Contacts of the helix formed by residues 28 - 46 (chain B) in PDB entry 2AR0
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 28 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 4.0 11.2 - - + -
25B SER* 3.2 23.2 + - - +
27B GLN* 1.3 98.3 + - - +
29B TYR* 1.3 66.9 + - - +
30B VAL 3.4 2.0 - - - -
31B ASN* 3.2 22.5 + - + +
32B GLU* 3.0 30.0 + - - +
98B THR* 4.0 27.1 + - + +
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Residues in contact with TYR 29 (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 TRP* 5.8 0.2 - - - -
16B CYS* 3.4 32.8 - - + -
19B LEU* 3.8 20.2 - - + -
20B ARG* 3.0 51.6 + - - +
24B VAL* 3.7 11.3 + - + -
25B SER 2.9 22.9 - - - -
26B TYR* 3.4 47.2 - + - +
27B GLN 3.5 1.8 - - - -
28B ASN* 1.3 77.9 - - - +
30B VAL* 1.3 68.3 + - + +
32B GLU* 3.1 2.8 + - - +
33B LEU* 3.0 26.6 + - - +
502B LEU* 5.8 0.2 - - + -
506B MSE 3.2 28.9 - - + -
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN 5.0 2.2 + - - +
28B ASN 3.4 0.4 - - - -
29B TYR* 1.3 77.8 - - + +
31B ASN* 1.3 59.1 + - - +
33B LEU* 3.2 8.5 + - - +
34B ALA* 2.7 38.3 + - + +
499B LEU* 3.9 29.4 - - + +
500B SER* 5.8 0.2 - - - -
502B LEU* 4.4 13.2 - - + -
503B ASP* 3.5 52.5 - - + +
506B MSE 5.9 3.8 - - + -
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Residues in contact with ASN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN 4.4 6.8 + - - +
28B ASN* 3.2 29.3 + - + +
30B VAL* 1.3 86.8 - - - +
32B GLU* 1.3 66.4 + - + +
34B ALA* 3.8 5.2 - - - +
35B SER* 3.1 25.3 + - - -
95B VAL* 5.6 4.5 - - + +
503B ASP* 4.6 5.5 + - - -
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.5 19.5 - - + -
24B VAL* 3.6 20.9 - - + -
28B ASN* 3.0 22.5 + - - +
29B TYR 3.4 5.2 - - - +
31B ASN* 1.3 78.3 - - - +
33B LEU* 1.3 63.0 + - - +
35B SER* 3.6 5.3 + - - -
36B LEU* 3.5 29.0 + - + +
73B TYR* 4.1 7.0 + - - -
96B SER 3.8 5.0 - - - +
97B THR* 2.7 34.6 + - - -
98B THR* 3.0 30.5 + - - +
99B ILE* 4.0 7.5 - - + +
108B LEU* 5.6 0.2 - - + -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.9 15.9 - - + +
15B LEU* 4.1 17.7 - - + -
16B CYS* 3.5 25.8 - - - -
19B LEU* 4.0 15.0 - - + -
29B TYR 3.0 16.6 + - - +
30B VAL 3.6 5.4 - - - +
32B GLU* 1.3 75.3 - - - +
34B ALA* 1.3 56.3 + - - +
36B LEU* 3.3 2.0 + - - +
37B LEU* 2.7 44.0 + - + +
108B LEU* 4.4 5.6 - - + -
112B MSE 3.6 27.8 - - + +
499B LEU* 4.2 15.0 - - + -
502B LEU* 4.0 16.8 - - + -
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 2.7 25.1 + - + +
31B ASN* 3.8 6.3 - - - +
33B LEU* 1.3 72.3 - - - +
35B SER* 1.3 58.5 + - - +
37B LEU* 3.7 1.9 - - - +
38B PHE* 2.9 33.4 + - - +
492B MSE 5.8 0.3 - - - +
499B LEU* 4.2 22.6 - - + +
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASN 3.1 13.4 + - - -
32B GLU* 3.7 5.0 - - - -
33B LEU 3.2 0.2 - - - -
34B ALA* 1.3 81.3 - - - +
36B LEU* 1.3 64.5 + - - +
38B PHE* 3.1 10.0 + - - +
39B LEU* 3.2 20.1 + - - +
73B TYR* 3.6 21.5 + - - -
77B LEU* 4.9 2.4 - - - +
91B VAL* 6.3 1.1 - - - -
92B PHE* 3.9 23.6 - - - -
95B VAL* 4.1 20.4 - - - +
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLU* 3.5 15.9 + - + +
33B LEU 3.3 4.1 + - - +
35B SER* 1.3 79.5 - - - +
37B LEU* 1.3 63.7 + - - +
38B PHE 3.3 0.2 + - - -
39B LEU* 3.3 4.1 + - + -
40B LYS* 3.0 19.8 + - - +
58B TRP* 3.4 14.1 - - + -
61B LEU* 3.8 21.3 - - + -
73B TYR* 3.6 37.2 - - + +
99B ILE* 5.7 2.9 - - + -
105B ILE* 6.0 2.0 - - + -
108B LEU* 3.9 28.9 - - + -
109B VAL* 4.5 16.6 - - + +
112B MSE 3.6 28.3 - - + -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.1 21.8 - - + -
33B LEU* 2.7 26.4 + - + +
34B ALA* 3.7 3.8 - - - +
36B LEU* 1.3 74.3 - - - +
38B PHE* 1.3 57.8 + - - +
40B LYS* 3.3 5.3 + - + +
41B MSE 2.8 43.7 + - + +
112B MSE 3.9 24.5 - - + -
115B LEU* 4.5 26.0 - - + -
492B MSE 5.4 3.1 - - - -
495B LEU* 4.7 21.1 - - + -
499B LEU* 3.9 29.2 - - + -
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Residues in contact with PHE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA 2.9 18.6 + - - +
