Contacts of the helix formed by residues 24 - 41 (chain B) in PDB entry 1AOC
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 THR 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B VAL 3.8 0.2 + - - -
23B THR* 1.3 72.7 - - - +
25B GLU* 1.3 67.7 + - - +
27B LYS* 3.8 21.2 - - + +
28B ASP* 3.1 40.1 + - - +
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Residues in contact with GLU 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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23B THR* 2.8 29.3 - - - +
24B THR* 1.3 93.9 + - - +
26B ILE* 1.3 69.7 + - + +
28B ASP* 4.1 3.3 - - - +
29B LYS* 3.4 23.1 + - - +
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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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21B ILE* 3.5 18.8 - - + +
22B VAL* 4.4 7.0 - - + -
23B THR* 2.7 33.2 + - + +
25B GLU* 1.3 71.2 - - + +
27B LYS* 1.3 66.3 + - - +
29B LYS* 2.8 34.0 + - + +
30B ILE* 3.0 31.1 + - + +
109B VAL* 4.7 10.1 - - + -
152B TYR* 5.2 3.4 - - + -
154B LEU* 4.7 26.5 - - + -
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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
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17B GLY 2.6 31.1 + - - -
18B ARG* 2.6 13.0 + - - +
19B THR* 4.8 0.2 - - - -
22B VAL* 2.5 48.4 + - + +
23B THR 2.8 17.2 + - - +
24B THR* 3.8 23.1 - - + +
26B ILE* 1.3 71.8 - - - +
28B ASP* 1.3 59.9 + - - +
30B ILE* 3.1 11.1 + - - +
31B GLU* 2.9 28.0 + - - +
98B VAL* 5.7 2.2 - - - +
112B GLN 6.0 2.7 - - - +
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Residues in contact with ASP 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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69A ARG* 5.5 1.2 + - - -
24B THR* 3.1 31.3 + - - +
25B GLU* 4.1 3.8 - - - +
27B LYS* 1.3 80.4 - - - +
29B LYS* 1.3 63.5 + - - +
31B GLU* 3.3 9.3 + - - +
32B LYS* 2.5 62.4 + - - +
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Residues in contact with LYS 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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25B GLU* 3.4 12.8 + - - +
26B ILE* 2.8 32.9 + - - +
28B ASP* 1.3 75.4 - - - +
30B ILE* 1.3 60.4 + - + +
32B LYS* 3.5 6.7 + - - +
33B ALA* 3.0 27.8 + - - +
152B TYR* 3.4 32.0 + - + +
154B LEU 6.1 0.7 - - - -
157B ASP* 4.5 10.8 - - + +
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Residues in contact with ILE 30 (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 VAL* 5.8 1.8 - - + -
26B ILE* 3.0 21.6 + - + +
27B LYS* 3.4 10.3 - - - +
29B LYS* 1.3 74.9 - - - +
31B GLU* 1.3 59.7 + - - +
33B ALA* 3.0 8.2 + - - +
34B VAL* 2.8 32.7 + - + +
109B VAL* 3.7 30.7 - - + -
110B ILE 5.3 0.2 - - - +
111B VAL* 3.9 37.0 - - + -
112B GLN 4.6 11.9 - - - +
113B ALA* 4.8 0.2 - - + -
152B TYR* 3.8 32.1 - - + -
159B PHE* 4.8 3.6 - - + -
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Residues in contact with GLU 31 (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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69A ARG* 4.7 5.4 - - - +
70A PRO* 4.2 0.7 - - - +
27B LYS 2.9 14.3 + - - +
28B ASP* 3.6 15.7 - - - +
30B ILE* 1.3 76.2 - - - +
32B LYS* 1.3 59.8 + - + +
34B VAL* 3.2 1.7 + - - +
35B GLU* 2.8 53.9 + - - +
113B ALA* 3.3 23.5 - - + +
114B PRO* 5.0 0.5 - - - +
115B ARG* 3.3 28.9 + - + +
116B ALA* 3.2 34.2 + - - +
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Residues in contact with LYS 32 (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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69A ARG* 4.0 31.6 - - - +
28B ASP* 2.5 55.4 + - - +
29B LYS* 4.0 6.2 - - - +
31B GLU* 1.3 79.1 - - + +
33B ALA* 1.3 55.9 + - - +
35B GLU* 3.2 9.5 + - - +
36B ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 33 (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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29B LYS 3.0 14.1 + - - +
30B ILE 3.0 8.1 + - - +
32B LYS* 1.3 76.4 - - - +
34B VAL* 1.3 62.6 + - - +
