Contacts of the helix formed by residues 31 - 45 (chain B) in PDB entry 6A5T
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 VAL 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLY 3.4 0.6 - - - -
30B LEU* 1.3 86.3 - - + +
32B SER* 1.3 63.4 + - - +
33B GLN* 2.9 16.8 + - - +
34B GLN* 3.2 21.4 + - + +
35B LEU* 4.1 11.9 + - + +
190B MET* 3.5 36.3 - - + +
192B GLY* 5.2 4.7 - - - -
485B LEU* 4.4 7.0 - - + -
488B LEU* 3.5 35.7 - - + +
489B ARG* 4.2 10.8 - - + +
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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
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28B LYS* 3.4 48.5 + - - +
29B GLY 3.9 1.4 + - - -
30B LEU 3.4 2.8 + - - -
31B VAL* 1.3 77.6 - - - +
33B GLN* 1.3 68.5 + - - +
35B LEU* 3.0 12.1 + - - +
36B ASP* 2.9 36.6 + - - +
536B SER 5.7 0.5 + - - -
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU 4.1 3.5 - - - +
31B VAL* 2.9 22.4 + - - +
32B SER* 1.3 74.4 + - - +
34B GLN* 1.3 76.6 - - + +
36B ASP* 4.0 5.8 - - - +
37B SER* 2.7 37.8 + - - -
401B LEU* 3.9 22.0 - - + -
488B LEU 4.8 5.3 + - - -
489B ARG* 4.8 15.9 + - - +
532B LEU* 4.8 15.9 - - + +
536B SER 5.4 6.0 - - - +
537B GLY* 5.9 0.9 - - - -
538B ILE* 4.3 28.0 - - + +
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 3.2 18.3 + - + +
33B GLN* 1.3 92.8 - - - +
35B LEU* 1.3 63.0 + - + +
37B SER* 3.9 3.4 - - - -
38B PHE* 2.8 33.1 + - - +
164B MET* 3.8 29.1 - - - +
192B GLY* 4.1 13.8 - - - +
202B VAL* 5.7 1.7 - - - +
203B LEU* 4.2 21.0 + - - +
205B ALA* 5.1 10.5 - - - +
401B LEU* 5.1 6.6 - - - +
402B ALA* 4.3 12.8 + - - +
488B LEU* 3.6 26.0 + - + +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 4.6 13.2 - - + +
32B SER* 3.0 11.0 + - - +
34B GLN* 1.3 76.0 - - + +
36B ASP* 1.3 63.1 + - - +
38B PHE* 4.4 1.8 - - + -
39B ASP* 2.9 42.3 + - - +
164B MET* 3.4 27.4 - - + -
165B LEU 3.7 16.4 - - - +
166B ARG* 3.7 32.1 - - + +
167B SER* 4.5 3.4 - - - +
173B ARG* 4.6 4.9 - - - +
190B MET* 4.4 11.0 - - + +
192B GLY* 4.4 4.7 - - - -
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B SER* 2.9 25.1 + - - +
33B GLN* 4.0 6.5 - - - +
35B LEU* 1.3 78.8 - - - +
37B SER* 1.3 61.3 + - - +
39B ASP* 3.8 7.7 - - - +
40B GLU* 3.0 24.4 + - - +
540B ILE* 3.5 23.4 - - + +
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Residues in contact with SER 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN 2.7 21.7 + - - -
34B GLN* 4.0 1.8 - - - -
36B ASP* 1.3 71.2 - - - +
38B PHE* 1.3 65.6 + - - +
40B GLU* 3.1 8.4 + - - +
41B PHE* 2.9 21.5 + - - +
401B LEU* 3.6 30.1 - - - +
402B ALA 5.1 0.4 - - - -
403B GLY* 3.1 28.3 + - - -
404B PRO* 3.9 5.4 - - - +
540B ILE* 4.2 6.6 - - - +
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Residues in contact with PHE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN 2.8 22.9 + - - +
35B LEU* 4.0 3.4 - - + +
37B SER* 1.3 72.8 + - - +
39B ASP* 1.3 71.9 + - - +
41B PHE* 3.1 9.2 - + - +
42B MET* 3.0 49.2 + - + +
161B VAL* 5.1 0.4 - - + -
162B PRO 3.4 13.0 - - - -
