Contacts of the helix formed by residues 22 - 40 (chain B) in PDB entry 2X06
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 22 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLY 3.5 5.5 - - - +
21B VAL* 1.3 91.0 - - + +
23B GLU* 1.3 67.3 + - - +
24B GLU* 3.0 5.3 + - + +
25B ASP* 3.0 31.8 + - - +
26B ALA 3.1 8.3 + - - -
63B PRO 3.3 15.9 - - - +
64B LYS* 4.6 14.8 - - + +
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Residues in contact with GLU 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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13B ILE* 4.5 5.7 - - + +
17B LYS* 3.0 49.1 + - + +
21B VAL 3.5 1.6 + - - -
22B PRO* 1.3 70.7 - - - +
24B GLU* 1.3 58.7 + - + +
26B ALA* 3.2 3.5 + - - +
27B LYS* 3.0 57.7 + - + +
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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
----------------------------------------------------------
22B PRO* 3.0 4.2 + - + +
23B GLU* 1.3 75.7 - - + +
25B ASP* 1.3 71.0 + - - +
27B LYS* 3.3 28.2 + - - +
28B ILE* 3.2 35.2 + - + +
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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
----------------------------------------------------------
21B VAL* 3.7 12.1 - - + +
22B PRO* 3.0 31.7 + - - +
24B GLU* 1.3 80.4 - - - +
26B ALA* 1.3 54.2 + - - +
28B ILE* 3.4 10.2 + - - +
29B THR* 2.8 37.0 + - - -
63B PRO 4.6 3.5 - - - +
65B PRO* 4.9 8.1 - - - +
67B ILE* 5.9 0.2 - - - +
88B VAL* 3.5 39.7 - - + +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 3.8 33.5 - - + +
16B LEU* 4.1 17.7 - - + +
17B LYS* 4.4 3.6 - - + -
21B VAL* 3.8 8.0 - - + +
22B PRO 3.1 10.6 + - - +
23B GLU* 3.5 11.9 - - - +
25B ASP* 1.3 74.4 - - - +
27B LYS* 1.3 55.2 + - - +
29B THR* 3.2 6.8 + - - -
30B ALA* 2.7 36.4 + - - +
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LYS* 4.2 13.1 + - - +
13B ILE* 3.6 30.0 - - + +
23B GLU* 3.0 45.2 + - + +
24B GLU* 3.6 31.9 - - - +
26B ALA* 1.3 74.4 - - - +
28B ILE* 1.3 57.4 + - + +
30B ALA* 3.1 3.6 + - - +
31B ASP* 2.8 36.7 + - - +
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.2 25.9 + - + +
25B ASP* 3.5 14.4 - - - +
27B LYS* 1.3 77.0 - - + +
29B THR* 1.3 64.5 + - - +
31B ASP* 3.1 19.2 + - - +
32B VAL* 3.2 16.0 + - + +
87B GLN* 3.7 27.8 - - + +
88B VAL* 4.7 6.5 - - + -
91B LYS* 4.0 40.4 - - + +
122B TYR* 4.4 9.8 + - + +
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Residues in contact with THR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.8 22.9 - - + -
25B ASP 2.8 21.9 + - - -
26B ALA 3.6 4.0 - - - -
28B ILE* 1.3 74.6 - - - +
30B ALA* 1.3 64.0 + - - +
32B VAL* 3.2 11.8 + - - +
33B PHE* 3.2 40.6 + - + -
85B LEU* 3.7 16.0 - - + +
87B GLN* 3.8 26.5 - - - +
88B VAL* 3.5 16.3 - - - +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LYS* 3.5 39.7 - - + +
12B ILE* 3.9 22.4 - - + +
13B ILE* 3.8 5.2 - - + -
26B ALA 2.7 20.1 + - - +
27B LYS 3.6 2.5 - - - +
29B THR* 1.3 73.3 - - - +
31B ASP* 1.3 65.3 + - - +
33B PHE* 3.2 2.4 + - - +
34B VAL* 3.0 28.7 + - - +
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Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LYS* 2.7 38.9 + - - +
27B LYS* 2.8 16.1 + - - +
28B ILE* 3.1 12.5 + - - +
30B ALA* 1.3 77.1 - - - +
32B VAL* 1.3 57.7 + - - +
34B VAL* 3.9 6.2 - - - +
35B ASP* 3.0 28.1 + - - +
122B TYR* 4.3 20.1 + - + +
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.3 15.5 - - + +
29B THR 3.2 6.4 + - - +
30B ALA 3.1 0.6 - - - -
31B ASP* 1.3 76.9 - - - +
33B PHE* 1.3 65.0 + - - +
35B ASP* 3.6 1.3 + - - +
36B ALA* 3.2 21.3 + - - +
44B HIS 5.0 0.2 - - - +
87B GLN* 3.8 22.0 - - + +
117B PHE 3.8 20.6 - - - +
118B GLY* 4.7 3.1 - - - -
