Contacts of the helix formed by residues 44 - 50 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D PHE* 2.9 18.5 + - + +
43D PRO* 1.3 76.7 - - - +
45D PHE* 1.3 61.7 + - - +
46D PRO* 3.5 2.2 - - - -
47D HIS* 3.3 13.3 + - - +
48D LEU* 2.9 27.4 + - - +
53D ARG* 4.3 3.8 - - - +
58D ILE* 3.6 29.6 - - + +
386D GLU* 3.7 19.3 - - - +
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Residues in contact with PHE 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D TYR* 5.3 2.0 - + - -
40D GLY* 4.1 18.6 - - - -
41D PHE 3.7 22.4 - - - -
42D THR* 2.9 42.8 + - + +
44D ALA* 1.3 75.3 - - - +
46D PRO* 1.4 60.7 - - + +
48D LEU* 3.3 3.5 + - + -
49D ALA* 3.0 24.6 + - - +
55D PHE* 5.8 0.9 - + - -
58D ILE* 3.9 16.6 - - + -
123D ILE* 3.2 17.9 - - - +
124D CYS 3.6 12.8 - - - -
125D THR* 3.7 13.0 - - - -
126D ALA* 3.5 37.9 - - + -
129D ALA* 3.5 12.1 - - + +
441D FAD 4.0 1.1 - - + -
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Residues in contact with PRO 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D THR 3.8 4.3 - - - +
43D PRO 3.7 11.2 - - - +
44D ALA 3.6 3.1 - - - -
45D PHE* 1.4 93.9 - - + +
47D HIS* 1.3 57.5 + - - +
49D ALA* 3.3 5.6 + - + +
50D MET* 3.1 31.7 + - - +
123D ILE* 3.8 29.4 - - + -
159D PRO* 4.4 5.8 - - + +
162D GLU* 3.8 22.7 - - + +
163D PHE* 4.3 4.4 - - + -
166D MET* 3.6 20.9 - - - -
441D FAD 4.1 12.8 - - + -
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Residues in contact with HIS 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PRO 3.4 25.5 + - - -
44D ALA* 3.4 10.6 - - - +
45D PHE 3.2 0.2 - - - -
46D PRO* 1.3 73.1 - - + +
48D LEU* 1.3 64.6 + - - +
50D MET* 3.1 6.8 + - - -
52D TRP* 2.8 39.5 + + + +
53D ARG* 3.6 46.8 + - + +
162D GLU* 4.1 5.4 - - - -
166D MET* 3.5 24.1 - - + +
350D ASP* 2.7 35.3 + - + +
379D HIS* 6.1 0.4 - - - -
382D LYS* 3.9 16.8 - - - +
386D GLU* 5.5 0.9 - - - -
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ALA 2.9 14.4 + - - +
45D PHE* 3.5 9.4 - - + +
47D HIS* 1.3 77.2 - - - +
49D ALA* 1.3 56.7 + - - +
51D GLY* 3.1 18.4 + - - -
53D ARG* 3.4 27.9 - - - +
54D LYS 4.0 1.8 - - - -
55D PHE* 3.7 28.0 - - + +
58D ILE* 4.0 16.8 - - + -
126D ALA* 3.8 40.6 - - + +
129D ALA* 4.0 6.3 - - + +
130D LEU* 3.8 28.2 - - + +
133D GLN* 4.1 7.3 - - - +
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D PHE 3.0 10.7 + - - +
46D PRO 3.5 8.5 - - - +
47D HIS 3.2 0.2 - - - -
48D LEU* 1.3 75.8 - - - +
50D MET* 1.3 56.1 + - - +
51D GLY 3.2 0.4 - - - -
123D ILE* 3.4 32.8 - - + -
129D ALA* 3.3 21.3 - - + +
132D THR* 3.9 7.9 - - + -
133D GLN* 3.1 22.0 - - - +
136D LEU* 3.1 15.3 - - - +
163D PHE* 4.0 3.8 - - + -
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Residues in contact with MET 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D PRO 3.1 9.0 + - - +
47D HIS 3.1 8.4 + - - +
49D ALA* 1.3 76.4 - - - +
51D GLY* 1.3 58.5 + - - +
52D TRP* 3.2 33.1 + - + -
133D GLN* 3.4 9.0 + - - +
136D LEU* 3.8 8.7 - - - -
140D TYR* 3.8 15.4 + - - +
163D PHE* 3.6 26.2 - - + -
166D MET* 3.2 40.6 - - + +
167D LEU* 3.8 16.6 - - + -
170D GLU* 3.4 37.4 - - + +
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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