Contacts of the helix formed by residues 36 - 44 (chain B) in PDB entry 2YYU
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 GLY 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A THR* 5.7 3.1 - - - -
11B LEU 4.7 3.8 + - - -
12B ASP* 5.3 6.1 + - - -
34B LYS* 3.8 12.7 + - - +
35B VAL* 1.3 77.3 - - - +
37B MET* 1.3 65.1 + - - -
38B GLU* 3.4 3.4 - - - -
39B LEU* 3.5 6.4 + - - +
40B TYR* 3.0 23.0 + - - +
61B ASP* 3.6 17.0 - - - -
62B LEU* 4.1 1.6 - - - -
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Residues in contact with MET 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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64A LEU* 4.0 28.9 - - - -
65A HIS 3.7 22.2 - - - +
66A ASP* 3.6 39.5 + - + +
70A THR* 4.5 10.6 - - + +
71A VAL* 5.1 2.0 - - - -
74A ALA* 3.9 11.9 - - + -
36B GLY* 1.3 68.7 - - - -
38B GLU* 1.3 67.9 + - - +
41B TYR* 2.9 52.0 + - + +
61B ASP 3.8 10.2 + - - +
62B LEU* 3.6 33.0 - - - +
63B LYS* 4.4 1.1 - - + +
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR* 5.0 8.0 - - + +
73A GLN* 3.4 46.0 + - + +
74A ALA* 4.2 12.7 - - - +
12B ASP* 3.3 33.6 - - - +
13B PHE* 3.6 15.9 - - - +
14B PRO* 3.8 16.4 - - + +
36B GLY* 3.4 1.3 - - - -
37B MET* 1.3 80.7 - - - +
39B LEU* 1.3 61.2 + - - +
42B GLN* 2.9 44.3 + - - +
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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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11B LEU* 3.6 36.3 - - + +
13B PHE 3.2 20.6 - - - +
14B PRO* 4.8 1.6 - - - -
15B SER 4.1 8.3 - - - +
19B VAL* 3.8 27.4 - - + -
35B VAL* 3.9 19.5 - - + -
36B GLY 3.5 8.0 + - - +
37B MET 3.3 0.2 - - - -
38B GLU* 1.3 78.6 - - - +
40B TYR* 1.3 65.1 + - - +
42B GLN* 3.3 1.9 + - - -
43B GLU* 3.1 40.8 + - + +
47B ILE* 4.0 18.8 - - + -
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Residues in contact with TYR 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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40A TYR* 5.3 2.0 - + - -
41A TYR* 2.9 50.8 + + - +
45A PRO* 4.9 0.2 - - - +
35B VAL* 3.7 7.0 - - + -
36B GLY 3.0 18.5 + - - +
39B LEU* 1.3 77.9 - - - +
41B TYR* 1.3 69.2 + + - +
44B GLY* 2.7 52.7 + - - +
45B PRO* 3.6 16.6 - - + +
47B ILE* 4.0 10.8 - - + -
48B VAL* 3.6 22.7 - - + -
60B LEU* 4.0 18.9 - - + +
62B LEU* 3.8 28.0 - - + -
78B LEU* 4.9 3.5 - - + +
81B VAL* 4.6 6.6 - - - +
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Residues in contact with TYR 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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40A TYR* 2.6 39.5 + + + -
41A TYR* 2.8 40.8 + + - -
45A PRO* 3.8 8.3 - - - +
62A LEU* 3.9 29.8 + - + +
64A LEU* 4.1 19.0 - - + +
74A ALA* 4.6 6.1 - - + +
78A LEU* 3.9 23.0 - - + +
81A VAL* 4.2 4.0 - - - +
37B MET* 2.9 50.4 + - + +
38B GLU 4.6 1.3 - - - +
40B TYR* 1.3 85.1 - + + +
42B GLN* 1.3 62.8 + - + +
62B LEU* 4.1 20.2 + - + +
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Residues in contact with GLN 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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45A PRO* 3.8 15.4 - - - +
73A GLN 4.0 5.7 + - - -
74A ALA 5.2 0.6 + - - +
77A GLY* 3.6 29.4 - - - +
80A ARG* 2.8 28.5 + - - +
81A VAL* 5.2 3.4 - - + -
14B PRO* 3.5 31.0 - - - +
38B GLU* 2.9 39.5 + - - +
39B LEU 3.3 2.5 + - - +
40B TYR 3.2 0.6 - - - -
41B TYR* 1.3 81.9 - - + +
43B GLU* 1.3 68.0 + - - +
44B GLY 3.8 0.2 - - - -
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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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45A PRO* 4.3 6.9 - - - +
14B PRO 4.5 0.7 - - - +
15B SER* 3.6 14.3 - - - -
16B LYS* 3.2 46.8 + - + +
17B GLN* 4.1 4.3 + - - +
39B LEU* 3.1 25.2 + - + +
42B GLN* 1.3 84.5 - - - +
44B GLY* 1.3 64.6 + - - +
45B PRO* 4.7 0.2 - - - +
46B ALA* 3.7 19.2 - - - +
47B ILE* 3.8 19.7 + - + +
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Residues in contact with GLY 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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44A GLY* 4.2 14.1 - - - -
45A PRO* 4.1 1.6 - - - +
40B TYR* 2.7 33.8 + - - -
42B GLN 3.8 0.2 - - - -
43B GLU* 1.3 69.6 - - - +
45B PRO* 1.3 69.6 - - - +
46B ALA 2.9 11.9 + - - -
47B ILE* 3.1 23.2 + - - +
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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