Contacts of the helix formed by residues 24 - 35 (chain A) in PDB entry 2OIL
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 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLY 3.4 0.8 + - - -
23A VAL* 1.3 79.3 - - - +
25A LYS* 1.3 62.2 + - - +
26A THR 3.4 1.8 - - - -
27A ASN* 3.3 2.6 + - - +
28A LEU* 2.9 38.2 + - - +
91A VAL* 4.8 0.2 - - - -
125A ASN* 3.7 3.7 + - - -
201A GDP 2.9 37.4 + - - -
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Residues in contact with LYS 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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17A LEU* 2.9 36.5 - - + +
18A ILE* 3.5 34.8 - - - +
19A GLY 3.1 10.3 + - - +
20A GLU 2.8 25.3 + - - -
21A SER* 3.7 6.7 - - - +
23A VAL* 3.7 13.0 - - + +
24A GLY* 1.3 77.2 - - - +
26A THR* 1.3 63.1 + - - +
28A LEU* 3.3 7.9 + - - +
29A LEU 3.1 9.7 + - - -
67A ASP* 3.8 9.2 - - - +
68A THR 4.4 16.2 - - - -
69A ALA* 6.1 0.9 - - - +
91A VAL* 4.0 13.0 - - + -
201A GDP 2.7 30.7 + - - +
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Residues in contact with THR 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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25A LYS* 1.3 76.2 - - - +
27A ASN* 1.3 58.3 + - - +
29A LEU* 3.4 7.4 + - + +
30A SER* 3.0 28.1 + - - +
34A ARG* 6.0 1.8 - - - +
41A SER* 3.8 29.6 - - - +
42A ARG 6.0 0.4 - - - +
43A THR* 5.7 6.3 - - - -
48A GLU* 5.4 5.8 - - - +
67A ASP* 2.8 23.9 + - - +
201A GDP 3.1 13.0 + - - -
301A MG 2.0 32.2 - - - -
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Residues in contact with ASN 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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24A GLY 3.9 3.6 - - - +
25A LYS 3.2 0.4 - - - -
26A THR* 1.3 76.2 - - - +
28A LEU* 1.3 59.5 + - - +
30A SER* 3.3 11.1 + - - -
31A ARG* 2.9 31.9 + - - +
36A GLU 4.1 0.7 - - - +
37A PHE* 3.2 26.8 - - + -
38A SER* 3.0 38.5 + - - -
39A HIS* 5.0 0.6 + - - +
41A SER* 3.7 16.2 + - - -
156A ALA* 3.7 7.6 - - + +
201A GDP 2.8 44.1 + - + +
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Residues in contact with LEU 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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17A LEU* 4.8 2.0 - - + -
24A GLY 2.9 21.8 + - - +
25A LYS* 3.6 4.9 - - - +
27A ASN* 1.3 73.2 - - - +
29A LEU* 1.3 65.8 + - - +
31A ARG* 4.0 2.0 - - - +
32A PHE* 3.0 26.5 + - - +
89A LEU* 5.0 5.2 - - + -
91A VAL* 3.8 38.8 - - + -
123A VAL* 4.3 7.9 - - + -
125A ASN* 3.8 12.8 - - - +
154A THR* 3.7 19.3 - - + +
156A ALA* 3.9 8.5 - - + -
162A VAL* 3.6 32.2 - - + +
165A ALA* 6.0 0.7 - - + -
166A PHE* 3.5 18.6 - - + -
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Residues in contact with LEU 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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17A LEU* 3.8 8.8 - - + +
25A LYS 3.1 12.9 + - - +
26A THR* 3.4 12.1 - - + +
27A ASN 3.3 0.2 - - - -
28A LEU* 1.3 77.8 - - - +
30A SER* 1.3 58.0 + - - +
32A PHE* 3.2 1.0 + - - -
33A THR* 2.8 43.1 + - + +
34A ARG* 3.9 13.5 - - - +
48A GLU* 4.9 7.6 - - + +
49A PHE* 4.9 0.4 - - - -
50A SER* 3.4 26.7 - - - +
65A ILE* 3.5 43.3 - - + +
67A ASP* 3.5 28.5 - - + +
166A PHE* 4.6 1.8 - - - -
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Residues in contact with SER 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 THR* 3.0 19.9 + - - +
27A ASN* 3.3 18.2 + - - -
29A LEU* 1.3 75.8 - - - +
31A ARG* 1.3 59.3 + - - +
33A THR* 4.1 1.1 - - - -
34A ARG* 2.8 55.6 + - - +
35A ASN 3.0 6.6 + - - -
36A GLU* 3.0 29.5 + - - -
37A PHE* 4.4 0.2 - - - -
38A SER* 4.9 1.2 + - - -
41A SER* 5.7 0.2 + - - -
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Residues in contact with ARG 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 ASN 2.9 20.9 + - - +
28A LEU* 4.0 3.1 - - - +
30A SER* 1.3 77.7 - - - +
32A PHE* 1.3 58.9 + - - +
35A ASN* 2.8 71.2 + - - +
36A GLU 3.1 10.1 + - - +
37A PHE* 3.4 22.3 - - - +
52A ARG* 5.1 0.5 + - - -
156A ALA* 2.8 23.7 + - + +
157A LEU 3.1 23.6 + - - -
159A SER* 3.3 26.2 + - - -
162A VAL* 3.6 27.8 - - + -
163A GLU* 6.0 0.3 - - - +
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Residues in contact with PHE 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 LEU 3.0 19.3 + - - +
29A LEU 3.9 1.3 - - - +
31A ARG* 1.3 80.6 - - - +
33A THR* 1.3 72.1 + - + +
35A ASN 4.6 0.5 + - - -
52A ARG* 2.7 69.0 + - + +
54A VAL* 3.8 25.8 - - + -
63A ALA* 4.3 5.6 - - + -
65A ILE* 4.1 13.7 - - + -
162A VAL* 4.0 5.8 - - + -
163A GLU* 4.0 22.9 - - + -
166A PHE* 3.4 56.1 - + + -
167A GLU* 4.8 3.8 - - + -
170A LEU* 4.3 4.3 - - + -
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Residues in contact with THR 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 LEU* 2.8 33.4 + - + +
30A SER* 4.1 0.5 - - - -
32A PHE* 1.3 81.1 - - + +
34A ARG* 1.3 68.9 + - - +
50A SER* 3.6 35.4 - - - +
51A THR 3.9 20.4 - - - +
52A ARG* 4.3 11.5 - - - +
65A ILE* 3.9 26.7 - - + -
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Residues in contact with ARG 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 THR* 6.0 2.6 - - - +
29A LEU* 3.9 7.9 - - - +
30A SER* 2.8 38.6 + - - +
33A THR* 1.3 87.3 + - - +
35A ASN* 1.3 70.8 + - - +
36A GLU* 3.3 38.0 + - + +
50A SER* 3.1 26.7 + - - -
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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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30A SER 3.0 2.6 + - - -
31A ARG* 2.8 59.1 + - - +
32A PHE 4.5 0.4 + - - -
33A THR 3.8 0.6 - - - -
34A ARG* 1.3 80.0 - - - +
36A GLU* 1.3 60.1 + - - +
159A SER* 4.3 2.4 + - - -
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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