Contacts of the helix formed by residues 165 - 178 (chain A) in PDB entry 2ZB8
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 GLY 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A GLY 3.1 9.0 + - - -
164A ALA* 1.3 79.0 - - - +
166A ALA* 1.3 55.0 + - - -
167A CYS 3.6 1.8 - - - -
168A GLY 4.1 1.1 - - - -
169A SER* 2.8 37.2 + - - -
337A ASN* 4.2 4.5 - - - -
339A GLY* 4.0 7.9 - - - -
700A NAP 3.3 26.9 - - - -
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLY* 5.5 0.9 - - - -
132A ALA* 5.8 0.9 + - - -
136A PRO* 3.8 18.5 - - + +
165A GLY* 1.3 70.6 - - - +
167A CYS* 1.3 65.4 + - - +
169A SER* 3.5 10.4 + - - -
170A VAL* 3.6 14.6 - - - +
339A GLY 3.7 2.4 + - - -
340A LYS* 3.6 43.5 - - + +
700A NAP 2.8 27.5 + - - +
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Residues in contact with CYS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PRO* 3.7 29.4 - - - -
139A THR* 4.2 7.0 - - - -
140A SER* 2.7 27.0 + - - +
166A ALA* 1.3 71.8 - - - +
168A GLY* 1.3 59.8 + - - +
170A VAL 3.2 2.4 + - - -
171A ALA* 2.8 19.4 + - - +
229A PHE* 4.3 4.5 - - + -
231A ASN* 3.9 17.0 - - - +
253A CYS* 4.3 2.2 - - - -
700A NAP 2.8 54.7 + - - +
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Residues in contact with GLY 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 3.7 15.4 - - - +
162A GLY 3.3 20.3 + - - -
163A ALA* 3.2 8.9 - - - +
165A GLY 3.7 2.4 + - - -
166A ALA 3.5 0.4 - - - -
167A CYS* 1.3 78.5 - - - +
169A SER* 1.3 62.4 + - - +
171A ALA* 3.7 2.4 - - - +
172A GLY 3.2 20.3 + - - -
202A PHE* 3.8 2.8 - - - -
231A ASN* 3.6 14.9 - - - +
700A NAP 4.7 0.8 + - - -
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ALA 3.0 14.1 + - - -
164A ALA* 4.3 7.6 - - - -
165A GLY 2.8 24.4 + - - -
166A ALA* 3.5 5.4 + - - -
168A GLY* 1.3 76.4 - - - +
170A VAL* 1.3 65.2 + - - +
173A GLN* 3.0 32.8 + - - +
196A LEU* 4.8 0.2 - - - -
200A LEU* 3.7 23.9 - - - +
202A PHE* 4.1 3.9 - - - -
313A LYS 5.4 1.3 + - - -
315A LYS* 5.1 9.4 + - - +
339A GLY* 4.4 9.5 - - - -
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA* 3.7 31.2 - - + +
137A GLY* 4.2 14.6 - - - -
140A SER* 4.0 10.5 - - - +
166A ALA 3.6 13.9 + - - +
167A CYS 3.2 6.8 + - - +
168A GLY 3.2 0.2 - - - -
169A SER* 1.3 82.2 + - - +
171A ALA* 1.3 66.1 + - - +
172A GLY 3.3 0.2 - - - -
173A GLN* 3.3 9.2 + - - +
174A ILE* 2.9 45.4 + - + +
303A LEU* 4.4 7.2 - - + -
312A LEU* 4.4 13.7 - - + -
313A LYS 5.2 2.0 - - - +
314A ILE* 6.2 0.4 - - - -
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A SER* 3.7 13.0 + - - +
144A ILE* 3.4 13.9 - - + +
158A MET* 3.8 3.2 - - - +
160A VAL* 4.4 3.8 - - + -
167A CYS 2.8 17.9 + - - +
168A GLY* 3.2 5.6 + - - +
170A VAL* 1.3 77.2 - - - +
172A GLY* 1.3 55.9 + - - +
174A ILE* 3.3 0.9 + - - -
175A GLY* 2.8 25.3 + - - -
