Contacts of the helix formed by residues 18 - 37 (chain A) in PDB entry 1INR
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 ASN 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 1.3 66.4 + - - +
20A PRO* 4.4 9.6 - - + -
21A ASN* 3.7 13.1 + - + +
22A MET* 3.3 29.9 + - - +
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Residues in contact with LEU 19 (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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18A ASN* 1.3 72.0 - - - +
20A PRO* 1.4 69.7 - - + +
22A MET* 3.4 15.9 + - - +
23A LEU* 3.2 38.1 + - + +
111A PHE* 4.5 22.7 - - + -
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Residues in contact with PRO 20 (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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18A ASN* 3.7 9.4 - - + -
19A LEU* 1.4 92.5 - - + +
21A ASN* 1.3 56.6 - - - +
23A LEU* 3.2 4.2 + - - +
24A ARG* 2.9 30.7 + - - +
27A ARG* 4.2 17.5 + - - +
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Residues in contact with ASN 21 (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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18A ASN* 3.7 14.9 + - + +
19A LEU 3.6 0.4 - - - -
20A PRO* 1.3 78.3 - - - +
22A MET* 1.4 61.2 + - - +
23A LEU 3.4 0.2 - - - -
24A ARG* 3.9 16.5 + - - +
25A ASP* 5.0 4.7 - - - +
104A ARG* 4.7 1.0 + - - -
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Residues in contact with MET 22 (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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18A ASN 3.3 21.7 + - - +
19A LEU* 3.5 23.3 - - - +
20A PRO 3.1 1.0 - - - -
21A ASN* 1.4 78.1 - - - +
23A LEU* 1.4 64.7 + - + +
24A ARG 3.6 0.6 + - - -
25A ASP* 4.8 5.9 + - - +
26A LEU* 5.5 1.6 + - - +
101A LEU* 4.3 8.5 - - + +
104A ARG* 2.7 56.1 + - + +
105A LEU* 4.1 18.8 - - + -
111A PHE* 4.0 30.1 - - + -
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Residues in contact with LEU 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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19A LEU* 3.2 28.9 - - + +
20A PRO 3.2 3.7 + - - +
22A MET* 1.4 79.4 - - + +
24A ARG* 1.3 57.5 + - - +
25A ASP 3.4 2.7 - - - -
26A LEU* 3.4 20.0 + - + +
27A ARG* 2.9 55.1 + - + +
101A LEU* 3.8 35.4 - - + -
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Residues in contact with ARG 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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20A PRO* 2.9 16.9 + - - +
21A ASN* 4.0 15.5 - - + +
22A MET 3.6 1.0 - - - -
23A LEU* 1.3 77.4 - - - +
25A ASP* 1.3 61.6 + - - +
27A ARG* 3.2 46.1 + - - +
28A ASP* 2.8 56.5 + - - +
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Residues in contact with ASP 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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21A ASN 5.0 4.0 + - - +
22A MET 4.8 5.2 + - - +
23A LEU 3.4 0.8 - - - -
24A ARG* 1.3 76.9 - - - +
26A LEU* 1.3 61.4 + - - +
28A ASP* 3.5 8.5 + - - +
29A ALA* 3.0 29.8 + - - +
97A ASN* 3.2 25.3 + - + +
104A ARG* 5.8 5.5 + - - +
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Residues in contact with LEU 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 MET 5.5 1.7 + - - +
23A LEU* 3.4 22.9 - - + +
25A ASP* 1.3 77.8 - - - +
27A ARG* 1.3 63.3 + - + +
29A ALA* 4.6 1.3 - - - -
30A PHE* 3.0 24.6 + - - +
94A LEU* 3.7 24.0 - - + +
97A ASN* 3.8 13.8 - - + +
98A LEU* 3.6 42.6 - - + +
101A LEU* 4.0 26.7 - - + -
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Residues in contact with ARG 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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20A PRO* 4.2 20.0 + - - +
