Contacts of the helix formed by residues 45 - 52 (chain B) in PDB entry 4PK5
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 HIS 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B PHE* 2.8 52.4 + + + +
42B ILE 3.1 5.6 + - - +
43B ALA 3.1 0.8 - - - -
44B LYS* 1.3 94.9 + - + +
46B LEU* 1.3 64.7 + - - +
47B PRO* 3.2 7.4 - - - -
48B ASP* 3.2 13.3 + - + +
49B LEU* 3.0 37.3 + - + +
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Residues in contact with LEU 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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42B ILE* 3.1 29.9 + - + +
43B ALA* 3.6 19.7 - - - +
45B HIS* 1.3 77.7 - - - +
47B PRO* 1.4 70.7 - - + +
49B LEU* 4.7 3.8 - - - -
50B ILE* 3.0 38.4 + - + +
55B LEU* 4.3 11.2 - - + -
85B CYS* 4.0 22.4 - - + +
86B ILE* 4.4 10.3 - - + +
89B ALA* 4.3 4.5 - - + -
152B PHE* 5.7 1.3 - - + -
153B SER 3.7 18.2 - - - +
154B PHE* 3.7 28.3 - - + -
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Residues in contact with PRO 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 ALA 5.1 0.2 - - - +
44B LYS 4.6 5.2 - - - +
45B HIS* 3.4 7.2 - - - -
46B LEU* 1.4 94.5 - - + +
48B ASP* 1.3 66.0 + - - +
50B ILE* 3.8 1.6 - - + +
51B GLU* 3.0 26.7 + - - +
153B SER* 4.2 13.9 - - - +
154B PHE 3.4 15.9 - - - +
155B ARG* 4.1 13.6 + - - +
156B ASP* 3.1 40.4 - - - +
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Residues in contact with ASP 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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45B HIS* 3.2 14.5 + - + +
47B PRO* 1.3 81.1 - - - +
49B LEU* 1.3 64.4 + - + +
51B GLU* 3.1 14.3 + - - +
52B SER* 2.8 35.3 + - - +
54B GLN* 5.7 2.0 - - - +
156B ASP* 5.2 5.2 - - - +
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Residues in contact with LEU 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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41B PHE* 4.9 4.3 - - + -
42B ILE* 3.8 44.0 - - + +
45B HIS* 3.0 26.5 + - + +
46B LEU* 4.4 2.5 - - - +
48B ASP* 1.3 79.2 - - + +
50B ILE* 1.3 61.5 + - - +
52B SER* 4.0 3.1 - - - -
53B GLY 3.2 2.8 + - - -
54B GLN* 3.2 27.3 + - + +
55B LEU* 3.0 42.1 + - + +
58B ARG* 3.3 34.8 - - + +
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Residues in contact with ILE 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 LEU* 3.0 29.5 + - + +
47B PRO 3.9 1.8 - - - +
49B LEU* 1.3 76.1 - - - +
51B GLU* 1.3 65.4 + - - +
53B GLY* 3.2 11.1 + - - -
55B LEU* 3.9 15.5 - - + -
89B ALA* 3.5 33.7 - - + -
93B GLY 3.5 23.1 - - - +
94B LYS* 3.7 22.2 - - + +
154B PHE* 3.4 18.2 - - + +
155B ARG* 3.7 25.8 - - - +
233B TYR* 3.7 7.0 - - + +
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Residues in contact with GLU 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 PRO* 3.0 17.6 + - - +
48B ASP* 3.4 15.2 - - - +
50B ILE* 1.3 78.4 - - - +
52B SER* 1.3 58.2 + - - +
53B GLY 3.3 3.2 + - - -
94B LYS* 4.0 20.4 + - + +
155B ARG* 4.8 16.3 + - - +
156B ASP* 5.4 5.7 - - - +
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Residues in contact with SER 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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48B ASP* 2.8 19.0 + - - -
51B GLU* 1.3 73.6 - - - +
53B GLY* 1.3 50.1 + - - +
54B GLN* 2.5 59.6 + - - +
94B LYS* 5.4 0.2 - - - -
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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