Contacts of the helix formed by residues 26 - 37 (chain A) in PDB entry 2OT7
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 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLU 4.9 1.2 + - - -
23A GLU 4.2 5.7 + - - +
24A PHE 3.2 2.6 + - - +
25A ARG* 1.3 74.3 - - + +
27A PHE* 1.3 60.0 + - - +
28A SER* 3.5 7.4 + - - -
29A ARG* 3.3 38.5 + - + +
30A TYR* 3.0 28.4 + - - +
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Residues in contact with PHE 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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25A ARG 3.4 6.0 + - - +
26A ASN* 1.3 70.3 + - - +
28A SER* 1.3 70.5 + - - +
30A TYR* 3.1 3.7 + - - +
31A ILE* 2.9 42.5 + - + +
148A TRP* 3.5 51.1 - + + +
153A LEU* 3.9 41.1 - - + +
155A THR* 3.8 14.8 - - + -
197A ILE* 3.7 22.0 - - + -
269A ILE* 4.3 0.7 - - + -
291A PHE* 3.8 44.0 - + - -
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Residues in contact with SER 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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26A ASN* 3.5 6.7 + - - -
27A PHE* 1.3 81.9 - - - +
29A ARG* 1.3 58.3 + - - +
31A ILE* 3.1 7.9 + - - +
32A ALA* 3.0 28.1 + - - +
153A LEU 4.8 1.4 + - - -
154A ARG 3.9 12.4 + - - -
155A THR* 3.8 26.2 - - - +
292A ALA 5.1 1.4 + - - -
293A THR* 5.6 6.6 - - - +
349A GLU* 5.7 2.5 - - - +
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Residues in contact with ARG 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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23A GLU 6.1 0.4 - - - +
26A ASN* 3.3 34.1 + - + +
27A PHE 3.2 0.6 - - - -
28A SER* 1.3 80.6 - - - +
30A TYR* 1.3 56.2 + - - +
32A ALA* 3.5 4.9 + - + +
33A TYR* 3.1 21.1 + - - +
352A GLU* 2.9 36.5 + - - +
353A PHE* 3.4 33.1 - - + -
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Residues in contact with TYR 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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17A PHE* 3.2 25.9 - - + +
18A TYR 4.3 1.0 + - - -
19A PRO* 3.5 31.8 - - + +
23A GLU* 3.6 36.8 + - + +
24A PHE* 5.1 0.4 - - - -
26A ASN 3.0 16.3 + - - +
27A PHE* 3.1 4.7 + - - +
29A ARG* 1.3 73.7 - - - +
31A ILE* 1.3 66.2 + - + +
33A TYR* 3.3 28.8 + + + +
34A ILE* 3.0 39.4 + - + +
47A VAL* 4.0 18.8 - - + -
148A TRP* 3.7 29.2 - + + +
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Residues in contact with ILE 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 PHE* 2.9 44.1 + - + +
28A SER* 3.1 7.8 + - - +
30A TYR* 1.3 79.2 - - + +
32A ALA* 1.3 61.5 - - - +
34A ILE* 3.3 22.4 - - + +
35A GLU* 3.1 27.3 + - + +
148A TRP* 4.3 9.0 - - + -
195A TYR* 4.1 26.2 - - + -
269A ILE* 3.7 30.7 - - + -
271A PHE* 4.9 1.6 - - + -
291A PHE* 4.0 6.3 - - + -
293A THR* 4.1 15.7 - - + -
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Residues in contact with ALA 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 SER 3.0 11.7 + - - +
29A ARG* 3.7 10.8 - - - +
31A ILE* 1.3 76.7 - - - +
33A TYR* 1.3 56.1 + - - +
35A GLU* 3.5 1.1 + - - +
36A SER* 2.9 23.2 + - - -
293A THR* 5.8 0.6 - - - +
347A THR* 4.0 13.9 - - + +
349A GLU* 3.7 20.9 - - + +
350A ALA* 3.3 35.8 - - - +
353A PHE* 4.2 4.5 - - + -
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Residues in contact with TYR 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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17A PHE* 4.2 11.1 - + - -
23A GLU* 4.9 10.2 + - - -
29A ARG 3.1 15.1 + - - +
30A TYR* 3.3 46.4 + + + +
32A ALA* 1.3 73.4 - - - +
34A ILE* 1.3 68.5 + - + +
36A SER* 2.5 29.4 + - - -
37A GLN* 3.2 44.7 + - + +
353A PHE* 3.7 35.6 - + + -
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Residues in contact with ILE 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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17A PHE* 3.7 31.6 - - + -
30A TYR* 3.0 42.5 + - + +
31A ILE* 3.3 34.5 - - + +
33A TYR* 1.3 77.3 - - + +
35A GLU* 1.3 62.3 + - - +
37A GLN* 3.1 9.9 + - - +
38A GLY 3.4 0.2 + - - -
39A ALA* 3.1 28.4 + - + +
45A ALA* 4.4 12.6 - - + -
47A VAL* 4.7 4.9 - - + -
269A ILE* 4.6 7.2 - - + -
271A PHE* 3.8 26.2 - - + -
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Residues in contact with GLU 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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8A LEU* 4.3 1.7 - - - +
31A ILE* 3.1 19.8 + - + +
32A ALA* 3.7 6.3 - - - +
34A ILE* 1.3 77.5 - - - +
36A SER* 1.3 55.6 + - - +
37A GLN 3.1 0.2 - - - -
38A GLY* 3.0 14.7 + - - -
39A ALA 4.4 0.4 - - - +
40A HIS* 3.0 28.6 - - - +
195A TYR* 2.6 35.5 + - - -
271A PHE* 3.5 16.9 - - + -
295A ARG* 2.9 27.2 + - - -
346A PRO* 3.5 13.6 - - + +
347A THR* 2.8 34.1 + - + +
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Residues in contact with SER 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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8A LEU* 3.1 26.3 - - - +
32A ALA 2.9 14.3 + - - -
33A TYR* 2.5 25.7 + - - -
35A GLU* 1.3 73.9 - - - +
37A GLN* 1.3 70.7 + - - +
38A GLY 3.3 0.4 - - - -
346A PRO* 4.6 0.4 - - - -
350A ALA* 4.0 8.6 - - - +
353A PHE* 3.6 24.8 + - - +
354A LEU* 3.8 27.5 - - - +
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Residues in contact with GLN 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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8A LEU* 4.1 9.6 - - - +
9A ASN* 4.0 6.8 + - - +
15A MET* 3.5 22.2 - - + +
17A PHE* 4.1 18.6 - - + -
33A TYR* 3.6 50.7 + - + +
34A ILE 3.1 10.1 + - - +
36A SER* 1.3 90.9 + - - +
38A GLY* 1.3 57.1 + - - +
39A ALA 3.4 0.4 - - - -
353A PHE 5.7 1.6 + - - -
354A LEU* 6.1 0.2 - - - +
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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