Contacts of the helix formed by residues 22 - 40 (chain A) in PDB entry 3O8H
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 GLY 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ASP* 1.3 64.9 + - - +
24A ASP* 3.3 15.1 + - - +
25A ARG* 3.3 26.0 + - - +
26A GLU* 3.4 2.4 + - - +
64A TYR* 3.2 42.5 + - - -
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY* 1.3 72.1 - - - +
24A ASP* 1.3 62.2 + - - +
25A ARG 3.1 0.2 - - - -
26A GLU* 3.3 18.2 + - - +
27A LEU* 2.9 54.3 + - - +
78A ARG* 6.0 0.2 + - - -
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Residues in contact with ASP 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY 3.8 10.1 + - - +
23A ASP* 1.3 79.6 + - - +
25A ARG* 1.3 55.7 + - + +
27A LEU* 3.6 9.6 + - - +
28A ALA* 2.8 31.1 + - - +
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY* 3.3 25.8 + - - +
23A ASP 3.1 0.8 - - - -
24A ASP* 1.3 78.1 - - + +
26A GLU* 1.3 62.6 - - - +
28A ALA* 3.4 7.0 + - - +
29A ILE* 3.0 31.4 + - - +
54A ALA* 4.6 2.0 - - - +
56A ILE* 3.8 25.5 - - + +
60A THR* 3.8 23.0 + - - +
63A PHE* 5.5 1.6 - - - -
64A TYR* 2.7 51.0 + - + -
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY 3.4 5.9 + - - +
23A ASP* 3.3 21.6 + - - +
25A ARG* 1.3 77.0 - - - +
27A LEU* 1.3 64.9 + - + +
29A ILE* 3.2 7.2 + - - +
30A LEU* 3.1 29.8 + - + +
64A TYR* 4.2 26.3 - - + +
65A PHE* 3.5 34.9 - - + -
74A THR* 4.9 2.6 - - - +
78A ARG* 3.7 20.3 + - - +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 2.9 39.9 + - - +
24A ASP* 4.0 8.7 - - - +
26A GLU* 1.3 74.9 - - + +
28A ALA* 1.3 61.0 + - - +
30A LEU* 3.2 11.4 + - + +
31A ALA* 2.9 31.0 + - - +
78A ARG* 3.8 29.4 - - - +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP 2.8 19.9 + - - +
25A ARG* 3.6 7.4 - - - +
26A GLU 3.3 0.4 - - - -
27A LEU* 1.3 77.0 - - - +
29A ILE* 1.3 59.1 + - - +
31A ALA* 4.0 5.0 - - - +
32A THR* 2.9 30.5 + - - -
53A GLY 5.5 0.4 - - - +
54A ALA* 3.9 24.9 - - + +
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG 3.0 19.6 + - - +
26A GLU 3.2 6.5 + - - +
28A ALA* 1.3 74.4 - - - +
30A LEU* 1.3 59.2 + - - +
32A THR* 3.4 4.7 + - - -
33A ALA* 2.9 27.9 + - - +
50A LEU* 4.5 8.5 - - + +
54A ALA* 3.8 19.5 - - + -
56A ILE* 3.7 22.0 - - + -
61A PHE* 3.8 32.1 - - + -
64A TYR* 3.7 30.7 - - + -
65A PHE* 3.8 17.5 - - + -
71A VAL* 3.9 11.2 - - + -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU* 3.1 24.7 + - + +
27A LEU* 3.2 15.7 + - + +
29A ILE* 1.3 75.6 - - - +
31A ALA* 1.3 57.1 + - - +
33A ALA* 3.3 2.1 + - - +
34A GLU* 2.9 25.5 + - - +
65A PHE* 3.9 7.9 - - + -
71A VAL* 3.8 34.3 - - + +
74A THR* 3.8 20.0 - - + -
75A LEU* 3.5 29.7 - - + +
78A ARG* 3.6 39.7 - - + +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU 2.9 19.8 + - - +
28A ALA* 4.0 6.7 - - - +
30A LEU* 1.3 69.4 - - - +
32A THR* 1.3 60.1 + - - +
34A GLU* 3.4 7.3 + - - +
35A ASN* 3.0 40.9 + - - +
