Contacts of the helix formed by residues 159 - 166 (chain T) in PDB entry 2P8Z
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 LYS 159 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29T ASP 3.1 27.5 + - - -
30T HIS* 3.8 11.2 - - - +
31T GLY 4.4 0.4 - - - +
130T ASP* 3.2 24.9 - - - +
131T THR* 3.6 7.8 + - - +
132T ILE* 6.4 0.4 - - + -
158T ASN* 1.3 106.5 + - - +
160T VAL* 1.3 64.7 + - - +
161T ASP* 3.1 15.5 - - - +
162T ARG* 3.1 48.8 + - + +
163T ALA 4.1 0.2 + - - -
212T GLY 3.3 1.8 + - - -
213T SER* 4.3 1.3 - - - +
843T GNP 3.1 40.6 + - + +
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Residues in contact with VAL 160 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131T THR* 3.3 20.0 - - - +
157T ILE 3.5 6.7 - - - +
159T LYS* 1.3 76.8 - - - +
161T ASP* 1.3 62.1 + - - +
163T ALA* 3.0 15.5 + - - +
164T LEU* 3.5 19.5 + - + +
174T LEU* 4.3 15.3 - - + -
178T PHE* 3.9 27.4 - - + -
211T PHE* 4.2 1.8 - - + -
212T GLY* 2.9 45.4 + - - +
213T SER* 5.2 0.2 - - - -
218T TRP* 4.9 11.7 - - + -
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Residues in contact with ASP 161 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159T LYS* 3.8 6.9 - - - -
160T VAL* 1.3 79.6 - - - +
162T ARG* 1.3 65.6 + - - +
164T LEU* 3.3 9.8 + - - +
165T LEU* 2.9 42.0 + - + +
166T GLU* 4.9 1.9 - - - +
213T SER* 2.6 11.1 + - - +
216T HIS* 3.7 21.7 + - + +
218T TRP* 5.7 3.1 - - + -
285T PHE* 5.4 6.1 - - + -
843T GNP 1.7 59.6 + - - +
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Residues in contact with ARG 162 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130T ASP* 4.4 18.4 + - - -
132T ILE* 4.3 27.3 - - + +
133T GLU* 4.4 14.8 + - - +
159T LYS* 3.1 41.9 + - + +
160T VAL 3.1 0.6 - - - -
161T ASP* 1.3 89.6 + - - +
163T ALA* 1.3 57.7 + - - +
165T LEU* 5.1 0.2 - - - -
166T GLU* 2.9 67.5 + - - +
167T LEU* 3.2 10.6 + - - +
843T GNP 5.1 1.3 - - - +
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Residues in contact with ALA 163 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131T THR* 4.0 23.6 - - + -
132T ILE* 5.0 2.4 - - + +
159T LYS 4.1 0.6 + - - -
160T VAL 3.0 11.2 + - - +
162T ARG* 1.3 79.8 - - - +
164T LEU* 1.3 61.3 + - + +
167T LEU* 4.2 7.9 - - + -
168T GLN 3.2 5.7 + - - -
169T VAL* 3.1 48.0 + - + +
174T LEU* 4.2 15.0 - - + -
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Residues in contact with LEU 164 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160T VAL* 3.7 21.5 - - + +
161T ASP* 3.3 6.4 + - - +
162T ARG 3.2 0.2 - - - -
163T ALA* 1.3 82.0 - - - +
165T LEU* 1.3 71.9 + - + +
168T GLN* 3.9 14.2 - - - +
169T VAL* 5.1 6.7 - - + +
174T LEU* 3.7 27.8 - - + -
218T TRP* 5.5 3.8 - - + -
281T ILE* 5.3 6.1 - - + -
282T PHE* 3.9 30.5 - - + -
285T PHE* 3.7 36.8 - - + -
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Residues in contact with LEU 165 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161T ASP* 2.9 24.0 + - + +
162T ARG* 5.1 0.2 - - - -
164T LEU* 1.3 89.4 - - + +
166T GLU* 1.3 70.3 + - + +
168T GLN* 4.5 5.9 + - - +
216T HIS* 4.1 23.1 - - + +
285T PHE* 4.6 17.9 - - + -
289T MET* 5.0 26.0 - - + -
317T LYS* 5.4 10.1 - - + -
320T LEU* 5.8 3.4 - - + -
843T GNP 5.7 0.2 - - - +
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Residues in contact with GLU 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161T ASP* 4.9 2.3 - - - +
162T ARG* 2.9 63.0 + - - +
165T LEU* 1.3 79.0 - - + +
167T LEU* 1.3 71.3 + - + +
168T GLN* 3.4 9.0 + - - +
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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