Contacts of the strand formed by residues 36 - 46 (chain B) in PDB entry 3QTA
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 ALA 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ALA* 3.7 22.3 + - - +
28B LEU* 4.0 15.5 - - + -
34B VAL* 3.7 4.7 + - + -
35B ASP* 1.3 79.7 + - - +
37B ALA* 1.3 61.0 + - - +
167B VAL* 3.8 17.9 - - + -
168B ASP 3.3 13.0 - - - +
169B ILE* 3.8 19.7 - - + -
170B LYS* 4.1 13.9 + - - +
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Residues in contact with ALA 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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25B ALA* 5.1 1.1 - - - -
36B ALA* 1.3 72.7 - - - +
38B VAL* 1.3 61.0 + - - +
39B GLU* 3.9 22.9 - - + +
166B LEU 3.5 1.7 - - - +
167B VAL* 3.6 1.9 - - - -
168B ASP* 2.9 42.0 + - + +
170B LYS* 4.1 15.0 - - + +
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Residues in contact with VAL 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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18B GLN* 4.7 7.3 + - - -
21B ALA* 3.6 40.8 - - + +
24B VAL* 3.7 31.2 - - + -
25B ALA* 3.9 21.8 - - + +
28B LEU* 4.1 10.5 - - + -
36B ALA 4.2 0.9 + - - +
37B ALA* 1.3 77.2 - - - +
39B GLU* 1.3 64.4 + - - +
40B ILE* 5.2 0.4 - - + -
119B PHE* 6.3 0.4 - - + -
165B SER* 3.6 18.8 - - - +
166B LEU 3.5 3.6 - - - +
167B VAL* 4.3 11.9 - - + -
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Residues in contact with GLU 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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18B GLN* 5.8 0.2 - - - -
37B ALA* 3.9 21.1 - - + +
38B VAL* 1.3 78.9 - - - +
40B ILE* 1.3 65.2 + - - +
41B LYS* 2.9 32.9 + - + +
165B SER* 3.1 5.5 + - - -
166B LEU* 2.9 45.7 + - + +
168B ASP* 4.6 11.7 - - - +
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Residues in contact with ILE 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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43A LEU* 3.6 22.6 - - - +
17B ILE* 3.7 33.0 - - + +
18B GLN* 4.2 20.7 + - - +
21B ALA* 4.3 17.5 - - + -
38B VAL* 5.2 0.4 - - + -
39B GLU* 1.3 72.0 - - - +
41B LYS* 1.3 63.2 + - - +
42B SER 3.6 24.9 - - - +
43B LEU* 4.8 6.1 - - + -
119B PHE* 4.7 5.4 - - + -
163B LEU* 4.4 10.8 - - + -
164B ASP 3.7 2.2 - - - +
165B SER* 3.9 23.8 - - - +
180B ILE* 6.0 0.2 - - + -
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Residues in contact with LYS 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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41A LYS* 4.0 27.3 + - - +
43A LEU* 3.3 18.2 - - - +
164A ASP* 5.1 0.9 - - - +
39B GLU* 2.9 37.3 + - + +
40B ILE* 1.3 77.0 - - - +
42B SER* 1.3 59.6 + - - +
164B ASP* 2.7 29.1 + - + +
165B SER 4.8 0.4 - - - -
166B LEU* 3.9 33.6 - - + +
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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
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41A LYS* 3.8 24.7 - - - -
42A SER 3.3 13.9 - - - -
43A LEU* 4.3 3.6 - - - +
40B ILE* 3.5 11.7 - - - +
41B LYS* 1.3 81.1 - - - +
43B LEU* 1.3 61.8 + - - +
44B SER* 4.5 7.5 + - - -
162B VAL* 4.3 2.0 + - - +
163B LEU* 3.3 5.2 - - - -
164B ASP* 2.8 46.6 + - - +
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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
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42A SER* 2.9 33.3 + - - +
43A LEU 4.1 13.2 + - - +
45A PHE* 3.6 22.6 - - + -
13B ILE* 4.0 13.5 - - + -
14B THR* 4.2 20.6 - - - +
17B ILE* 3.6 32.8 - - + -
40B ILE* 4.8 4.3 - - + -
42B SER* 1.3 74.9 - - - +
44B SER* 1.3 61.8 + - - +
45B PHE* 3.7 22.9 - - + -
161B ILE* 4.1 6.1 - - + -
162B VAL 3.4 4.7 - - - -
163B LEU* 3.7 13.5 - - + -
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Residues in contact with SER 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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14A THR* 3.9 18.6 - - - +
41A LYS* 5.0 4.2 - - - +
42A SER* 4.7 9.4 + - - -
42B SER* 4.5 9.5 + - - -
43B LEU* 1.3 78.4 + - - +
45B PHE* 1.3 70.0 + - - +
46B VAL* 4.9 3.6 - - - -
54B GLU* 5.7 3.6 - - - -
161B ILE* 3.4 6.1 - - - +
162B VAL* 2.8 41.4 + - - -
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Residues in contact with PHE 45 (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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10A LEU* 3.5 48.2 - - + +
11A THR* 3.6 9.5 - - - +
13A ILE* 4.7 6.5 - - + -
14A THR* 2.9 34.6 + - - +
45A PHE* 3.6 30.5 - + - -
10B LEU* 4.3 9.2 - - + -
13B ILE* 4.4 12.6 - - + -
43B LEU* 3.7 25.8 - - + -
44B SER* 1.3 80.9 - - - +
46B VAL* 1.3 63.8 + - - +
159B LEU* 3.8 33.2 - - + -
160B THR 3.4 2.5 - - - -
161B ILE* 4.1 19.3 - - + -
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Residues in contact with VAL 46 (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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11A THR* 3.5 12.6 - - - +
14A THR* 4.7 9.4 - - + -
44B SER* 4.9 2.7 - - - -
45B PHE* 1.3 82.6 - - - +
47B GLN* 1.3 70.1 + - - +
48B PRO* 4.0 0.2 - - - +
50B ASP* 4.8 10.8 - - + +
51B ILE* 4.0 9.4 - - + -
54B GLU* 4.4 22.2 - - + +
158B SER 4.4 0.2 - - - +
160B THR* 3.0 44.8 + - + -
162B VAL* 3.8 29.8 - - + -
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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