229A PHE* 3.7 42.6 - - + -
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Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A MET* 4.5 0.9 - - - -
160A VAL* 3.9 7.5 - - - +
168A GLY 3.2 8.3 + - - -
171A ALA* 1.3 76.1 - - - +
173A GLN* 1.3 65.1 + - - +
175A GLY 3.3 7.3 + - - -
176A HIS* 3.4 11.4 + - - +
183A VAL* 3.6 26.8 - - - +
202A PHE* 3.5 24.0 - - - -
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Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A SER 3.0 23.3 + - - +
170A VAL* 3.3 5.6 + - - +
172A GLY* 1.3 70.8 - - - +
174A ILE* 1.3 67.8 + - - +
176A HIS* 3.2 9.8 + - - +
177A PHE* 2.9 43.6 + - + -
200A LEU* 3.6 40.7 - - + +
202A PHE* 4.4 0.4 - - + -
311A LYS 3.6 9.7 - - - +
312A LEU* 3.7 10.9 - - + +
313A LYS* 2.8 53.4 + - - +
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Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A SER 4.4 0.7 - - - -
141A LEU* 3.8 40.4 - - + +
144A ILE* 3.6 18.4 - - + -
170A VAL* 2.9 42.8 + - + +
171A ALA 3.6 4.3 - - - +
173A GLN* 1.3 74.3 - - + +
175A GLY* 1.3 64.9 + - - +
177A PHE* 3.1 11.9 + - + +
178A LEU* 3.0 43.6 + - + +
303A LEU* 4.0 4.9 - - + -
306A TRP* 3.8 21.8 - - + -
312A LEU* 5.2 1.1 - - + -
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 4.3 1.3 - - - +
150A ILE* 4.8 4.0 - - - -
158A MET* 3.7 30.3 - - - -
171A ALA 2.8 13.0 + - - -
172A GLY 3.3 3.3 + - - -
173A GLN 3.2 0.8 - - - -
174A ILE* 1.3 77.4 - - - +
176A HIS* 1.3 58.9 + - - +
178A LEU* 3.3 2.4 + - - +
179A GLY 3.3 5.4 + - - -
180A CYS* 3.0 33.0 + - - +
183A VAL* 4.4 0.4 - - - -
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Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLY 3.4 6.6 + - - +
173A GLN* 3.2 11.5 + - - +
175A GLY* 1.3 72.5 - - - +
177A PHE* 1.3 68.6 + - + +
178A LEU 3.2 0.7 + - - -
179A GLY* 3.2 11.4 + - - -
180A CYS 3.2 23.1 - - - +
181A SER* 3.6 9.3 + - - -
183A VAL* 3.6 25.0 + - + +
200A LEU 5.4 1.0 + - - -
201A GLY* 3.1 29.6 + - - -
202A PHE* 5.1 0.2 - - - -
203A ASP* 2.9 32.1 + - - -
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLN* 2.9 34.5 + - + -
174A ILE* 3.1 13.4 + - + +
176A HIS* 1.3 78.9 - - + +
178A LEU* 1.3 62.7 + - - +
179A GLY 3.7 0.7 + - - -
306A TRP* 3.5 57.8 - + + +
311A LYS* 3.4 63.7 - - + +
312A LEU* 3.8 15.5 - - + -
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU* 4.6 1.1 - - + -
144A ILE* 4.1 16.6 - - + -
145A GLN* 3.8 39.3 - - + +
150A ILE* 3.7 22.7 - - + +
151A THR* 3.8 11.6 - - - +
152A ALA* 3.8 5.4 + - - +
174A ILE* 3.0 35.5 + - + +
175A GLY 3.7 3.6 - - - +
177A PHE* 1.3 83.9 - - + +
179A GLY* 1.3 55.5 + - - +
180A CYS 3.9 0.4 - - - -
306A TRP* 4.0 22.2 - - + -
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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