Contacts of the helix formed by residues 23 - 35 (chain A) in PDB entry 5A0Q
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 TYR 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASP 4.4 6.7 - - - +
11A ARG* 3.6 55.4 + - + -
14A THR* 6.4 0.2 - - - +
15A ILE 4.7 4.1 + - - +
17A SER* 3.4 35.1 - - - -
18A PRO* 5.4 2.3 - - + +
19A GLU* 4.8 6.6 + - - +
21A ARG* 3.5 29.2 + - - -
22A LEU* 1.3 71.8 - - - +
24A GLN* 1.3 65.3 + - - +
25A VAL 3.2 0.2 - - - -
26A GLU* 3.1 25.2 - - - +
27A TYR* 3.0 56.6 + + + +
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Residues in contact with GLN 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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11A ARG 3.2 24.2 + - - +
12A HIS* 4.0 23.0 - - - +
13A ILE 4.8 0.4 - - - -
14A THR* 3.6 32.8 - - + +
22A LEU 3.5 0.2 - - - -
23A TYR* 1.3 77.0 - - + +
25A VAL* 1.4 56.8 + - - +
27A TYR* 3.3 17.0 + - - +
28A ALA* 3.1 20.4 + - - +
132A ARG* 4.9 0.2 - - - +
133A PRO* 3.7 19.0 - - + +
12G SER 3.8 7.6 - - - +
13G THR* 3.9 2.9 - - - +
14G PHE* 3.2 53.9 + - - +
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Residues in contact with VAL 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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14A THR* 5.3 2.0 - - + -
22A LEU* 3.6 37.7 + - + +
23A TYR 3.2 0.6 - - - -
24A GLN* 1.4 75.9 - - + +
26A GLU* 1.3 60.8 + - - +
28A ALA* 3.0 20.8 + - - +
29A PHE* 3.1 38.8 + - + -
126A THR* 3.8 21.1 - - + +
133A PRO* 4.6 6.5 - - + -
156A PRO 4.6 4.3 - - - +
157A ALA* 3.9 19.3 - - + +
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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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21A ARG* 3.5 31.1 + - - +
22A LEU 3.2 13.4 + - - +
23A TYR* 3.1 44.1 - - - +
25A VAL* 1.3 75.4 - - - +
27A TYR* 1.4 67.6 + - + +
29A PHE* 3.2 22.0 + - + +
30A LYS* 2.9 36.4 + - + +
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Residues in contact with TYR 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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11A ARG* 3.5 40.6 + - + +
23A TYR* 3.0 46.0 + + + +
24A GLN* 3.3 35.4 - - - +
26A GLU* 1.4 79.3 - - + +
28A ALA* 1.3 56.9 + - - +
30A LYS* 3.3 34.2 + - - +
31A ALA* 2.9 27.0 + - - +
14G PHE* 3.5 29.5 - - + -
15G SER 4.3 3.6 - - - +
16G PRO* 3.9 28.4 - - + +
18G GLY* 4.2 4.5 - - - -
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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 GLN 3.1 11.7 + - - +
25A VAL 3.0 12.9 + - - +
27A TYR* 1.3 73.9 - - - +
29A PHE* 1.4 56.7 + - - +
31A ALA* 3.2 10.5 + - - +
32A ILE* 3.0 29.8 + - - +
133A PRO* 3.8 23.6 - - + +
135A GLY* 4.2 4.8 - - - -
156A PRO* 3.6 20.2 - - + -
14G PHE* 4.4 9.8 - - + -
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Residues in contact with PHE 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 VAL* 3.1 34.2 + - + -
26A GLU* 3.2 21.3 + - + +
28A ALA* 1.4 74.0 - - - +
30A LYS* 1.4 62.4 + - + +
32A ILE* 3.2 12.6 + - + +
33A ASN* 2.8 30.4 + - - +
155A ASP* 4.0 16.8 - - + -
156A PRO* 3.6 30.5 - - + -
157A ALA* 3.9 16.2 - - + -
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Residues in contact with LYS 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* 2.9 22.2 + - - +
27A TYR* 3.6 35.2 - - - +
28A ALA 3.3 0.2 - - - -
29A PHE* 1.4 77.0 - - + +
31A ALA* 1.3 57.6 + - - +
33A ASN* 3.4 10.4 + - - +
34A GLN* 3.1 32.4 + - + +
16G PRO* 3.0 34.4 + - - +
17G ASP* 3.8 15.5 - - - +
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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 TYR 2.9 13.2 + - - +
28A ALA* 3.2 10.5 + - - +
30A LYS* 1.3 73.9 - - - +
32A ILE* 1.3 58.3 + - - +
34A GLN* 3.4 3.8 + - - +
35A GLY* 3.1 23.2 + - - -
82A GLY* 4.4 2.9 - - - -
83A MET* 4.5 15.8 + - + +
135A GLY* 5.0 2.0 - - - -
14G PHE* 3.8 17.9 - - + -
18G GLY* 3.0 31.0 - - - +
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Residues in contact with ILE 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 3.0 13.8 + - - +
29A PHE* 3.2 14.6 + - + +
31A ALA* 1.3 74.6 - - - +
33A ASN* 1.4 67.6 + - - +
35A GLY* 3.2 12.6 + - - -
36A GLY 4.2 1.9 + - - -
37A LEU 5.0 0.2 - - - +
81A THR* 3.5 17.1 - - - +
82A GLY* 3.9 10.4 + - - -
135A GLY 3.7 18.8 - - - -
136A CYS 3.7 2.5 - - - +
137A CYS* 3.4 31.2 - - + +
155A ASP* 5.1 2.9 - - - +
156A PRO* 3.5 34.8 - - + -
168A ALA* 5.3 0.9 - - + -
169A GLY* 4.7 21.0 - - - +
172A GLN* 6.1 0.9 - - - +
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Residues in contact with ASN 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 PHE* 2.8 24.4 + - - +
30A LYS* 3.5 11.7 - - - +
31A ALA 3.3 0.2 - - - -
32A ILE* 1.4 78.8 - - - +
34A GLN* 1.4 66.7 + - - +
35A GLY 3.3 0.7 - - - -
36A GLY* 3.7 0.7 + - - -
169A GLY 3.7 18.5 + - - +
170A VAL* 3.5 38.4 + - + +
172A GLN* 3.5 27.1 + - - +
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Residues in contact with GLN 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 LYS 3.1 19.3 + - - +
31A ALA* 3.4 8.7 + - - +
32A ILE 3.2 0.2 - - - -
33A ASN* 1.4 80.5 - - + +
35A GLY* 1.4 58.7 + - - +
36A GLY* 3.1 7.2 + - - -
17G ASP* 3.9 18.2 - - + +
18G GLY* 4.7 5.6 - - - +
19G ARG* 4.2 26.6 + - - +
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Residues in contact with GLY 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 3.1 11.8 + - - -
32A ILE 3.2 10.4 + - - -
34A GLN* 1.4 76.6 - - - +
36A GLY* 1.3 56.3 + - - +
37A LEU* 3.2 19.6 + - - +
82A GLY* 3.6 25.6 - - - +
83A MET* 4.6 1.6 - - - -
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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