119B ILE* 4.4 12.6 - - + +
122B TYR* 3.5 51.8 - - + -
123B TYR* 4.2 2.9 - - + +
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 3.7 5.8 - - - +
12B ILE* 3.5 29.8 - - + -
29B THR* 3.2 42.4 + - + -
30B ALA* 3.2 2.8 + - - +
32B VAL* 1.3 78.8 - - - +
34B VAL* 1.3 63.2 + - - +
36B ALA* 3.1 9.8 - - - +
37B ASP* 3.0 23.9 + - - +
44B HIS 3.9 8.5 - - - -
45B GLY* 3.3 31.7 - - - -
46B ILE* 3.9 4.3 - - - -
48B ARG* 4.5 1.8 - - + -
49B PHE* 3.8 36.8 - + + -
52B TYR* 3.6 33.4 - + - -
87B GLN* 4.0 9.6 - - - -
116B HIS* 6.4 0.4 - + - -
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 3.7 28.3 - - + +
8B GLU* 3.5 32.1 - - + +
9B LYS* 4.1 12.8 - - + +
30B ALA 3.0 19.6 + - - +
31B ASP* 3.9 6.7 - - - +
33B PHE* 1.3 74.6 - - - +
35B ASP* 1.3 67.9 - - - +
37B ASP* 2.9 1.9 + - - -
38B LEU* 2.8 53.0 + - + +
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Residues in contact with ASP 35 (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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31B ASP 3.0 18.2 + - - +
32B VAL 3.8 4.3 - - - +
34B VAL* 1.3 76.3 - - - +
36B ALA* 1.3 63.2 + - - +
38B LEU* 3.9 5.2 - - - +
39B LYS* 3.0 53.0 + - - +
119B ILE* 3.6 12.4 - - + +
122B TYR* 3.9 27.5 - - + +
125B GLU* 4.4 5.3 - - - +
311B LYS* 3.3 26.0 + - - -
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Residues in contact with ALA 36 (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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32B VAL 3.2 9.5 + - - +
33B PHE 3.1 11.4 + - - +
35B ASP* 1.3 79.7 - - - +
37B ASP* 1.3 61.4 + - - +
39B LYS* 3.3 0.9 + - - -
40B GLY 3.1 3.6 + - - -
41B PHE* 2.9 37.5 + - - +
44B HIS* 3.6 30.7 - - + +
45B GLY* 3.8 0.7 - - - +
119B ILE* 3.9 23.4 - - + +
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Residues in contact with ASP 37 (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 GLU* 2.8 19.4 - - - +
33B PHE 3.0 5.8 + - - +
34B VAL 2.9 6.7 + - - +
36B ALA* 1.3 72.7 - - - +
38B LEU* 1.3 66.0 + - - +
40B GLY* 3.1 6.1 + - - -
41B PHE 5.0 1.8 - - - +
42B THR* 4.5 16.6 - - - +
45B GLY* 3.5 8.6 - - - -
46B ILE* 2.8 37.3 + - - +
314B ARG* 2.7 30.1 + - - +
318B PHE* 3.5 34.6 - - + -
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Residues in contact with LEU 38 (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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5B PRO* 3.6 33.4 - - + -
34B VAL* 2.8 41.9 + - + +
35B ASP* 4.0 3.8 - - - +
37B ASP* 1.3 72.8 - - - +
39B LYS* 1.3 60.3 + - - +
40B GLY 3.3 0.9 + - - -
310B ASN* 3.3 9.0 - - - +
311B LYS* 3.3 58.0 + - + +
314B ARG* 3.5 25.0 + - - +
315B LYS* 4.2 6.1 - - + +
318B PHE* 4.3 10.8 - - + -
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Residues in contact with LYS 39 (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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35B ASP* 3.0 47.7 + - - +
36B ALA 3.8 3.8 - - - +
38B LEU* 1.3 76.7 - - - +
40B GLY* 1.3 59.3 + - - +
41B PHE* 3.4 29.8 - - + -
119B ILE* 3.8 8.5 - - + -
121B GLY* 5.8 1.8 - - - -
122B TYR 5.6 1.1 - - - +
125B GLU* 3.9 26.3 + - - -
304B GLY 5.7 0.6 + - - -
307B GLU* 3.8 39.4 + - + +
308B GLU* 4.6 8.3 + - - -
310B ASN* 3.0 20.5 + - - +
311B LYS* 3.1 22.8 - - - +
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Residues in contact with GLY 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 ALA 3.1 0.4 + - - -
37B ASP 3.1 15.0 + - - -
38B LEU 3.1 1.0 + - - -
39B LYS* 1.3 80.4 - - - +
41B PHE* 1.3 58.9 + - - +
42B THR* 2.9 19.6 + - - -
310B ASN* 4.2 7.9 - - - -
314B ARG* 4.3 13.2 - - - -
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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