Contacts of the helix formed by residues 44 - 54 (chain A) 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 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TYR* 2.7 32.6 + - - -
42A GLN 3.8 0.4 - - - -
43A GLU* 1.3 70.5 - - - +
45A PRO* 1.3 68.6 - - - +
46A ALA 2.8 12.8 + - - -
47A ILE* 3.1 22.2 + - - +
44B GLY* 4.2 2.9 - - - -
45B PRO* 4.1 12.9 - - - +
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Residues in contact with PRO 45 (chain A).
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* 3.4 27.9 - - + +
44A GLY* 1.3 80.9 - - - +
46A ALA* 1.3 62.6 + - + +
47A ILE 3.3 0.2 - - - -
48A VAL* 3.1 17.6 + - + +
49A ALA* 3.3 11.6 + - - +
81A VAL* 3.8 23.3 - - + +
40B TYR 4.9 0.2 - - - +
41B TYR 3.8 7.6 - - - +
42B GLN 3.8 19.3 - - - +
43B GLU 4.3 2.5 - - - +
44B GLY* 4.1 15.9 - - - +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 6.6 0.2 - - - -
43A GLU* 4.0 14.6 - - + +
44A GLY 2.8 0.6 + - - -
45A PRO* 1.3 82.4 - - + +
47A ILE* 1.3 62.4 + - - +
48A VAL 3.2 0.2 + - - -
49A ALA* 3.2 9.0 + - - +
50A PHE* 3.0 23.1 + - - +
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 4.2 34.8 - - + -
19A VAL* 4.6 7.2 - - + -
35A VAL* 4.2 10.3 - - + -
39A LEU* 4.1 22.4 - - + -
40A TYR* 3.8 21.3 - - + -
43A GLU* 3.6 22.9 - - + +
44A GLY 3.1 16.8 + - - +
46A ALA* 1.3 78.8 - - - +
48A VAL* 1.3 67.8 + - + +
50A PHE* 3.6 14.3 - - + +
51A LEU* 3.0 43.9 + - + +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 5.5 0.9 - - + -
40A TYR* 3.8 28.3 - - + -
45A PRO* 3.1 10.3 + - + +
47A ILE* 1.3 78.9 - - + +
49A ALA* 1.3 65.8 + - - +
50A PHE 3.2 0.2 + - - -
51A LEU* 3.2 9.2 + - - +
52A LYS* 2.9 34.0 + - + +
58A VAL* 4.5 17.0 - - + -
60A LEU* 4.3 17.7 - - + -
81A VAL* 3.5 26.9 - - + +
82A GLY 4.3 0.2 - - - -
83A ALA* 4.1 14.4 - - - +
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Residues in contact with ALA 49 (chain A).
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 3.3 7.1 + - - +
46A ALA* 3.2 10.7 + - - +
48A VAL* 1.3 79.6 - - - +
50A PHE* 1.3 61.7 + - - +
52A LYS* 3.4 13.0 + - - +
53A GLU* 2.9 39.3 + - + +
81A VAL 4.6 4.4 + - - +
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Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LYS* 3.7 33.2 - - + +
19A VAL* 4.6 5.2 - - + -
20A GLU* 3.7 33.4 - - + -
23A LEU* 4.6 9.4 - - + -
46A ALA 3.0 12.8 + - - +
47A ILE* 3.6 17.3 - - + +
48A VAL 3.1 0.2 - - - -
49A ALA* 1.3 76.2 - - - +
51A LEU* 1.3 94.8 + - + +
53A GLU* 2.8 26.2 + - + +
54A GLN* 3.0 49.5 + - + +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.0 11.9 - - + -
19A VAL* 3.9 9.9 - - + -
23A LEU* 3.6 30.5 - - + -
33A VAL* 4.1 9.0 - - + -
35A VAL* 3.5 32.5 - - + -
47A ILE* 3.0 27.7 + - + +
48A VAL* 3.6 4.7 - - - +
50A PHE* 1.3 91.4 - - + +
52A LYS* 1.3 62.7 + - - +
54A GLN* 2.9 17.2 + - - +
56A HIS* 3.3 23.4 + - + +
58A VAL* 3.7 15.9 - - + -
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 2.9 36.9 + - + +
49A ALA* 3.6 9.0 - - - +
51A LEU* 1.3 74.6 - - - +
53A GLU* 1.3 54.5 - - + +
55A GLY* 2.7 28.1 + - - -
56A HIS 3.8 12.0 + - - +
58A VAL* 4.5 9.6 - - + -
81A VAL 3.9 4.3 - - - +
82A GLY* 3.3 39.2 + - - +
84A ASP* 5.0 8.3 + - - +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA* 2.9 34.7 + - + +
50A PHE* 2.8 16.6 + - + +
52A LYS* 1.3 75.1 - - + +
54A GLN* 1.3 64.5 + - + +
55A GLY 3.3 1.5 + - - -
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 5.5 2.0 - - + -
27A ALA 5.2 5.0 - - - +
30A PRO* 5.8 0.2 - - - +
50A PHE* 3.0 55.2 - - + +
51A LEU* 2.9 8.9 + - - +
52A LYS 2.8 1.6 + - - -
53A GLU* 1.3 85.2 + - - +
55A GLY* 1.3 62.8 + - - +
56A HIS* 3.5 27.0 + - + +
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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