Contacts of the helix formed by residues 27 - 44 (chain A) in PDB entry 3AYU
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 ASP 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 1.3 75.1 - - - +
28A PRO* 1.3 81.7 - - - +
29A GLU* 2.9 36.3 + - - +
30A THR* 3.0 28.8 + - - +
31A VAL* 3.0 11.6 + - - +
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Residues in contact with PRO 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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22A TYR* 3.8 35.0 - - + +
26A LEU 4.0 4.3 - - - +
27A ASP* 1.3 93.2 - - - +
29A GLU* 1.3 54.8 + - - +
31A VAL* 3.2 2.4 + - + +
32A ASP* 2.8 38.4 + - - +
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Residues in contact with GLU 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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27A ASP* 2.9 16.9 + - - +
28A PRO* 1.3 78.6 - - - +
30A THR* 1.3 58.1 + - - +
32A ASP* 3.5 8.6 + - + +
33A ASP* 2.9 30.3 + - + +
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Residues in contact with THR 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 LEU* 4.2 27.1 - - + +
27A ASP* 3.0 28.4 + - - +
29A GLU* 1.3 76.1 - - - +
31A VAL* 1.3 58.8 + - - +
33A ASP* 3.8 6.4 - - + +
34A ALA* 3.0 28.4 + - - +
37A ARG* 5.6 0.2 + - - -
106A LEU* 4.3 24.2 - - + -
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Residues in contact with VAL 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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22A TYR* 3.7 28.5 - - + -
23A THR* 3.9 19.3 - - + -
26A LEU* 3.8 22.7 - - + +
27A ASP 3.0 16.4 + - - +
28A PRO 3.2 7.4 + - - +
30A THR* 1.3 73.2 - - - +
32A ASP* 1.3 65.1 + - - +
34A ALA* 3.2 5.0 + - - +
35A PHE* 3.0 49.6 + - + -
64A PHE* 4.1 6.7 - - + -
114A LEU* 4.1 15.9 - - + -
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Residues in contact with ASP 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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17A TYR* 5.1 1.6 + - - -
19A ILE* 3.3 17.0 - - + +
22A TYR* 2.6 29.6 + - - -
28A PRO* 2.8 24.4 + - - +
29A GLU* 3.7 9.2 - - + +
31A VAL* 1.3 71.3 - - - +
33A ASP* 1.3 56.1 + - - +
35A PHE* 3.4 3.3 + - - +
36A ALA* 2.9 29.6 + - - +
52A ARG* 3.0 35.2 + - - +
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Residues in contact with ASP 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 GLU* 2.9 19.6 + - + +
30A THR* 3.8 7.2 - - - +
32A ASP* 1.3 75.8 - - - +
34A ALA* 1.3 58.5 + - - +
36A ALA* 3.2 7.5 + - - +
37A ARG* 2.8 76.9 + - - +
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Residues in contact with ALA 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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26A LEU* 5.9 0.2 - - + -
30A THR* 3.0 19.0 + - + +
31A VAL 3.2 4.9 + - - +
33A ASP* 1.3 77.6 + - - +
35A PHE* 1.3 59.1 + - - +
37A ARG* 3.8 12.8 - - - +
38A ALA* 3.0 27.9 + - - +
106A LEU* 4.7 7.6 - - + -
114A LEU* 4.0 21.1 - - + -
115A PHE* 3.7 29.0 - - + +
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Residues in contact with PHE 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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17A TYR* 5.0 1.6 - - + -
19A ILE* 3.7 31.9 - - + -
31A VAL* 3.0 36.7 + - + -
32A ASP 3.8 4.7 - - - +
34A ALA* 1.3 73.8 - - - +
36A ALA* 1.3 64.4 - - - +
38A ALA* 3.1 5.2 + - - +
39A PHE* 3.0 32.1 + - + -
62A ILE* 3.6 27.4 - - + -
64A PHE* 3.9 24.7 - + - -
98A PHE* 3.5 30.1 - + - -
114A LEU* 4.0 12.3 - - + -
118A ALA* 3.7 17.5 - - + -
122A PHE* 3.7 16.0 - + + -
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Residues in contact with ALA 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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17A TYR* 4.2 18.7 + - - +
