Contacts of the helix formed by residues 44 - 50 (chain B) in PDB entry 1YQZ
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 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A TYR* 3.4 40.8 + - + -
41B ALA* 2.9 22.7 + - + +
43B CYS* 1.3 77.0 - - - +
45B LEU* 1.3 64.9 + - + +
46B PRO* 3.4 2.0 - - - -
47B TYR* 2.9 19.0 + - - +
48B VAL* 3.0 20.8 + - + +
53B VAL* 4.9 2.7 - - + -
58B TYR 4.4 4.0 - - - +
59B ALA* 5.4 0.2 - - - -
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Residues in contact with LEU 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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40B PHE* 4.2 2.9 - - + -
41B ALA* 3.4 13.5 - - + +
42B ASN* 3.2 25.3 + - - +
44B ALA* 1.3 78.6 - - + +
46B PRO* 1.3 67.7 - - + +
48B VAL* 3.1 10.5 + - + +
49B ILE* 3.1 24.9 + - - +
59B ALA* 5.0 3.8 - - + +
130B LEU* 4.1 12.1 - - + -
131B ARG 3.8 10.1 - - - +
132B ASN* 3.6 35.0 - - - +
133B LEU* 4.0 26.0 - - + +
136B THR* 3.3 21.6 - - + +
440B FAD 4.3 4.7 - - + -
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Residues in contact with PRO 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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43B CYS 3.6 11.7 - - - +
44B ALA 3.6 4.0 - - - -
45B LEU* 1.3 92.1 - - + +
47B TYR* 1.3 57.8 + - + +
49B ILE* 3.3 8.1 + - + +
50B GLY 3.0 14.9 + - - -
130B LEU* 4.2 10.5 - - + -
159B VAL* 4.9 2.0 - - - +
162B GLU* 3.5 38.8 - - + +
163B VAL* 4.2 6.5 - - + +
166B ASN* 3.0 33.8 - - + +
440B FAD 3.8 23.1 - - + -
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Residues in contact with TYR 47 (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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361A TYR* 4.7 1.8 - + - -
362A TYR* 3.5 33.4 - + - -
421A PRO* 4.0 18.6 - - + -
422A PRO* 3.9 17.1 - - + +
43B CYS 3.6 24.7 - - - -
44B ALA* 2.9 10.8 + - - +
46B PRO* 1.3 77.2 - - + +
48B VAL* 1.3 62.4 + - - +
50B GLY 3.4 0.6 + - - -
51B GLU 3.2 2.4 + - - -
52B VAL* 2.9 40.6 + - + +
53B VAL* 3.0 23.3 + - + -
162B GLU* 3.6 33.2 + - + +
165B GLU* 6.2 2.2 - - - -
166B ASN* 3.4 26.9 - - - -
327B LYS* 4.9 13.0 + - - +
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Residues in contact with VAL 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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44B ALA* 3.0 22.5 + - + +
45B LEU* 3.1 12.5 + - + +
47B TYR* 1.3 75.4 - - - +
49B ILE* 1.3 64.6 + - - +
51B GLU* 3.0 17.3 + - - +
53B VAL* 3.5 33.1 - - + +
56B ARG* 5.9 1.8 - - - +
59B ALA* 4.5 22.0 - - + -
133B LEU* 5.3 1.8 - - + -
136B THR* 3.7 21.8 - - + -
137B ASP* 5.8 1.8 - - - +
140B ASP* 5.5 5.9 - - + +
170B ARG* 4.7 1.2 + - - -
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Residues in contact with ILE 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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45B LEU 3.1 11.1 + - - +
46B PRO* 3.5 9.4 - - + +
48B VAL* 1.3 77.4 - - - +
50B GLY* 1.3 58.2 + - - +
51B GLU 3.2 0.4 + - - -
130B LEU* 3.8 39.3 - - + -
136B THR* 4.0 14.8 - - + +
139B ILE* 4.0 33.9 - - + -
140B ASP* 5.6 3.8 - - + +
143B ILE* 4.7 4.3 - - + -
163B VAL* 4.8 10.8 - - + -
166B ASN* 5.0 2.7 - - + -
167B LEU* 3.9 30.7 - - + -
170B ARG* 2.9 34.4 + - - +
234B ILE* 5.1 0.9 - - + -
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Residues in contact with GLY 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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46B PRO 3.0 11.7 + - - -
47B TYR 3.4 0.6 + - - -
48B VAL 3.2 0.6 - - - -
49B ILE* 1.3 74.6 - - - +
51B GLU* 1.3 67.9 + - - +
52B VAL* 3.1 12.9 + - - +
166B ASN* 3.3 38.2 - - - +
169B GLU* 4.6 2.3 - - - +
170B ARG* 4.0 16.9 + - - +
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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