Contacts of the helix formed by residues 29 - 39 (chain A) in PDB entry 1RE0
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ALA 3.2 0.6 - - - -
28A ALA* 1.3 80.7 - - - +
30A LYS* 1.3 67.4 + - - +
32A THR* 3.4 1.4 + - - -
33A ILE* 3.0 33.9 + - - +
91A VAL* 4.4 0.7 - - - -
126A ASN* 4.0 9.0 - - - -
700A GDP 3.0 32.8 + - - -
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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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22A MET* 3.1 43.9 - - + +
23A VAL* 3.7 25.4 - - - +
24A GLY* 3.0 23.5 + - - +
25A LEU 3.3 9.3 + - - -
26A ASP* 4.3 2.6 - - - +
28A ALA* 4.9 0.4 - - + -
29A GLY* 1.3 79.0 - - - +
31A THR* 1.3 62.1 + - - +
33A ILE* 3.3 1.9 + - - -
34A LEU* 3.1 19.6 + - - +
65A VAL* 3.7 22.2 - - + -
66A TRP 5.2 2.5 - - - -
67A ASP* 4.6 10.8 - - - +
91A VAL* 4.1 18.2 - - + -
700A GDP 2.8 33.0 + - - +
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Residues in contact with THR 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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30A LYS* 1.3 73.2 - - - +
32A THR* 1.3 65.3 + - - +
34A LEU* 3.2 4.9 + - - +
35A TYR* 2.9 23.5 + - + +
54A GLU* 2.9 26.7 + - - +
700A GDP 2.9 21.8 + - - +
701A MG 1.8 33.7 - - - -
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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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29A GLY 3.7 4.5 - - - -
31A THR* 1.3 73.4 - - - +
33A ILE* 1.3 63.2 + - - +
35A TYR* 3.1 20.1 + - + +
36A LYS* 3.2 16.2 + - + +
160A ALA* 3.6 28.3 - - + +
161A THR* 3.9 14.1 - - + +
700A GDP 2.7 59.8 + - + +
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Residues in contact with ILE 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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22A MET* 4.6 11.9 - - + -
29A GLY 3.0 21.9 + - - +
30A LYS* 3.6 5.2 - - - +
32A THR* 1.3 76.8 - - - +
34A LEU* 1.3 57.1 + - + +
36A LYS* 3.4 3.6 + - - +
37A LEU* 3.1 43.3 + - + +
91A VAL* 4.0 28.7 - - + -
124A PHE* 4.1 20.4 - - + -
126A ASN* 4.7 6.1 - - - -
158A THR* 5.2 0.2 - - - +
160A ALA* 3.4 22.0 - - + -
166A LEU* 3.7 33.4 - - + +
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Residues in contact with LEU 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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22A MET* 3.2 38.8 - - + -
30A LYS 3.1 11.0 + - - +
31A THR* 3.8 5.2 - - - +
33A ILE* 1.3 77.9 - - + +
35A TYR* 1.3 60.6 + - - +
37A LEU* 3.9 9.3 - - + +
38A LYS* 3.0 34.6 + - + +
54A GLU* 3.1 51.4 - - + +
55A THR* 3.3 16.8 - - - +
56A VAL* 4.3 14.1 - - + +
63A PHE* 4.6 7.9 - - + +
65A VAL* 3.6 5.4 - - + +
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Residues in contact with TYR 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 THR* 2.9 14.7 + - + +
32A THR* 3.1 17.7 + - + +
34A LEU* 1.3 76.6 - - - +
36A LYS* 1.3 82.4 + - + +
38A LYS* 3.1 22.7 + - + +
39A LEU* 3.7 3.5 + - - +
42A ILE* 4.5 23.0 - - + +
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Residues in contact with LYS 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* 3.2 8.4 + - + +
33A ILE 3.4 6.7 + - - +
35A TYR* 1.3 94.4 - - + +
37A LEU* 1.3 63.2 + - + +
38A LYS 3.2 0.9 + - - -
39A LEU* 3.3 25.8 - - + +
160A ALA 3.1 19.7 - - - +
161A THR* 2.7 31.9 + - - +
162A SER* 4.4 11.6 + - - +
163A GLY* 4.6 4.0 - - - +
166A LEU* 4.1 14.4 - - + -
167A TYR* 4.5 4.4 + - + -
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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 ILE* 3.1 37.3 + - + +
34A LEU* 4.2 10.1 - - + +
36A LYS* 1.3 77.9 - - + +
38A LYS* 1.3 66.7 + - - +
39A LEU* 4.0 7.4 - - - +
56A VAL* 4.0 35.8 - - + +
58A TYR* 5.7 2.9 - - + -
63A PHE* 6.0 3.6 - - + -
166A LEU* 4.6 12.6 - - + -
167A TYR* 3.7 33.2 + - + +
170A LEU* 3.6 36.6 - - + -
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Residues in contact with LYS 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 LEU* 3.0 20.3 + - + +
35A TYR* 3.1 17.7 - - + +
36A LYS 3.1 1.6 - - - -
37A LEU* 1.3 79.2 - - - +
39A LEU* 1.3 65.7 + - - +
40A GLY* 2.7 29.8 + - - +
42A ILE* 6.3 2.7 - - + -
43A VAL* 6.5 1.8 - - - -
53A VAL 5.9 0.2 + - - -
54A GLU* 5.7 0.6 - - - +
55A THR 2.5 33.3 + - - +
56A VAL* 4.5 11.3 - - + +
269B GLN* 3.2 25.6 + - - +
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Residues in contact with LEU 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 TYR 3.7 4.2 + - - +
36A LYS* 3.3 21.1 - - + +
37A LEU 4.0 6.5 - - - +
38A LYS* 1.3 80.6 - - - +
40A GLY* 1.3 64.6 + - - +
167A TYR* 4.3 12.3 - - - +
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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