Contacts of the helix formed by residues 169 - 179 (chain B) in PDB entry 2ZA5
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 GLU 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B THR* 5.7 3.8 - - - +
135B PRO* 5.1 4.2 - - - +
136B PRO* 3.6 30.6 - - + +
168B MET* 1.3 79.2 - - - +
170B ASN* 1.3 63.6 + - - +
171B HIS* 3.3 33.1 + - + +
172B ILE* 2.8 27.0 - - + +
173B CYS* 3.0 7.7 + - - -
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Residues in contact with ASN 170 (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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168B MET 4.6 2.0 + - - -
169B GLU* 1.3 72.9 - - - +
171B HIS* 1.3 53.8 + - - +
173B CYS* 3.3 6.7 + - - +
174B ASP* 2.7 36.9 + - - +
188B ARG* 4.0 12.7 + - - +
190B VAL* 4.0 10.0 - - + +
191B ARG 3.1 18.9 - - - +
192B ASP* 4.1 8.8 - - - +
194B MET 2.9 21.1 + - - +
195B LEU* 3.9 7.3 - - - +
196B CYS 4.4 3.4 - - - +
244B ARG* 2.9 30.4 + - - +
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Residues in contact with HIS 171 (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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169B GLU* 3.5 36.5 + - + +
170B ASN* 1.3 79.0 - - - +
172B ILE* 1.3 78.0 + - + +
174B ASP* 3.5 1.7 + - - +
175B ALA* 3.0 29.3 + - + +
188B ARG* 3.5 25.1 + - - +
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Residues in contact with ILE 172 (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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168B MET* 4.0 10.8 - - + -
169B GLU* 2.8 46.2 - - + +
171B HIS* 1.3 90.2 - - + +
173B CYS* 1.3 61.3 + - - +
175B ALA* 3.3 5.0 + - + +
176B LYS* 2.8 56.2 + - + +
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Residues in contact with CYS 173 (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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168B MET* 3.9 10.5 - - - -
169B GLU 3.0 15.9 + - - +
170B ASN 3.6 4.7 - - - +
172B ILE* 1.3 76.4 - - - +
174B ASP* 1.3 64.7 + - - +
176B LYS* 3.3 4.4 + - - +
177B TYR* 3.2 35.4 + - - -
190B VAL* 3.7 11.0 - - + -
196B CYS* 2.0 56.1 - - + -
239B PRO* 3.8 14.6 - - - -
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Residues in contact with ASP 174 (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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170B ASN 2.7 22.2 + - - +
171B HIS 3.8 3.7 - - - +
173B CYS* 1.3 72.4 - - - +
175B ALA* 1.3 58.9 + - - +
177B TYR* 3.2 10.0 + - - +
178B HIS* 2.6 44.7 + - - -
185B ASP 4.9 4.0 - - - +
187B VAL 4.4 0.2 - - - +
188B ARG* 3.4 36.9 + - - +
189B ILE* 2.8 30.5 + - - +
190B VAL* 3.0 20.9 + - + +
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Residues in contact with ALA 175 (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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171B HIS* 3.0 19.4 + - + +
172B ILE* 3.9 5.8 - - - +
174B ASP* 1.3 74.7 - - - +
176B LYS* 1.3 66.5 + - - +
178B HIS* 2.9 23.6 + - - +
179B LEU* 3.2 16.1 + - + +
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Residues in contact with LYS 176 (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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168B MET* 4.2 14.8 - - - -
172B ILE* 2.8 45.9 + - + +
173B CYS* 3.6 6.7 - - - +
174B ASP 3.3 0.2 - - - -
175B ALA* 1.3 73.3 - - - +
177B TYR* 1.3 56.3 + - - +
179B LEU* 3.0 28.5 + - + +
237B ASN* 3.2 38.1 - - - +
238B ARG* 3.0 16.1 + - - -
239B PRO* 3.9 23.8 - - + -
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Residues in contact with TYR 177 (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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1B 2FF 3.3 41.3 - + - -
173B CYS* 3.2 23.0 + - - +
174B ASP* 3.6 9.0 - - - +
175B ALA 3.2 0.8 - - - -
176B LYS* 1.3 79.0 - - - +
178B HIS* 1.3 60.4 + - - +
179B LEU 3.3 0.2 - - - -
181B ALA* 3.6 4.3 - - - +
189B ILE* 4.0 24.1 - - + +
190B VAL* 4.4 3.6 - - + -
229B TRP* 4.1 12.3 - + - -
230B GLY* 3.2 18.4 - - - -
231B GLU* 3.3 16.4 + - + -
237B ASN 4.1 3.6 - - - -
238B ARG* 3.5 37.5 + - - +
239B PRO* 2.6 46.0 + - + -
241B ILE* 3.7 14.5 - - + +
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Residues in contact with HIS 178 (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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174B ASP* 2.6 49.6 + - - -
175B ALA* 2.9 12.3 + - - +
177B TYR* 1.3 76.7 - - - +
179B LEU* 1.3 65.9 + - + +
180B GLY 3.3 0.9 + - - -
181B ALA* 3.1 25.8 + - - +
183B THR* 3.7 15.7 + - + +
184B GLY 3.0 22.6 + - - -
185B ASP* 3.7 28.7 + - - +
187B VAL 2.7 30.8 + - - -
189B ILE* 3.8 15.6 - - + +
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Residues in contact with LEU 179 (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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175B ALA 3.2 12.0 + - - +
176B LYS* 3.0 19.4 + - + +
178B HIS* 1.3 77.2 - - + +
180B GLY* 1.3 60.0 + - - +
237B ASN* 3.7 36.0 - - - +
238B ARG* 2.9 30.3 + - - -
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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