Contacts of the helix formed by residues 26 - 37 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLU 4.5 2.5 + - - +
23B GLU 3.8 7.6 + - - +
24B PHE 3.2 2.2 - - - -
25B ARG* 1.3 76.9 - - + +
27B PHE* 1.3 58.9 + - - +
28B SER* 3.4 19.1 + - - -
29B ARG* 3.4 35.6 + - + +
30B TYR* 3.1 28.6 + - - +
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Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ARG 3.6 6.2 + - - +
26B ASN* 1.3 71.5 + - - +
28B SER* 1.3 71.5 + - - +
30B TYR* 3.1 5.2 + - - +
31B ILE* 3.0 39.8 + - + +
148B TRP* 3.4 53.6 - + + +
153B LEU* 4.0 32.8 - - + +
155B THR* 3.9 19.3 - - + -
197B ILE* 3.6 28.3 - - + -
269B ILE* 4.4 0.7 - - + -
291B PHE* 3.8 45.1 - + - -
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASN* 3.4 9.7 + - - -
27B PHE* 1.3 86.6 - - - +
29B ARG* 1.3 58.1 + - - +
31B ILE* 3.3 8.5 + - - +
32B ALA* 3.0 26.9 + - - +
153B LEU 5.2 0.8 + - - -
154B ARG 4.1 17.6 + - - -
155B THR* 4.8 7.6 - - - -
292B ALA 6.0 0.7 - - - -
293B THR* 5.6 6.2 - - - +
349B GLU* 5.5 2.5 - - - +
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU 6.0 1.1 - - - +
26B ASN* 3.4 38.3 + - + +
27B PHE 3.2 0.4 - - - -
28B SER* 1.3 81.5 + - - +
30B TYR* 1.3 56.4 + - - +
32B ALA* 3.3 8.8 + - - +
33B TYR* 2.9 25.2 + - - +
352B GLU* 2.7 40.6 + - - +
353B PHE* 3.8 16.4 - - + -
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Residues in contact with TYR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.4 22.9 - - + +
18B TYR 4.1 1.2 + - - -
19B PRO* 3.4 42.2 - - + +
23B GLU* 3.6 36.1 + - + +
24B PHE* 5.4 0.2 - - - -
26B ASN 3.1 16.8 + - - +
27B PHE 3.1 6.3 + - - +
29B ARG* 1.3 73.9 - - - +
31B ILE* 1.3 60.1 + - - +
33B TYR* 3.2 32.9 + + + +
34B ILE* 2.8 47.5 + - + +
47B VAL* 4.1 5.4 - - + -
148B TRP* 3.8 28.5 - + + +
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Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 3.0 40.3 + - + +
28B SER* 3.6 8.1 - - - +
30B TYR* 1.3 74.8 - - - +
32B ALA* 1.3 65.3 + - - +
34B ILE* 3.4 20.3 + - + +
35B GLU* 3.1 29.7 + - + +
148B TRP* 4.6 6.3 - - + -
195B TYR* 4.0 18.2 - - + -
269B ILE* 3.8 29.8 - - + -
271B PHE* 5.0 1.6 - - + -
291B PHE* 4.1 6.7 - - + -
293B THR* 3.9 25.1 - - + -
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B SER 3.0 12.0 + - - +
29B ARG* 3.3 11.2 + - - +
31B ILE* 1.3 77.1 - - - +
33B TYR* 1.3 57.7 + - - +
35B GLU* 3.5 0.7 + - - +
36B SER* 3.0 22.3 + - - -
293B THR* 5.7 0.2 - - - +
347B THR* 3.9 13.4 - - + +
349B GLU* 3.6 22.2 - - + +
350B ALA* 3.2 38.0 - - - +
353B PHE* 4.1 4.3 - - + -
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Residues in contact with TYR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 4.2 15.0 - + - -
23B GLU* 5.6 2.9 - - - -
29B ARG 2.9 15.0 + - - +
30B TYR* 3.4 48.9 - + + +
31B ILE 3.2 0.4 - - - -
32B ALA* 1.3 73.8 - - - +
34B ILE* 1.3 68.8 + - + +
36B SER* 2.6 29.2 + - - -
37B GLN* 3.2 39.2 + - + +
353B PHE* 3.6 35.3 - + + -
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.7 34.5 - - + -
30B TYR* 2.8 48.2 + - + +
31B ILE* 3.6 32.5 - - + +
33B TYR* 1.3 74.3 - - + +
35B GLU* 1.3 61.8 + - - +
37B GLN* 3.2 9.4 + - - +
39B ALA* 3.1 29.5 + - + +
45B ALA* 4.3 12.1 - - + -
47B VAL* 4.5 12.3 - - + -
269B ILE* 4.5 2.9 - - + -
271B PHE* 3.9 24.0 - - + -
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.2 2.3 - - - +
31B ILE* 3.1 19.9 + - - +
32B ALA* 3.8 5.4 - - - +
34B ILE* 1.3 73.2 - - - +
36B SER* 1.3 56.3 + - - +
37B GLN 3.1 5.2 - - - -
38B GLY 2.9 15.1 + - - -
39B ALA 4.4 0.4 - - - +
40B HIS* 3.1 31.4 - - - +
195B TYR* 2.5 37.1 + - - -
271B PHE* 3.5 15.1 - - + -
295B ARG* 3.0 23.8 + - - -
346B PRO* 3.6 12.3 - - + +
347B THR* 2.8 33.0 + - - +
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.1 26.3 - - - +
32B ALA 3.0 12.9 + - - -
33B TYR* 2.6 35.3 + - - -
35B GLU* 1.3 75.2 - - - +
37B GLN* 1.3 60.0 + - - +
38B GLY 3.4 0.2 - - - -
346B PRO* 4.6 1.6 - - - -
350B ALA* 4.0 8.9 - - - +
353B PHE* 3.7 23.3 - - - +
354B LEU* 3.7 24.3 - - - +
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Residues in contact with GLN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A LYS* 3.4 25.6 - - - +
8B LEU* 4.1 8.3 - - - +
9B ASN* 4.0 10.0 + - - +
15B MET* 3.5 17.0 - - + +
17B PHE* 4.0 18.5 - - + -
33B TYR* 3.2 47.1 + - + +
34B ILE 3.2 9.4 + - - +
35B GLU 3.1 0.8 - - - -
36B SER* 1.3 81.6 + - - +
38B GLY* 1.3 58.6 + - - +
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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