36B ALA* 3.3 9.1 + - - +
37B VAL* 3.2 23.4 + - - +
152B TYR* 4.1 18.2 - - + +
157B ASP 5.7 1.6 - - - +
158B GLY* 6.2 0.2 - - - -
159B PHE* 3.6 22.0 - - + -
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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
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30B ILE 2.8 23.5 + - - +
31B GLU 3.7 3.6 - - - +
33B ALA* 1.3 71.9 - - - +
35B GLU* 1.3 63.1 + - - +
37B VAL* 3.1 7.5 + - - +
38B ALA* 3.0 19.6 + - - +
51B PHE* 3.7 24.6 - - + -
57B PHE* 4.7 5.4 - - + -
111B VAL* 3.8 25.4 - - + -
113B ALA* 3.9 12.3 - - + -
116B ALA* 3.6 18.2 - - + -
118B PHE* 4.0 13.5 - - + -
159B PHE* 3.7 19.3 - - + -
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Residues in contact with GLU 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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69A ARG* 2.7 54.7 + - - +
70A PRO* 3.6 23.0 - - + +
71A GLU* 4.3 0.2 - - - +
123A TRP* 4.4 5.6 - - + -
31B GLU* 2.8 43.4 + - - +
32B LYS* 3.2 10.3 + - - +
34B VAL* 1.3 75.8 - - - +
36B ALA* 1.3 58.0 + - - +
38B ALA* 3.1 7.0 + - - +
39B GLN* 2.8 42.2 + - - +
115B ARG* 5.5 0.7 + - - -
116B ALA* 3.7 11.4 - - + -
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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 LYS 2.9 12.9 + - - +
33B ALA* 3.5 12.8 - - - +
34B VAL 3.2 0.2 - - - -
35B GLU* 1.3 74.9 - - - +
37B VAL* 1.3 65.5 + - + +
39B GLN* 3.3 14.4 + - - +
40B GLU* 2.9 35.9 + - - +
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Residues in contact with VAL 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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33B ALA 3.2 12.7 + - - +
34B VAL* 3.1 9.2 + - - +
36B ALA* 1.3 78.8 - - + +
38B ALA* 1.3 53.5 + - - +
40B GLU* 3.5 12.2 - - + +
41B SER* 2.7 45.1 + - - -
51B PHE* 3.7 23.6 - - + -
54B HIS* 3.9 42.2 - - + +
57B PHE* 4.3 4.9 - - + -
159B PHE* 3.8 20.6 - - + -
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Residues in contact with ALA 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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94A ASP* 4.4 4.3 - - + +
121A CYS* 6.0 0.3 - - - -
123A TRP* 3.6 29.4 - - + -
34B VAL 3.0 12.2 + - - +
35B GLU 3.5 7.9 - - - +
37B VAL* 1.3 77.0 - - - +
39B GLN* 1.3 61.1 + - - +
41B SER* 4.5 0.4 - - - -
42B GLY* 3.1 23.2 + - - -
50B ILE* 3.6 25.1 - - + +
51B PHE* 4.0 17.2 - - + -
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Residues in contact with GLN 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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65A CYS* 3.5 19.7 + - - +
66A ARG* 3.9 22.2 + - - +
67A THR* 4.2 1.8 - - - +
68A VAL 2.9 31.3 + - - +
69A ARG* 4.2 13.7 - - - +
94A ASP* 4.4 10.5 - - - +
96A GLU* 5.1 0.2 - - - +
119A ARG* 2.9 32.4 + - - -
121A CYS* 5.4 0.8 - - - -
123A TRP* 4.6 4.4 - - + +
35B GLU* 2.8 28.9 + - - +
36B ALA* 3.6 17.4 + - - +
38B ALA* 1.3 73.2 - - - +
40B GLU* 1.3 56.6 + - - +
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Residues in contact with GLU 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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119A ARG* 4.2 12.5 + - - +
36B ALA* 2.9 27.1 + - - +
37B VAL* 3.5 18.4 - - + +
39B GLN* 1.3 75.7 - - - +
41B SER* 1.3 71.8 + - - +
53B HIS* 4.1 15.5 - - + -
54B HIS* 4.9 8.3 - - - -
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Residues in contact with SER 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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119A ARG* 4.7 3.1 + - - -
37B VAL* 2.7 32.2 + - - +
38B ALA* 3.9 1.1 - - - -
40B GLU* 1.3 78.6 - - - +
42B GLY* 1.3 60.7 + - - +
43B VAL* 2.8 21.5 + - - +
50B ILE* 2.7 27.6 + - - -
51B PHE* 4.7 0.5 - - - -
53B HIS* 2.8 39.1 + - - +
54B HIS 4.8 0.3 + - - -
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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
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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