Contacts of the helix formed by residues 163 - 173 (chain A) in PDB entry 1ZX1
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 ASP 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A TYR 3.6 8.9 - - - +
156A THR* 3.5 6.9 + - - -
157A LYS* 4.0 17.8 + - - +
161A ASN 4.9 0.9 - - - +
162A GLY* 1.3 72.0 - - - -
164A SER* 1.3 76.5 + - - +
165A ARG* 3.3 25.5 + - - +
166A TYR* 2.9 54.5 + - + +
167A PHE* 4.2 2.4 + - - -
169B TRP* 5.0 0.3 + - - -
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Residues in contact with SER 164 (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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155A TYR* 3.4 25.2 + - - -
162A GLY 3.6 0.2 + - - -
163A ASP* 1.3 78.2 + - - +
165A ARG* 1.3 64.7 + - - +
166A TYR 3.2 0.2 - - - -
167A PHE* 3.3 44.7 + - - -
168A LEU* 3.3 15.3 - - - +
188A ILE* 3.5 23.2 - - - +
190A PHE* 4.3 8.0 - - - -
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Residues in contact with ARG 165 (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 ASP* 3.0 18.4 + - - +
164A SER* 1.3 81.6 + - - +
166A TYR* 1.3 61.9 + - - +
168A LEU* 3.2 18.5 + - + -
169A TRP* 3.6 0.3 + - - +
226A TRP* 2.7 87.9 + - + +
227A HIS* 3.3 39.8 - - - +
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Residues in contact with TYR 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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157A LYS* 4.5 15.3 + - - +
162A GLY* 4.3 2.9 - - - -
163A ASP* 2.9 47.2 + - + +
165A ARG* 1.3 77.5 - - - +
167A PHE* 1.3 61.1 + - - +
168A LEU 3.4 0.5 + - - -
169A TRP* 3.6 13.5 + - - +
170A PRO* 4.1 3.5 - - - +
227A HIS 3.4 18.8 - - - -
228A PHE* 3.7 34.0 + + + -
166B TYR 4.9 3.1 - - - +
169B TRP* 3.4 34.7 - + + +
170B PRO* 5.0 0.9 - - - +
224B ALA* 4.1 14.2 - - + +
228B PHE* 3.6 31.8 - + + -
230B GLN* 4.0 20.5 + - - +
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Residues in contact with PHE 167 (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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101A PHE* 6.5 0.2 - + - -
103A LEU* 3.7 36.6 - - + -
106A PHE* 3.4 44.3 - + + +
146A VAL* 4.8 13.7 - - + -
148A THR* 4.9 6.3 - - + -
155A TYR* 3.6 26.5 - + - -
163A ASP 4.2 1.1 + - - -
164A SER* 3.3 42.9 + - - -
166A TYR* 1.3 78.4 - - - +
168A LEU* 1.3 83.7 + - + +
169A TRP 3.3 0.4 - - - -
170A PRO* 3.4 11.4 - - - +
171A LEU* 4.2 13.0 - - + +
188A ILE* 5.0 3.6 - - + -
169B TRP* 4.2 1.5 - - - -
170B PRO* 4.5 9.0 - - + +
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Residues in contact with LEU 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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101A PHE* 6.4 0.2 - - + -
144A LEU* 4.1 24.5 - - + -
146A VAL* 5.2 6.1 - - + -
164A SER* 3.3 19.1 - - - +
165A ARG* 3.6 24.7 - - + +
166A TYR 3.2 1.4 - - - -
167A PHE* 1.3 98.5 - - + +
169A TRP* 1.3 55.5 + - - +
170A PRO 3.4 0.2 - - - -
171A LEU* 3.1 8.6 + - + +
172A GLN* 2.7 54.6 + - - +
186A PRO* 3.5 32.8 - - + -
188A ILE* 4.8 7.0 - - + -
226A TRP* 4.4 0.7 - - + -
227A HIS* 4.1 2.2 - - + -
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Residues in contact with TRP 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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165A ARG 3.6 3.2 + - - +
166A TYR 3.9 5.6 - - - +
167A PHE 3.3 0.2 - - - -
168A LEU* 1.3 77.5 - - - +
170A PRO* 1.3 74.0 - - + +
173A HIS* 2.9 72.3 + + + +
174A GLY 3.2 5.4 + - - -
223A THR 3.5 7.6 - - - -
224A ALA* 3.4 38.8 - - + -
227A HIS* 3.3 36.1 - + + -
228A PHE* 3.4 24.9 - + + -
106B PHE* 4.1 15.5 - + - -
161B ASN 3.5 22.4 + - - -
162B GLY* 4.3 2.2 - - - -
163B ASP 5.1 0.2 + - - -
166B TYR* 3.6 40.6 - + + +
167B PHE* 4.5 1.1 - - - +
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Residues in contact with PRO 170 (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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166A TYR 4.1 3.8 - - - +
167A PHE 3.4 17.5 - - - +
169A TRP* 1.3 95.6 - - + +
171A LEU* 1.3 61.8 + - + +
174A GLY* 3.3 4.7 + - - +
175A THR* 3.2 28.8 + - - -
105B TRP 3.9 6.5 - - - +
106B PHE* 3.8 36.6 - - + +
107B SER* 5.1 4.0 - - - -
166B TYR 5.1 0.7 - - - +
167B PHE* 4.4 15.5 - - + +
170B PRO* 4.2 20.4 - - + -
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Residues in contact with LEU 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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101A PHE* 4.3 9.9 - - + -
103A LEU* 5.7 0.2 - - + -
107A SER* 4.3 23.8 - - - +
108A VAL* 3.8 31.6 - - + -
113A LYS* 6.0 0.4 - - + -
116A MET* 4.1 21.3 - - + -
144A LEU* 3.9 27.4 - - + -
167A PHE* 4.2 22.7 - - + +
168A LEU* 3.1 8.6 + - + +
170A PRO* 1.3 82.8 - - + +
172A GLN* 1.3 60.8 + - - +
175A THR* 3.3 9.5 - - - -
176A LEU* 3.0 32.6 + - + +
105B TRP 6.1 0.4 - - - +
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Residues in contact with GLN 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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144A LEU* 3.7 21.2 - - + +
168A LEU* 2.7 32.7 + - + +
171A LEU* 1.3 74.4 - - - +
173A HIS* 1.3 51.9 + - - +
176A LEU* 3.4 9.6 - - + +
177A HIS* 2.8 33.4 + - - +
183A VAL* 3.6 27.9 - - + +
184A LEU 4.1 1.0 - - - +
186A PRO* 3.6 27.0 - - - +
220A ILE* 3.8 5.5 - - - +
222A CYS* 3.8 7.6 - - - -
226A TRP* 3.2 35.4 - - - -
227A HIS* 3.3 13.8 + - - +
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Residues in contact with HIS 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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132A TYR* 3.3 35.0 + + - -
169A TRP* 2.9 62.4 + + + +
172A GLN* 1.3 75.3 - - - +
174A GLY* 1.3 68.3 + - - +
175A THR 3.2 1.8 - - - -
177A HIS* 3.4 6.4 + + - +
178A PHE 3.2 21.7 + - - -
222A CYS* 3.6 6.3 + - - -
223A THR* 5.5 0.9 - - - -
231A ZN 2.1 38.3 - - - -
106B PHE* 4.3 2.9 - + - -
160B VAL 3.2 24.1 + - - -
161B ASN 4.1 4.0 - - - -
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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