Contacts of the helix formed by residues 30 - 43 (chain B) in PDB entry 5T8Y
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 PHE 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B THR* 5.5 0.7 - - + -
28B ASP 4.0 1.6 - - - -
29B THR* 1.3 70.0 - - - +
31B ASP* 1.3 64.6 + - - +
32B SER 3.3 2.7 - - - -
33B LEU* 3.1 24.7 + - + +
34B LYS* 3.1 22.2 + - - +
57B ARG 4.7 3.8 - - - -
58B VAL* 3.0 28.4 + - - +
60B PRO* 3.9 17.0 - - + -
70B ILE* 4.8 3.4 - - + -
138B LEU* 4.6 6.7 - - + -
139B SER 6.0 0.9 - - - -
142B ALA* 3.6 35.7 - - + -
143B VAL* 3.6 30.7 - - + -
146B ARG* 3.3 45.5 - - - +
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Residues in contact with ASP 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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29B THR* 3.0 31.1 + - - +
30B PHE* 1.3 72.5 - - - +
32B SER* 1.3 62.3 + - - +
33B LEU 3.3 0.7 + - - -
34B LYS* 3.5 13.7 + - - +
35B ASP* 3.4 23.8 + - - +
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Residues in contact with SER 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 3.3 0.8 - - - -
31B ASP* 1.3 79.9 - - - +
33B LEU* 1.3 60.2 + - - +
35B ASP* 4.1 4.5 + - - +
36B ARG* 3.4 13.3 + - - +
503B B12 3.1 32.1 + - - -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 3.1 26.4 + - + +
32B SER* 1.3 79.3 - - - +
34B LYS* 1.3 54.9 + - - +
36B ARG* 3.1 3.5 + - - +
37B LEU* 2.8 60.2 + - + +
57B ARG* 3.8 20.9 - - + +
58B VAL* 3.9 8.7 - - + -
139B SER* 3.6 35.4 - - - +
142B ALA* 4.3 12.1 - - + -
503B B12 3.5 33.6 - - + +
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A GLU* 4.7 9.4 - - - -
372A ILE* 6.1 2.6 - - - +
373A GLU* 5.6 1.6 - - - -
30B PHE 3.1 12.1 + - - +
31B ASP* 3.5 8.9 + - - +
33B LEU* 1.3 76.7 - - - +
35B ASP* 1.3 68.7 + - - +
37B LEU* 3.4 5.1 + - - +
38B ILE* 3.2 42.0 + - + +
54B ILE* 4.2 13.9 - - + +
55B GLU* 4.0 24.6 + - - -
58B VAL* 3.7 28.6 - - + +
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Residues in contact with ASP 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 2.9 36.0 - - - +
31B ASP* 3.4 17.4 + - - +
32B SER* 4.5 4.3 - - - +
33B LEU 3.3 0.2 - - - -
34B LYS* 1.3 82.4 - - - +
36B ARG* 1.3 57.5 + - - +
38B ILE* 3.5 3.1 + - - +
39B LEU* 3.0 28.1 + - - +
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Residues in contact with ARG 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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32B SER 3.4 17.4 + - - +
33B LEU* 3.1 5.1 + - - +
35B ASP* 1.3 78.0 - - - +
37B LEU* 1.3 59.4 + - - +
39B LEU* 3.3 27.0 + - - +
40B GLN* 2.9 54.0 + - + +
205B ASN* 5.5 0.4 - - - +
207B GLY 4.7 0.6 + - - -
208B GLN* 3.3 39.2 + - - +
503B B12 3.3 91.5 - - + +
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Residues in contact with LEU 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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33B LEU* 2.8 40.1 + - + +
34B LYS 3.7 4.7 - - - +
35B ASP 3.3 0.2 - - - -
36B ARG* 1.3 77.5 - - - +
38B ILE* 1.3 60.8 + - - +
40B GLN* 4.0 3.4 - - - +
41B GLU* 3.1 24.8 + - - +
46B LEU* 4.2 16.1 - - + +
50B GLU* 5.6 0.4 - - + -
54B ILE* 3.8 34.2 - - + +
57B ARG* 4.1 43.1 - - + +
58B VAL* 4.2 2.2 - - + -
503B B12 3.8 27.4 - - + +
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Residues in contact with ILE 38 (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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366A LEU* 5.3 4.0 - - + -
369A GLU* 4.2 26.7 - - + +
370A LYS* 4.4 25.5 - - + -
373A GLU* 3.4 30.1 - - + +
34B LYS* 3.2 31.9 + - + +
35B ASP* 3.8 4.7 - - - +
36B ARG 3.3 0.2 - - - -
37B LEU* 1.3 75.4 - - - +
39B LEU* 1.3 59.7 + - - +
41B GLU* 3.3 6.7 + - - +
42B SER* 2.9 30.5 + - - -
54B ILE* 3.8 20.0 - - + -
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Residues in contact with LEU 39 (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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35B ASP 3.0 19.0 + - - +
36B ARG* 3.5 36.6 - - - +
38B ILE* 1.3 78.3 - - - +
40B GLN* 1.3 62.8 + - - +
42B SER* 3.2 9.2 + - - -
43B LEU* 3.2 44.6 + - + +
208B GLN* 4.9 4.3 - - - +
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Residues in contact with GLN 40 (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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36B ARG* 2.9 36.7 + - - +
37B LEU* 4.0 1.6 - - - +
39B LEU* 1.3 76.5 - - - +
41B GLU* 1.3 57.6 + - - +
43B LEU* 3.5 2.6 + - - -
44B GLY 3.2 3.3 + - - -
45B TYR* 2.8 45.7 + - + +
46B LEU* 3.7 21.9 - - + +
208B GLN* 2.7 41.7 + - - +
209B LEU* 3.2 29.3 + - - +
503B B12 4.3 16.3 - - + +
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Residues in contact with GLU 41 (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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366A LEU* 3.4 32.7 - - + +
367A GLU* 5.6 0.2 - - - +
370A LYS* 3.2 32.0 + - - -
37B LEU 3.1 19.5 + - - +
38B ILE* 3.6 6.3 - - - +
39B LEU 3.2 0.2 - - - -
40B GLN* 1.3 74.4 - - - +
42B SER* 1.3 59.5 + - - +
44B GLY* 3.0 19.0 + - - -
45B TYR 4.8 0.7 - - - +
46B LEU* 3.8 24.0 - - + +
54B ILE* 6.0 0.7 - - + -
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Residues in contact with SER 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASP* 3.3 47.5 + - - +
228A GLU* 4.9 3.5 + - - +
370A LYS* 5.1 3.4 - - - -
38B ILE* 2.9 20.6 + - - -
39B LEU* 3.5 12.3 - - - -
41B GLU* 1.3 82.9 + - - +
43B LEU* 1.3 64.3 + - - +
44B GLY 3.3 0.6 + - - -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLU* 6.4 2.0 - - + -
39B LEU* 3.2 32.3 + - + +
40B GLN* 3.5 0.9 + - - +
41B GLU 3.1 0.6 - - - -
42B SER* 1.3 83.0 - - - +
44B GLY* 1.3 63.0 + - - +
45B TYR* 3.4 49.2 - - + +
208B GLN* 3.7 17.0 - - - +
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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