35B SER* 3.1 6.3 + - - +
37B LEU* 1.3 76.7 - - - +
39B LEU* 1.3 61.0 + - + +
41B MSE 3.2 3.0 + - + +
42B CYS* 2.9 58.0 + - - -
51B TYR* 5.4 7.6 - + + -
52B LEU* 4.5 4.9 - - + -
88B VAL* 4.3 17.0 - - + -
91B VAL* 4.8 21.3 - - + -
92B PHE* 3.8 30.3 - + + -
492B MSE 3.2 33.1 - - + +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER 3.2 15.8 + - - +
36B LEU* 3.7 7.4 - - - +
38B PHE* 1.3 76.7 - - + +
40B LYS* 1.3 63.2 + - - +
42B CYS* 3.3 4.0 + - - +
43B LYS* 3.3 16.3 + - - +
52B LEU* 3.9 35.9 - - + +
56B TYR 5.2 2.0 - - - +
58B TRP* 3.7 27.3 - - + +
61B LEU* 4.1 16.6 - - + -
73B TYR* 4.7 8.3 - - + -
76B MSE 3.9 26.2 - - + -
77B LEU* 5.9 0.9 - - + -
80B LEU* 4.1 11.0 - - + -
92B PHE* 4.0 22.9 - - + -
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Residues in contact with LYS 40 (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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36B LEU 3.0 18.0 + - - +
37B LEU* 3.5 9.4 - - + +
39B LEU* 1.3 77.9 - - - +
41B MSE 1.3 71.0 + - + +
43B LYS* 3.3 4.6 + - + +
44B GLU* 3.1 59.5 + - - +
58B TRP* 3.4 43.0 - - + +
112B MSE 2.8 30.4 + - - +
113B ASP* 3.1 23.7 + - - -
115B LEU* 3.3 19.0 + - + +
117B TRP* 5.9 0.8 - - - -
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Residues in contact with MSE 41 (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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37B LEU* 2.8 26.1 + - + +
38B PHE* 3.2 5.4 + - + +
40B LYS* 1.3 103.5 - - + +
42B CYS* 1.3 59.9 + - - +
44B GLU* 3.2 6.8 + - + +
45B THR* 2.9 31.1 + - - -
115B LEU* 4.5 13.9 - - + -
117B TRP* 3.9 34.3 - - + -
488B ALA* 4.3 18.0 - - + +
491B ALA* 4.7 1.3 - - - -
492B MSE 3.9 32.5 - - + -
495B LEU* 3.8 25.8 - - + -
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Residues in contact with CYS 42 (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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38B PHE* 2.9 58.4 + - - -
39B LEU 3.6 6.5 - - - +
40B LYS 3.3 0.2 - - - -
41B MSE 1.3 76.9 - - - +
43B LYS* 1.3 65.1 + - - +
45B THR* 3.2 22.3 - - - +
48B GLU* 3.5 17.7 + - + +
51B TYR* 4.3 22.2 - - + -
52B LEU* 3.9 21.5 - - + -
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Residues in contact with LYS 43 (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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39B LEU 3.3 3.2 + - - -
40B LYS* 3.6 8.7 - - - +
41B MSE 3.1 0.4 - - - -
42B CYS* 1.3 79.5 - - - +
44B GLU* 1.3 66.1 + - - +
46B GLY* 2.7 29.6 + - - -
48B GLU* 3.3 32.0 + - - +
58B TRP* 3.5 35.9 - - + +
59B ASP* 3.7 25.6 + - - +
62B LYS* 4.8 9.3 - - - +
113B ASP* 5.1 3.6 + - - -
318B PHE* 5.7 9.2 - - - -
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Residues in contact with GLU 44 (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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40B LYS* 3.1 42.5 + - - +
41B MSE 3.2 10.7 + - + +
43B LYS* 1.3 86.9 + - - +
45B THR* 1.3 61.0 + - - +
46B GLY* 3.2 0.7 + - - -
117B TRP* 3.3 43.3 - - + -
484B PRO* 3.9 16.3 - - - +
488B ALA* 4.0 8.4 - - + +
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Residues in contact with THR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B MSE 2.9 10.1 + - - -
42B CYS* 3.2 12.5 - - - +
43B LYS 2.9 0.2 + - - -
44B GLU* 1.3 77.4 - - - +
46B GLY* 1.3 59.4 + - - +
47B GLN* 3.1 32.7 + - + +
51B TYR* 3.4 35.0 + - + +
484B PRO* 3.7 3.3 - - - +
485B ASP* 3.2 29.4 + - + +
488B ALA* 3.6 20.4 - - - +
489B ALA* 5.0 1.0 + - - +
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Residues in contact with GLY 46 (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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43B LYS 2.7 15.9 + - - -
44B GLU 3.2 2.2 - - - -
45B THR* 1.3 77.1 - - - +
47B GLN* 1.3 67.8 + - - +
48B GLU* 3.8 2.2 - - - -
484B PRO* 5.1 4.9 - - - -
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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