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA 2.9 22.6 + - - -
29A ILE 3.6 4.5 - - - -
31A ALA* 1.3 75.2 - - - +
33A ALA* 1.3 54.0 + - - +
35A ASN* 3.2 10.2 + - + +
36A LEU* 2.8 56.9 + - + +
49A ASP 4.0 0.2 - - - +
50A LEU* 3.8 18.8 - - - +
53A GLY* 3.2 41.2 + - - -
54A ALA 3.4 0.3 + - - -
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE 2.9 18.0 + - - +
30A LEU 3.5 4.7 - - - +
32A THR* 1.3 76.1 - - - +
34A GLU* 1.3 62.7 + - - +
36A LEU* 3.4 2.3 + - - +
37A LEU* 3.0 33.4 + - + +
42A LEU* 6.1 4.0 - - + -
45A ILE* 5.7 0.9 - - + -
50A LEU* 3.5 20.8 - - + +
71A VAL* 3.6 24.0 - - + -
72A LEU* 5.8 0.4 - - - +
75A LEU* 3.8 10.5 - - + -
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU 2.9 16.3 + - - +
31A ALA* 3.9 7.8 - - - +
32A THR 3.3 0.2 - - - -
33A ALA* 1.3 78.5 - - - +
35A ASN* 1.3 63.8 + - - +
37A LEU* 3.3 11.6 + - - +
38A GLU* 3.4 21.4 + - - +
75A LEU* 3.7 20.9 - - + +
116A SER 4.8 0.5 - - - +
117A HIS* 2.7 42.2 + - - +
119A ALA* 4.2 5.0 - - + +
120A VAL* 3.6 23.5 - - + +
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Residues in contact with ASN 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.0 24.1 + - - +
32A THR* 3.4 11.2 - - + +
34A GLU* 1.3 77.3 - - - +
36A LEU* 1.3 65.8 + - + +
38A GLU* 3.0 33.1 + - - +
39A ASP* 4.1 3.5 + - - +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A THR* 2.8 41.5 + - + +
33A ALA* 4.0 2.2 - - - +
35A ASN* 1.3 78.6 - - + +
37A LEU* 1.3 61.5 + - - +
39A ASP* 3.3 6.8 + - + +
40A ARG* 3.2 46.6 + - - +
45A ILE* 3.7 37.0 - - + -
49A ASP* 3.8 20.9 - - + +
50A LEU* 4.2 2.9 - - + -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 3.0 27.0 + - + +
34A GLU* 3.8 6.5 - - - +
35A ASN 3.2 0.4 - - - -
36A LEU* 1.3 75.0 - - - +
38A GLU* 1.3 63.5 + - - +
39A ASP 3.2 1.0 + - - -
40A ARG 3.4 14.3 + - - +
41A PRO* 4.7 0.9 - - + -
42A LEU* 3.7 38.8 - - + +
45A ILE* 3.7 12.8 - - + -
72A LEU* 4.1 9.9 - - + -
75A LEU* 4.1 21.3 - - + -
119A ALA* 3.4 24.0 - - + +
120A VAL* 4.9 4.3 - - + -
122A ARG* 4.6 7.1 + - - -
123A ALA* 3.9 27.6 - - + -
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 3.4 19.9 + - - +
35A ASN* 3.0 29.6 + - - +
37A LEU* 1.3 79.2 - - - +
39A ASP* 1.3 69.4 + - - +
118A LYS* 5.7 1.6 + - - +
119A ALA* 3.6 19.0 + - - +
122A ARG* 4.7 11.3 + - - +
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Residues in contact with ASP 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASN 5.1 1.8 - - - +
36A LEU* 3.3 8.5 + - + +
37A LEU 3.2 0.2 - - - -
38A GLU* 1.3 92.8 - - - +
40A ARG* 1.3 65.2 + - + +
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.2 43.8 + - - +
37A LEU* 3.4 27.4 + - - +
38A GLU 3.8 0.6 - - - -
39A ASP* 1.3 83.6 - - + +
41A PRO* 1.4 77.1 - - + +
44A ASP* 2.7 45.3 + - + +
45A ILE* 3.5 19.4 - - + +
49A ASP* 2.9 28.5 + - - -
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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