Contacts of the helix formed by residues 42 - 54 (chain B) in PDB entry 5Y7G
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 ASP 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B LEU* 1.3 72.3 - - - +
43B ASP* 1.3 65.8 + - - +
44B GLN* 3.1 16.3 + - - +
45B GLU* 2.8 52.8 + - - +
46B ARG* 3.1 33.6 + - - +
215B ARG* 3.4 19.6 + - - +
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Residues in contact with ASP 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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42B ASP* 1.3 73.9 - - - +
44B GLN* 1.3 74.5 + - - +
46B ARG* 2.8 23.9 + - - +
47B ALA* 2.9 28.6 + - + +
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Residues in contact with GLN 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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42B ASP* 3.1 16.6 + - - +
43B ASP* 1.3 80.1 - - - +
45B GLU* 1.3 57.0 + - - +
47B ALA* 3.6 5.3 - - - +
48B PHE* 3.0 27.0 + - - +
171B LEU* 4.0 20.5 - - + +
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Residues in contact with GLU 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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41B LEU* 3.4 22.9 - - + +
42B ASP* 2.8 33.1 + - - +
44B GLN* 1.3 70.3 - - - +
46B ARG* 1.3 58.8 + - - +
48B PHE* 2.7 29.1 + - - +
49B ILE* 2.9 16.9 + - - +
171B LEU* 3.6 36.9 - - + +
174B ARG* 3.8 10.6 - - - -
175B LEU* 4.9 9.2 - - + -
178B MET* 5.0 0.3 - - - +
215B ARG* 2.4 49.1 + - - -
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Residues in contact with ARG 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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38B ALA 5.1 3.8 + - - -
41B LEU* 3.1 53.2 + - + +
42B ASP* 3.1 18.5 + - - +
43B ASP* 2.8 29.1 + - - +
45B GLU* 1.3 78.4 - - - +
47B ALA* 1.3 58.0 + - - +
49B ILE* 3.3 6.6 + - + +
50B ALA* 3.0 29.0 + - - +
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Residues in contact with ALA 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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43B ASP 2.9 20.7 + - - +
44B GLN* 3.6 5.2 - - - +
46B ARG* 1.3 75.9 - - - +
48B PHE* 1.3 59.3 + - - +
50B ALA* 3.5 7.2 - - - +
51B ALA* 2.8 30.2 + - - +
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Residues in contact with PHE 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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26B PHE* 4.9 9.2 - + - -
30B LEU* 4.7 8.7 - - + -
44B GLN 3.0 13.6 + - - +
45B GLU* 2.7 19.2 + - - +
47B ALA* 1.3 68.7 - - - +
49B ILE* 1.3 71.7 + - + +
51B ALA* 2.9 5.4 + - - +
52B PHE* 2.8 41.0 + + + +
63B LEU* 4.7 6.5 - - + -
99B TRP* 3.3 50.9 - + + -
168B CYS* 4.3 14.6 - - + -
171B LEU* 5.7 12.1 - - + -
172B CYS* 4.7 17.0 - - - -
175B LEU* 4.2 26.9 - - + -
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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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27B ARG* 5.6 0.5 + - - -
30B LEU* 3.9 61.2 - - + +
33B ILE* 4.5 11.9 - - + -
34B GLY* 5.0 3.6 - - - +
41B LEU* 4.0 30.1 - - + -
45B GLU 2.9 18.5 + - - +
46B ARG* 3.8 6.5 - - + +
48B PHE* 1.3 79.3 - - + +
50B ALA* 1.3 63.4 + - - +
52B PHE* 3.5 8.5 + - - +
53B ALA* 3.5 12.6 + - - +
175B LEU* 4.9 5.2 - - + -
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Residues in contact with ALA 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 ARG 3.0 18.4 + - - +
47B ALA* 3.5 8.7 - - - +
49B ILE* 1.3 79.5 - - - +
51B ALA* 1.3 62.1 + - - +
52B PHE 3.4 0.5 + - - -
53B ALA* 3.5 11.0 + - - +
54B GLU* 3.7 16.0 + - - +
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Residues in contact with ALA 51 (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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47B ALA 2.8 21.2 + - - +
48B PHE 2.9 2.9 + - - +
50B ALA* 1.3 71.5 - - - +
52B PHE* 1.3 65.8 + - - +
54B GLU* 3.3 17.2 + - - +
55B LEU* 3.6 13.3 + - - +
97B LEU* 4.1 14.4 - - + +
99B TRP* 3.7 23.6 - - + -
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Residues in contact with PHE 52 (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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23B LEU* 3.8 5.6 - - + -
26B PHE* 3.7 28.7 - + - -
27B ARG* 3.1 45.3 - - + -
30B LEU* 3.8 18.8 - - + -
48B PHE* 2.8 27.0 + + + +
49B ILE* 3.7 5.6 - - - +
50B ALA 3.3 0.2 - - - -
51B ALA* 1.3 77.7 - - - +
53B ALA* 1.3 62.5 + - - +
55B LEU* 2.9 28.8 + - + +
60B GLN* 2.9 57.2 - - + +
63B LEU* 4.0 22.4 - - + -
64B VAL* 4.2 1.3 - - + -
99B TRP* 4.1 4.4 - + + -
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Residues in contact with ALA 53 (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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27B ARG* 3.2 35.2 + - - +
49B ILE 3.5 7.4 + - - +
50B ALA* 3.5 9.9 + - - +
51B ALA 3.4 0.4 - - - -
52B PHE* 1.3 79.3 - - - +
54B GLU* 1.3 68.5 + - - +
55B LEU 3.5 7.3 + - - +
60B GLN* 4.0 2.6 + - - +
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Residues in contact with GLU 54 (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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50B ALA 3.7 14.1 - - - +
51B ALA* 3.3 11.4 + - - +
52B PHE 3.0 1.2 + - - -
53B ALA* 1.3 81.3 - - - +
55B LEU* 1.3 65.7 + - - +
56B PRO* 3.8 3.6 - - - +
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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