163B ILE* 3.9 9.6 - - + -
164B MET* 3.2 62.4 - - + -
167B SER* 4.3 6.3 - - - -
194B PHE* 3.5 19.3 - + - -
402B ALA* 4.4 6.9 - - + +
403B GLY* 4.6 4.4 - - - +
406B LEU* 3.8 17.7 - - + -
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Residues in contact with ASP 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 2.9 30.3 + - - +
36B ASP* 3.8 8.7 - - - +
38B PHE* 1.3 78.7 - - - +
40B GLU* 1.3 67.4 + - - +
41B PHE 3.2 0.2 + - - -
42B MET* 3.2 3.8 + - - +
43B GLU* 3.0 40.8 + - - +
167B SER* 3.4 27.2 - - - -
168B LYS* 3.5 35.8 + - + +
169B PHE* 4.4 5.0 - - - -
173B ARG* 4.8 1.9 + - - -
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Residues in contact with GLU 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 ASP 3.0 14.7 + - - +
37B SER* 3.4 9.4 - - - +
39B ASP* 1.3 74.6 - - - +
41B PHE* 1.3 67.7 + - - +
43B GLU* 3.9 5.0 - - - +
44B THR* 3.0 38.1 + - - +
45B SER* 3.5 9.6 + - - +
540B ILE* 4.2 33.7 - - + +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER 2.9 11.8 + - - +
38B PHE* 3.1 15.0 - + - +
39B ASP 3.1 0.2 - - - -
40B GLU* 1.3 78.6 - - - +
42B MET* 1.3 91.1 + - + +
43B GLU 2.7 12.6 + - - -
45B SER* 2.9 41.5 + - - +
46B ILE* 3.5 31.7 + - + -
49B LEU* 5.5 0.4 - - + -
161B VAL* 4.2 6.3 - - + -
403B GLY* 3.9 23.6 - - - -
406B LEU* 3.4 47.8 - - + -
407B ALA* 3.6 13.7 - - - -
410B PHE* 4.9 5.4 - + + -
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Residues in contact with MET 42 (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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38B PHE* 3.0 38.2 + - + +
39B ASP* 3.2 4.0 + - - +
41B PHE* 1.3 103.0 - - + +
43B GLU* 1.3 60.6 + - - +
46B ILE* 4.5 14.7 - - + +
47B GLN 5.7 0.3 + - - -
84B LEU* 3.8 40.8 - - + +
113B SER* 5.6 2.9 - - - -
161B VAL* 3.4 30.1 - - + -
163B ILE* 3.7 20.9 - - + -
169B PHE* 4.4 23.5 - - + -
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Residues in contact with GLU 43 (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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39B ASP* 3.0 23.5 + - - +
40B GLU* 4.2 5.2 - - - +
41B PHE 2.7 6.5 + - - -
42B MET* 1.3 77.9 - - - +
44B THR* 1.3 66.3 + - - +
46B ILE 5.2 0.2 - - - -
47B GLN* 4.4 9.6 - - - +
168B LYS* 4.1 19.9 + - - +
169B PHE* 3.6 34.8 - - + -
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Residues in contact with THR 44 (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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40B GLU* 3.0 25.1 + - - +
43B GLU* 1.3 86.1 + - - +
45B SER* 1.3 68.9 + - - +
46B ILE 3.3 2.2 - - - -
47B GLN* 3.4 6.8 + - + +
48B ASP* 3.0 41.3 + - + +
237B LYS* 5.9 1.6 - - - +
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLU* 3.7 8.1 + - - +
41B PHE* 2.9 43.7 + - - -
44B THR* 1.3 79.7 - - - +
46B ILE* 1.3 57.4 + - - +
48B ASP* 3.4 2.7 + - - +
49B LEU* 2.8 32.6 + - - +
403B GLY 5.8 1.0 - - - -
407B ALA* 4.6 13.5 - - - +
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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