32A ASP 2.9 17.6 + - - +
33A ASP* 3.2 9.8 + - - +
35A PHE* 1.3 76.1 - - - +
37A ARG* 1.3 64.9 + - + +
39A PHE* 3.4 6.2 + - - +
40A GLN* 3.1 22.1 + - - +
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Residues in contact with ARG 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 ASP* 2.8 64.3 + - - +
34A ALA* 3.8 15.4 - - - +
36A ALA* 1.3 74.1 - - + +
38A ALA* 1.3 62.5 + - - +
40A GLN* 3.2 9.2 + - - +
41A VAL* 3.2 24.8 + - - +
106A LEU* 5.0 11.9 - - - +
115A PHE* 3.3 48.5 - - + +
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Residues in contact with ALA 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 ALA 3.0 18.1 + - - +
35A PHE 3.1 5.8 + - - +
37A ARG* 1.3 76.6 - - - +
39A PHE* 1.3 60.6 + - - +
41A VAL* 3.3 18.2 - - - +
42A TRP* 3.5 13.0 + - - -
115A PHE* 3.6 12.7 - - - +
118A ALA* 3.7 6.1 - - + -
119A ALA* 3.5 30.8 - - - +
122A PHE* 3.6 15.7 - - + -
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Residues in contact with PHE 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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17A TYR* 3.3 59.5 - + + -
35A PHE 3.0 23.4 + - - -
36A ALA* 3.7 6.5 - - - +
38A ALA* 1.3 74.5 - - - +
40A GLN* 1.3 65.8 + - - +
42A TRP* 3.0 6.9 + + - -
43A SER* 3.0 20.2 + - - -
50A PHE* 3.5 45.1 - + + -
60A ILE* 3.7 26.7 - - + -
62A ILE* 3.9 4.3 - - + -
122A PHE* 3.5 41.7 - + - -
126A MET* 4.4 2.9 - - + -
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Residues in contact with GLN 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 ALA 3.1 13.6 + - - +
37A ARG* 3.2 13.8 + - - +
39A PHE* 1.3 73.9 - - - +
41A VAL* 1.3 65.3 + - - +
43A SER* 3.3 23.4 + - - -
44A ASP* 2.6 63.4 + - - +
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Residues in contact with VAL 41 (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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37A ARG 3.2 15.6 + - - +
38A ALA* 3.3 12.3 - - - +
40A GLN* 1.3 77.7 - - - +
42A TRP* 1.3 66.4 + - + +
44A ASP* 3.5 18.6 - - - +
45A VAL* 4.1 1.0 - - - +
115A PHE* 3.9 17.7 - - + -
119A ALA* 4.4 4.3 - - + -
137A LEU* 4.0 10.8 - - + -
148A PHE* 3.8 25.8 - - + -
150A LEU* 3.5 43.3 - - + +
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Residues in contact with TRP 42 (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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38A ALA 3.5 17.4 + - - -
39A PHE* 3.0 8.7 + - - +
41A VAL* 1.3 76.8 - - + +
43A SER* 1.3 63.9 + - - +
44A ASP 3.1 1.8 - - - -
45A VAL* 3.2 14.1 + - - +
46A THR* 3.0 21.7 + - - +
48A LEU* 5.2 1.8 - - + -
50A PHE* 4.4 12.6 - - + -
119A ALA 3.0 20.1 + - - -
122A PHE* 4.1 14.4 - - + -
123A GLY* 3.6 25.0 - - - +
126A MET* 4.9 11.2 - - + -
128A LEU* 3.7 21.8 - - + -
137A LEU* 3.4 24.7 - - + +
138A MET* 4.0 7.6 - - - -
150A LEU* 4.0 23.8 - - + -
154A ASP* 4.1 11.7 - - + -
158A ILE* 3.7 40.6 - - + -
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Residues in contact with SER 43 (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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39A PHE 3.0 8.8 + - - -
40A GLN* 3.3 36.7 + - - -
42A TRP* 1.3 77.5 - - - +
44A ASP* 1.3 58.4 + - - +
46A THR* 3.0 20.7 - - - +
48A LEU 2.9 27.4 - - - -
49A ARG* 3.2 17.4 + - - -
50A PHE* 4.1 11.6 - - - -
165A SER* 4.8 0.2 + - - -
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Residues in contact with ASP 44 (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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40A GLN* 2.6 55.0 + - - +
41A VAL* 3.5 14.1 - - - +
43A SER* 1.3 77.8 - - - +
45A VAL* 1.3 67.9 + - + +
46A THR 3.8 0.2 - - - -
165A SER* 6.0 0.4 - - - -
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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