23A LEU* 2.9 47.2 + - + +
24A ARG* 3.2 44.9 + - - +
26A LEU* 1.3 76.8 - - + +
28A ASP* 1.3 57.6 + - - +
30A PHE* 3.4 7.3 + - - +
31A SER* 3.1 26.7 + - - -
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Residues in contact with ASP 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 ARG* 2.8 54.9 + - - +
25A ASP* 3.5 9.0 + - - +
26A LEU 3.4 0.2 - - - -
27A ARG* 1.3 67.8 - - - +
29A ALA* 1.3 62.5 + - - +
31A SER* 2.7 14.5 + - - -
32A ARG* 2.7 39.1 + - - +
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Residues in contact with ALA 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 ASP 3.0 18.3 + - - +
26A LEU* 3.9 4.0 - - - +
28A ASP* 1.3 72.6 - - - +
30A PHE* 1.4 66.4 + - - +
32A ARG* 3.1 24.1 + - - +
33A VAL* 3.2 11.9 + - - +
90A HIS* 4.7 1.5 - - - +
93A SER* 4.4 7.4 - - - +
94A LEU* 4.0 31.9 - - + +
97A ASN* 4.0 11.0 - - - +
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Residues in contact with PHE 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 3.0 18.7 + - - +
27A ARG* 3.7 7.6 - - - +
29A ALA* 1.4 72.8 - - - +
31A SER* 1.4 57.7 + - - +
32A ARG 2.8 11.7 + - - -
33A VAL* 2.9 36.5 + - + -
34A LYS* 2.9 52.2 + - + -
37A PHE* 5.3 4.0 - + + -
94A LEU* 3.7 21.3 - - + +
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Residues in contact with SER 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 ARG 3.1 12.9 + - - -
28A ASP* 2.7 24.1 + - - -
30A PHE* 1.4 73.4 - - - +
32A ARG* 1.3 67.5 + - - +
34A LYS* 3.6 19.3 - - - +
35A THR* 3.3 22.2 - - - +
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Residues in contact with ARG 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 ASP* 2.7 48.8 + - - +
29A ALA* 3.1 12.2 + - - +
30A PHE 2.8 1.4 + - - -
31A SER* 1.3 88.7 + - - +
33A VAL* 1.3 62.6 + - - +
34A LYS 3.4 0.2 - - - -
35A THR* 3.1 22.2 + - - -
36A PHE* 3.3 13.0 - - - -
90A HIS* 3.4 37.9 - - + +
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Residues in contact with VAL 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 ALA 3.4 12.8 - - - +
30A PHE* 2.9 24.2 + - + +
32A ARG* 1.3 75.4 - - - +
34A LYS* 1.3 59.4 + - - +
36A PHE* 3.0 26.8 + - - +
37A PHE* 3.1 32.6 - - + -
87A ILE* 4.2 5.4 - - + -
90A HIS* 3.5 34.3 - - + +
91A VAL* 4.1 8.7 - - + +
94A LEU* 4.3 18.4 - - + -
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A PHE* 2.9 42.2 + - + +
31A SER* 3.6 23.6 - - - +
32A ARG 3.4 0.2 - - - -
33A VAL* 1.3 77.4 - - - +
35A THR* 1.3 62.5 + - + +
37A PHE* 2.8 38.6 + - + +
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Residues in contact with THR 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 SER 3.3 21.3 - - - +
32A ARG* 3.1 14.7 + - - +
33A VAL 3.2 0.2 - - - -
34A LYS* 1.3 76.3 - - + +
36A PHE* 1.3 67.6 + - - +
37A PHE 3.2 5.0 - - - -
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Residues in contact with PHE 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 ARG 3.3 23.3 - - - -
33A VAL 3.0 12.5 + - - +
35A THR* 1.3 84.3 - - - +
37A PHE* 1.3 67.6 + - + +
84A ASP* 4.3 17.1 - - - +
86A ASP* 3.6 29.8 - - + -
87A ILE* 3.6 29.4 - - + -
90A HIS* 3.4 31.9 - + - -
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Residues in contact with PHE 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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30A PHE* 5.3 4.7 - + + -
33A VAL* 3.1 48.7 - - + -
34A LYS* 2.8 21.1 + - + +
35A THR 4.5 2.9 - - - -
36A PHE* 1.3 87.5 - - - +
80A ALA* 5.0 15.7 - - + -
87A ILE* 3.5 21.3 - - + -
91A VAL* 5.6 1.1 - - + -
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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