Contacts of the helix formed by residues 43 - 52 (chain B) in PDB entry 3U44
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 MET 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B THR* 4.3 21.1 - - + +
39B VAL* 3.9 11.0 - - + -
40B PRO* 2.9 17.7 + - + +
42B GLN* 1.3 79.4 - - - +
44B THR* 1.3 63.7 + - - +
45B PHE 3.6 1.8 - - - -
46B LEU* 3.4 11.4 + - + +
47B MET* 3.2 41.9 + - + +
208B ASP* 4.0 11.9 - - - +
209B GLY* 3.9 27.1 - - - -
597B ARG* 3.8 29.6 - - + +
598B MET 4.9 11.7 - - - +
599B TYR* 5.1 5.4 - - + -
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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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1027A ASP* 4.9 0.2 + - - -
1029A TYR* 4.0 12.5 - - - -
39B VAL* 3.9 9.9 - - + -
40B PRO 3.4 11.4 + - - +
41B ASP 2.8 25.8 + - - +
42B GLN 3.4 0.2 - - - -
43B MET* 1.3 76.7 - - - +
45B PHE* 1.3 67.8 + - - +
46B LEU 3.2 0.7 + - - -
47B MET 3.2 2.8 + - - -
48B GLU* 3.1 26.5 + - - +
65B VAL* 3.5 13.3 - - + +
67B SER* 4.0 23.1 - - - +
70B ARG* 3.1 30.6 + - - +
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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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1012A THR* 5.8 7.4 - - + +
1013A LYS* 3.9 15.3 - - + +
1027A ASP* 5.7 0.2 - - - +
1029A TYR* 3.3 49.6 - + + -
42B GLN 3.4 22.9 - - - -
44B THR* 1.3 81.2 + - - +
46B LEU* 1.3 91.5 + - + +
47B MET 3.4 0.2 - - - -
48B GLU* 3.5 13.8 - - - +
49B TYR* 3.3 21.7 + - + +
371B PHE* 4.6 11.9 - + - -
583B PRO* 3.4 36.3 - - + -
589B PHE* 5.1 10.1 - + - -
597B ARG 5.6 0.2 - - - -
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Residues in contact with LEU 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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42B GLN 4.1 9.9 - - - +
43B MET* 3.4 13.7 + - + +
44B THR 3.1 0.4 - - - -
45B PHE* 1.3 111.9 - - + +
47B MET* 1.3 66.3 + - + +
49B TYR* 3.5 6.1 + - - +
50B GLU* 3.3 25.7 + - - +
589B PHE* 6.2 2.2 - - + -
597B ARG* 3.2 39.3 - - + +
598B MET* 3.6 14.8 - - - +
599B TYR* 4.8 14.4 - - + +
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Residues in contact with MET 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 3.3 34.3 - - + -
19B ILE* 3.4 22.4 - - + -
37B PHE* 3.2 39.7 - - + -
39B VAL* 4.2 14.4 - - + -
43B MET* 3.2 36.3 - - + +
44B THR 3.2 4.8 + - - +
46B LEU* 1.3 77.5 - - - +
48B GLU* 1.3 60.4 + - - +
50B GLU* 3.8 3.3 - - - +
51B LEU* 2.9 35.5 + - - +
65B VAL* 4.2 12.8 - - + -
208B ASP* 4.9 0.2 - - - +
599B TYR* 4.9 7.2 - - - -
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Residues in contact with GLU 48 (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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1013A LYS* 2.8 34.4 + - + +
1027A ASP* 4.4 0.3 - - - +
1153A LEU* 3.4 19.4 - - + +
1155A GLN* 3.5 16.7 + - - +
44B THR 3.1 17.1 + - - +
45B PHE* 3.5 11.6 + - - +
47B MET* 1.3 78.8 - - - +
49B TYR* 1.3 60.8 + - - +
52B ALA 3.5 7.4 + - - -
60B MET* 3.3 29.3 - - + +
65B VAL* 3.7 21.6 + - + +
70B ARG* 3.5 25.5 + - - -
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Residues in contact with TYR 49 (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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1012A THR* 3.7 23.8 - - + -
1013A LYS* 6.4 0.2 - - + -
1150A GLU* 5.3 4.0 - - - +
1151A PRO* 3.6 36.0 + - + +
1153A LEU* 3.8 20.1 - - + +
45B PHE* 3.3 15.1 + - + +
46B LEU* 3.8 5.2 - - - +
47B MET 3.2 0.4 - - - -
48B GLU* 1.3 80.4 - - - +
50B GLU* 1.3 66.7 + - + +
52B ALA* 4.0 2.4 - - - +
53B LYS* 3.4 50.7 + - + +
343B LYS* 3.8 22.8 + - - -
585B LEU* 4.0 17.1 + - + +
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Residues in contact with GLU 50 (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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19B ILE* 3.8 21.2 - - + +
23B GLN* 3.2 9.9 + - - -
46B LEU 3.3 15.8 + - - +
47B MET* 3.2 6.3 + - - +
49B TYR* 1.3 80.6 - - + +
51B LEU* 1.3 68.9 + - - +
53B LYS* 2.9 55.8 + - - +
599B TYR* 3.8 40.7 - - + +
600B GLY* 5.7 0.9 - - - -
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Residues in contact with LEU 51 (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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19B ILE* 3.7 40.2 - - + +
22B ILE* 4.1 28.7 - - + -
23B GLN* 3.0 25.6 + - + +
26B LEU* 5.4 4.9 - - + +
37B PHE* 4.2 13.2 - - + -
47B MET 2.9 21.6 + - - +
50B GLU* 1.3 71.8 - - - +
52B ALA* 1.3 58.9 + - - +
53B LYS 2.9 5.9 + - - -
54B THR* 3.9 6.9 + - - +
57B MET* 5.7 1.0 - - - +
59B GLY 5.0 2.0 - - - +
60B MET* 3.6 23.6 - - + -
63B ALA* 4.6 10.3 - - + -
65B VAL* 4.0 25.6 - - + -
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Residues in contact with ALA 52 (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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1133A SER* 4.2 5.6 - - - +
1135A ALA* 3.9 9.7 - - + +
1153A LEU* 4.3 16.8 - - + -
48B GLU 3.5 15.7 + - - +
49B TYR 4.0 3.8 - - - +
50B GLU 3.3 1.0 - - - -
51B LEU* 1.3 76.7 - - - +
53B LYS* 1.3 56.5 + - - +
54B THR* 3.1 1.5 + - - -
58B GLY* 3.0 27.3 - - - -
59B GLY* 3.5 29.8 - - - +
60B MET* 3.6 8.0 - - - -
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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