 - - + +
76B PHE* 3.3 37.9 - - + -
77B ALA* 4.9 4.0 - - - +
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Residues in contact with VAL 14 (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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10B ARG 3.0 21.0 + - - +
11B HIS* 3.9 9.2 - - + +
13B LEU* 1.3 76.1 - - - +
15B HIS* 1.3 63.3 + - + +
17B LEU* 3.4 9.6 + - - +
18B GLU* 3.0 47.9 + - + +
41B ALA* 3.8 15.7 - - - +
44B LEU* 3.7 36.6 - - + +
45B GLU* 4.0 18.4 - - - +
47B LEU* 4.9 3.4 - - + -
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Residues in contact with HIS 15 (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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11B HIS* 3.0 57.6 + + - +
12B ARG* 4.0 6.7 - - - +
13B LEU 3.4 0.2 - - - -
14B VAL* 1.3 81.6 - - + +
16B ALA* 1.3 60.6 + - - +
18B GLU* 3.6 20.9 + - - +
19B ARG* 2.8 63.6 + - - +
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Residues in contact with ALA 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 ARG* 3.1 22.9 + - - +
13B LEU 3.6 5.6 - - - +
14B VAL 3.2 0.2 - - - -
15B HIS* 1.3 77.0 - - - +
17B LEU* 1.3 54.1 + - - +
19B ARG* 4.1 4.4 - - - +
20B THR* 2.7 38.2 + - - -
76B PHE* 3.6 23.1 - - + -
82B PHE* 3.9 19.1 - - + -
85B LEU* 3.4 14.8 - - + +
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Residues in contact with LEU 17 (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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13B LEU 3.1 17.9 + - - +
14B VAL* 3.7 5.6 - - - +
16B ALA* 1.3 74.3 - - - +
18B GLU* 1.3 65.0 + - - +
20B THR* 3.2 7.1 + - - -
21B ALA* 3.0 22.3 + - - +
37B TYR* 3.8 28.6 - - + +
40B ALA* 3.9 27.6 - - + +
41B ALA* 3.9 16.8 - - + +
44B LEU* 4.4 10.1 - - + -
69B ILE* 4.1 15.5 - - + -
73B LEU* 4.3 19.5 - - + -
82B PHE* 3.6 26.0 - - + -
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Residues in contact with GLU 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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14B VAL* 3.0 37.3 + - - +
15B HIS* 3.6 29.2 + - - +
17B LEU* 1.3 75.9 - - - +
19B ARG* 1.3 63.7 + - - +
21B ALA* 3.0 18.7 + - - +
22B ASP* 3.0 22.2 + - - +
38B ARG* 5.3 8.1 - - + -
41B ALA* 4.0 16.3 - - + +
45B GLU* 4.4 9.2 - - - +
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Residues in contact with ARG 19 (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 ARG* 4.0 23.9 - - - +
15B HIS* 2.8 70.1 + - - +
16B ALA* 4.0 5.9 - - - +
18B GLU* 1.3 73.2 - - - +
20B THR* 1.3 60.4 + - - +
22B ASP* 3.5 15.5 + - + +
23B LEU* 3.2 25.7 + - + +
85B LEU* 4.3 16.5 - - + +
100B LEU* 6.1 1.6 - - + -
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Residues in contact with THR 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 ALA 2.7 22.9 + - - -
17B LEU 3.4 5.6 - - - -
19B ARG* 1.3 75.8 - - - +
21B ALA* 1.3 64.8 + - - +
23B LEU* 3.2 6.9 + - + +
24B LEU* 3.1 31.4 + - + +
37B TYR* 3.8 31.6 - - + -
82B PHE* 3.3 8.5 - - - -
84B PRO* 4.3 13.6 - - + +
85B LEU* 3.1 26.2 - - + +
370B TYR* 5.2 7.4 - - + -
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Residues in contact with ALA 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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17B LEU 3.0 12.4 + - - +
18B GLU 3.0 8.9 + - - +
20B THR* 1.3 76.2 - - - +
22B ASP* 1.3 57.8 + - - +
24B LEU* 3.1 13.6 + - - +
25B ASP* 2.9 34.7 + - - +
34B SER* 3.7 23.6 - - - +
37B TYR* 4.1 2.9 - - + +
38B ARG* 3.8 29.4 - - + +
