Contacts of the helix formed by residues 44 - 50 (chain A) in PDB entry 3HYW
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.0 17.8 + - + +
43A PRO* 1.3 77.5 - - - +
45A PHE* 1.3 61.8 + - - +
46A PRO* 3.4 2.5 - - - -
47A HIS* 3.2 13.7 + - - +
48A LEU* 2.9 26.7 + - - +
53A ARG* 4.2 4.1 - - - +
58A ILE* 3.6 31.5 - - + +
386A GLU* 3.6 19.3 - - - +
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Residues in contact with PHE 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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38A TYR* 5.2 2.2 - + - -
40A GLY* 4.0 18.8 - - - -
41A PHE 3.5 22.4 - - - -
42A THR* 2.9 36.6 + - + +
44A ALA* 1.3 75.5 - - - +
46A PRO* 1.4 60.7 - - + +
48A LEU* 3.2 5.9 + - + +
49A ALA* 2.9 29.8 + - - +
55A PHE* 5.9 0.9 - + - -
58A ILE* 3.7 18.4 - - + -
123A ILE 3.3 17.0 - - - +
124A CYS 3.6 20.6 - - - -
125A THR* 3.7 12.8 - - - -
126A ALA* 3.4 36.8 - - + -
129A ALA* 3.5 6.2 - - + +
441A FAD 4.2 1.1 - - + -
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Residues in contact with PRO 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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42A THR 3.8 4.3 - - - +
43A PRO 3.6 12.8 - - - +
44A ALA 3.5 3.8 - - - -
45A PHE* 1.4 92.4 - - + +
47A HIS* 1.3 57.2 + - - +
49A ALA* 3.4 6.0 + - + +
50A MET* 3.1 31.4 + - - +
123A ILE* 4.0 30.0 - - + -
159A PRO* 4.5 3.6 - - + +
162A GLU* 3.7 24.9 - - + +
163A PHE* 4.4 4.6 - - + +
166A MET* 4.0 20.0 - - + -
441A FAD 4.1 13.5 - - + -
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Residues in contact with HIS 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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43A PRO 3.4 26.2 + - - -
44A ALA* 3.2 11.6 + - - +
46A PRO* 1.3 75.6 - - + +
48A LEU* 1.3 63.6 + - - +
50A MET* 3.1 4.7 + - - -
51A GLY 3.1 3.6 + - - -
52A TRP* 2.8 43.4 + + + +
53A ARG* 3.6 47.2 + - + +
162A GLU* 4.4 2.2 - - - -
166A MET* 3.2 24.4 - - + +
350A ASP* 2.8 28.6 + - - -
379A HIS* 6.2 0.2 - - - -
382A LYS* 4.1 16.8 - - + +
386A GLU* 5.3 0.9 - - - -
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Residues in contact with LEU 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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44A ALA 2.9 13.7 + - - +
45A PHE* 3.2 11.0 + - + +
47A HIS* 1.3 75.6 - - - +
49A ALA* 1.3 56.8 + - - +
51A GLY* 3.0 7.3 + - - -
53A ARG* 3.4 29.1 - - + +
54A LYS 4.0 2.2 - - - -
55A PHE* 3.7 26.2 - - + +
58A ILE* 4.2 13.7 - - + -
126A ALA* 3.6 44.0 - - + +
129A ALA* 4.2 4.6 - - + +
130A LEU* 3.9 26.7 - - + -
133A GLN* 2.8 26.9 - - - +
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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 PHE 2.9 10.2 + - - +
46A PRO 3.5 9.6 - - - +
47A HIS 3.2 0.2 - - - -
48A LEU* 1.3 76.6 - - - +
50A MET* 1.3 60.1 + - - +
123A ILE* 3.5 31.4 - - + -
129A ALA* 3.3 22.1 - - + +
132A THR* 4.1 3.4 - - + -
133A GLN* 3.2 24.5 - - - -
136A LEU* 3.3 10.9 - - - +
163A PHE* 3.9 9.6 - - + -
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Residues in contact with MET 50 (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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46A PRO 3.1 17.8 + - - +
47A HIS 3.1 8.4 + - - +
49A ALA* 1.3 76.3 - - - +
51A GLY* 1.3 60.8 + - - +
52A TRP* 3.4 29.5 + - + -
133A GLN* 4.6 2.4 - - - +
136A LEU* 3.8 17.0 - - - -
140A TYR* 3.6 21.4 + - - +
163A PHE* 3.8 16.4 - - + -
166A MET* 3.9 28.7 - - + +
167A LEU* 4.0 18.6 - - + -
170A GLU* 3.5 36.5 - - + +
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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