Contacts of the helix formed by residues 85 - 95 (chain B) in PDB entry 4ZPK
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 GLN 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A ASP* 4.9 1.6 - - - +
162A GLN* 4.4 18.6 + - + +
83B ALA 3.6 2.3 + - - +
84B ASP* 1.3 70.7 - - - +
86B GLN* 1.3 74.9 + - + +
87B MET 3.2 1.8 - - - -
88B ASP* 3.4 17.0 + - - +
89B ASN* 2.8 19.2 + - - +
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Residues in contact with GLN 86 (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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84B ASP* 3.5 3.9 - - + +
85B GLN* 1.3 88.6 - - + +
87B MET* 1.3 77.6 + - - +
89B ASN* 3.0 30.0 - - - +
90B LEU* 3.1 15.5 + - + +
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Residues in contact with MET 87 (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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165A LYS* 5.7 0.2 - - - -
176A LEU* 3.3 17.1 - - + +
178A ILE* 3.7 29.2 - - + -
188A TYR* 3.7 33.0 - - + +
83B ALA* 6.2 0.2 - - + -
84B ASP* 3.4 29.6 - - + +
85B GLN 3.2 0.6 - - - -
86B GLN* 1.3 95.9 - - - +
88B ASP* 1.3 64.7 + - - +
90B LEU* 3.5 17.9 + - + +
91B TYR* 2.9 29.5 + - + -
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Residues in contact with ASP 88 (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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161A ASP* 3.6 27.3 - - + +
162A GLN* 3.8 27.6 + - + +
165A LYS* 3.2 30.2 - - + +
82B GLU* 6.1 0.3 - - - -
83B ALA* 5.1 2.6 - - - +
84B ASP 2.6 23.8 - - - +
85B GLN* 3.7 9.1 - - - +
86B GLN 3.1 0.4 - - - -
87B MET* 1.3 75.9 - - - +
89B ASN* 1.3 66.9 + - - +
90B LEU 3.0 1.3 - - - -
91B TYR* 2.8 20.6 + - + +
92B LEU* 3.0 18.5 + - - +
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Residues in contact with ASN 89 (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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161A ASP* 3.0 25.5 + - - -
85B GLN* 2.8 20.7 + - - +
86B GLN* 3.0 18.7 - - - +
88B ASP* 1.3 79.1 - - - +
90B LEU* 1.3 62.9 + - + +
92B LEU* 3.7 17.7 + - - +
93B LYS* 4.0 14.5 + - - +
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Residues in contact with LEU 90 (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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176A LEU* 5.1 2.9 - - + -
178A ILE* 5.1 1.3 - - + -
311A TYR* 3.4 23.6 + - - +
313A LYS* 4.8 11.4 - - + +
338A VAL* 4.2 22.4 - - + -
86B GLN* 3.1 18.5 + - + +
87B MET* 3.7 31.6 - - + +
88B ASP 3.0 0.8 - - - -
89B ASN* 1.3 78.4 - - + +
91B TYR* 1.3 64.9 + - - +
93B LYS* 3.2 9.9 + - + +
94B ALA* 3.0 27.3 + - - +
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Residues in contact with TYR 91 (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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164A LEU* 5.1 4.3 - - + -
165A LYS* 3.3 47.5 + - + -
168A ILE* 4.0 28.4 - - + +
174A GLY 4.8 0.5 + - - -
175A PHE* 3.6 8.6 - - - -
176A LEU* 3.0 48.3 + - + -
188A TYR* 5.3 0.4 - - - -
190A SER* 3.2 16.1 + - - -
192A SER* 4.4 5.0 + - - -
340A ILE* 3.5 43.6 - - + +
87B MET* 2.9 21.6 + - + +
88B ASP* 2.8 16.0 + - + +
90B LEU* 1.3 75.9 - - - +
92B LEU* 1.3 66.0 - - - +
94B ALA* 3.7 1.4 + - - -
95B LEU* 4.1 1.2 + - - +
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Residues in contact with LEU 92 (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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161A ASP* 3.3 30.7 - - + +
164A LEU* 3.7 36.1 - - + +
168A ILE* 5.7 0.4 - - - -
88B ASP 3.0 29.0 + - - +
89B ASN* 3.7 9.9 - - - +
91B TYR* 1.3 81.0 - - - +
93B LYS* 1.3 67.6 + - + +
95B LEU* 3.5 17.2 + - - +
113B GLU* 6.0 7.2 - - + -
114B ASN* 5.4 5.9 + - - +
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Residues in contact with LYS 93 (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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260A ARG* 2.7 30.5 + - - -
311A TYR* 4.0 17.4 - - + +
313A LYS* 3.7 28.2 - - - +
89B ASN* 4.0 14.8 - - - +
90B LEU* 3.2 12.7 + - + +
92B LEU* 1.3 82.4 - - + +
94B ALA* 1.3 54.7 + - - +
95B LEU 3.0 5.7 - - - +
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Residues in contact with ALA 94 (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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176A LEU* 4.7 0.9 - - + -
260A ARG* 3.0 13.2 + - - +
309A THR* 2.9 24.2 - - - +
311A TYR* 3.6 17.9 - - + -
338A VAL* 4.3 3.6 - - + +
339A ALA* 4.0 20.0 - - - +
340A ILE* 3.6 28.9 - - + -
90B LEU 3.0 15.8 + - - +
92B LEU 3.4 0.4 - - - -
93B LYS* 1.3 76.8 - - - +
95B LEU* 1.3 57.9 + - - +
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Residues in contact with LEU 95 (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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168A ILE* 4.8 12.3 - - + -
260A ARG* 3.1 10.2 + - - -
309A THR* 4.1 7.6 - - + +
340A ILE* 3.9 17.8 - - + +
342A ARG* 5.4 0.7 - - - +
91B TYR 4.6 1.1 - - - +
92B LEU 3.5 14.7 + - - +
93B LYS 3.0 14.7 + - - +
94B ALA* 1.3 78.6 - - - +
96B GLU* 1.3 64.6 + - - +
97B GLY 3.5 22.1 + - - +
99B ILE* 3.5 32.8 - - + -
114B ASN* 4.5 6.1 + - - +
225B MET* 3.0 42.8 - - + -
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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