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Residues in contact with ASP 22 (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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18B GLU* 3.0 22.3 + - - +
19B ARG* 3.6 19.0 - - + +
20B THR 3.2 0.2 - - - -
21B ALA* 1.3 78.0 - - - +
23B LEU* 1.3 61.9 + - - +
25B ASP* 3.3 10.7 + - - +
26B ILE* 3.1 29.5 + - + +
38B ARG* 5.4 5.4 + - - -
100B LEU* 6.2 3.6 - - + -
107B PRO* 3.6 29.2 - - + +
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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 ARG* 3.2 10.5 + - + +
20B THR* 3.2 10.6 + - + +
22B ASP* 1.3 78.8 - - - +
24B LEU* 1.3 63.4 + - + +
26B ILE* 3.1 29.1 + - + +
27B LEU* 3.9 8.1 + - + +
28B GLY* 5.1 0.2 - - - -
85B LEU* 4.2 19.3 - - + -
88B ALA* 3.6 31.6 - - + -
92B LEU* 3.5 26.9 - - + -
96B LEU* 5.0 2.7 - - + -
100B LEU* 4.0 22.2 - - + -
370B TYR* 5.2 12.5 - - + +
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Residues in contact with LEU 24 (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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20B THR* 3.1 23.8 + - + +
21B ALA 3.1 6.3 + - - +
23B LEU* 1.3 73.8 - - + +
25B ASP* 1.3 65.8 + - - +
26B ILE 3.3 0.5 + - - -
28B GLY* 3.4 23.0 - - - -
29B GLY 4.1 0.5 + - - -
30B GLU* 3.9 32.7 + - + +
33B LYS* 3.9 16.4 - - + -
34B SER* 3.9 30.7 - - - +
37B TYR* 4.1 17.0 - - + -
369B TYR* 4.6 10.1 - - + -
370B TYR* 4.3 24.7 - - + -
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Residues in contact with ASP 25 (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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21B ALA 2.9 12.9 + - - +
22B ASP* 3.5 16.2 - - - +
24B LEU* 1.3 75.7 - - - +
26B ILE* 1.3 63.1 + - - +
28B GLY* 4.4 3.3 - - - -
30B GLU 4.4 2.2 - - - +
31B ASP* 4.6 5.7 - - - +
34B SER* 3.0 14.9 + - - -
38B ARG* 2.8 42.9 + - - -
107B PRO* 4.2 16.5 - - + +
111B ARG* 4.9 5.4 + - - -
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Residues in contact with ILE 26 (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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22B ASP* 3.1 21.9 + - + +
23B LEU* 3.1 19.0 + - + +
24B LEU 3.1 1.8 - - - -
25B ASP* 1.3 79.1 - - - +
27B LEU* 1.3 80.8 + - + +
28B GLY* 3.8 0.2 - - - -
96B LEU* 5.1 15.0 - - + -
100B LEU* 3.8 29.4 - - + -
107B PRO* 3.9 24.9 - - + +
110B ILE* 4.0 20.9 - - + -
111B ARG* 3.0 39.2 + - + +
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Residues in contact with LEU 27 (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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23B LEU* 3.9 6.2 + - + +
26B ILE* 1.3 89.9 - - + +
28B GLY* 1.3 56.4 + - - +
92B LEU* 4.1 12.8 - - + -
96B LEU* 5.1 7.2 - - + -
111B ARG* 2.8 21.9 + - - +
114B TRP* 5.1 11.7 - - + +
338B SER 5.0 2.4 - - - +
339B ASP* 4.0 38.1 - - + +
340B GLY 5.5 1.8 - - - +
370B TYR 3.3 27.1 - - - +
371B ALA* 4.1 4.5 - - - -
372B ASN* 4.8 20.5 + - + +
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Residues in contact with GLY 28 (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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23B LEU 5.1 0.2 - - - -
24B LEU* 3.4 15.0 - - - -
25B ASP 4.4 2.9 - - - -
26B ILE 3.8 1.1 - - - -
27B LEU* 1.3 85.1 + - - +
29B GLY* 1.3 59.3 + - - +
30B GLU* 3.3 21.9 + - - +
111B ARG* 3.4 4.8 - - - +
372B ASN* 5.4 4.8 - - - +
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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
------------------------------------------------------------
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