Contacts of the helix formed by residues 162 - 179 (chain A) in PDB entry 1Z0X
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A GLN* 2.9 40.5 + - + +
158A VAL* 3.2 5.4 + - - +
161A GLY* 1.3 70.1 - - - +
163A ASP* 1.3 60.5 + - - +
164A TYR* 3.1 10.3 + - - +
165A LEU* 2.7 47.2 + - + +
166A LYS* 3.1 21.9 + - - +
49B ASN* 5.4 4.4 + - - -
51B GLN* 6.1 0.9 - - - +
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Residues in contact with ASP 163 (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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161A GLY 3.1 10.9 + - - +
162A ASP* 1.3 70.2 + - - +
164A TYR* 1.3 66.3 + - - +
166A LYS* 3.4 25.0 + - - +
167A GLU* 3.0 22.9 + - - +
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Residues in contact with TYR 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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162A ASP* 3.1 6.6 + - - +
163A ASP* 1.3 78.1 - - - +
165A LEU* 1.3 66.3 + - + +
167A GLU* 3.0 20.3 + - - +
168A GLN* 3.0 50.6 + - + +
48B LYS* 3.8 34.1 - - + -
49B ASN* 4.2 18.6 - - - +
51B GLN* 3.8 21.8 - - + -
52B ALA* 3.2 43.4 + - + +
55B GLN* 3.4 21.6 - - + +
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Residues in contact with LEU 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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154A LEU* 3.9 24.9 - - + +
157A GLN* 3.4 34.1 - - + +
158A VAL* 3.9 13.7 - - + -
162A ASP* 2.7 28.1 + - - +
164A TYR* 1.3 71.5 - - + +
166A LYS* 1.3 65.3 + - - +
168A GLN* 3.2 6.8 + - + +
169A VAL* 3.0 29.9 + - + +
51B GLN* 4.0 33.7 - - + +
55B GLN* 4.5 2.0 - - - +
103B VAL* 3.7 28.3 - - + -
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Residues in contact with LYS 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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158A VAL* 4.0 38.7 + - + +
159A LEU 5.8 0.4 + - - -
161A GLY* 4.4 11.5 - - - -
162A ASP 3.1 18.6 + - - +
163A ASP* 3.6 23.8 + - - +
164A TYR 3.2 0.2 - - - -
165A LEU* 1.3 76.5 - - - +
167A GLU* 1.3 62.8 + - - +
169A VAL* 3.5 6.5 + - + +
170A LEU* 3.2 21.1 + - - +
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Residues in contact with GLU 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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163A ASP 3.0 12.4 + - - +
164A TYR* 3.0 13.2 + - - +
166A LYS* 1.3 78.4 - - - +
168A GLN* 1.3 79.7 + - - +
170A LEU* 3.1 13.7 - - + +
171A HIS* 2.9 56.7 + - + +
48B LYS* 3.6 22.5 + - - -
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Residues in contact with GLN 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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164A TYR* 3.0 55.5 + - + +
165A LEU* 3.2 9.6 + - + +
167A GLU* 1.3 98.3 + - - +
169A VAL* 1.3 65.7 + - - +
171A HIS* 3.0 11.2 + - - +
172A MSE 2.9 19.8 + - - +
55B GLN* 4.6 12.7 + - + +
103B VAL* 4.1 14.1 - - + -
105B ALA* 3.3 34.4 + - + +
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Residues in contact with VAL 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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158A VAL* 4.5 15.9 - - + -
165A LEU* 3.0 17.2 + - + +
166A LYS* 3.7 8.3 - - - +
168A GLN* 1.3 75.5 - - - +
170A LEU* 1.3 62.9 + - - +
172A MSE 3.3 33.8 - - + +
173A LYS* 3.4 23.9 + - + +
103B VAL* 4.3 16.6 - - + +
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Residues in contact with LEU 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 LYS 3.2 11.0 + - - +
167A GLU* 3.1 16.1 + - + +
168A GLN 3.0 0.4 - - - -
169A VAL* 1.3 78.3 - - - +
171A HIS* 1.3 72.0 + - + +
173A LYS* 3.2 13.2 + - + +
174A GLN* 3.1 20.4 + - + +
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Residues in contact with HIS 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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167A GLU* 2.9 47.3 + - + +
168A GLN* 3.0 15.6 + - - +
170A LEU* 1.3 82.9 - - + +
172A MSE 1.3 65.2 + - - +
174A GLN* 3.0 21.0 + - - +
175A TYR* 2.9 48.9 + + + -
105B ALA* 4.2 7.9 + - + +
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Residues in contact with MSE 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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168A GLN 2.9 11.2 + - - +
169A VAL* 3.3 29.2 - - + +
171A HIS* 1.3 76.8 - - - +
173A LYS* 1.3 87.0 + - + +
175A TYR* 3.2 3.7 + - - +
176A VAL* 3.1 24.8 + - + +
184A MSE 4.7 14.1 - - + -
188A ILE* 5.9 4.3 - - + -
103B VAL* 4.6 6.7 - - + -
104B PRO* 3.5 43.5 - - - +
105B ALA* 4.1 11.1 - - + +
110B LEU* 3.8 14.2 - - + +
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Residues in contact with LYS 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 VAL* 3.4 22.0 + - + +
170A LEU* 3.2 13.5 + - + +
172A MSE 1.3 96.7 - - + +
174A GLN* 1.3 62.8 + - - +
176A VAL* 3.5 10.0 + - + +
177A SER* 3.2 22.0 + - - -
188A ILE* 4.6 30.1 - - + +
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Residues in contact with GLN 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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170A LEU* 3.1 11.5 + - + +
171A HIS* 3.0 24.2 + - - +
173A LYS* 1.3 76.9 - - - +
175A TYR* 1.3 62.4 + - - +
177A SER* 3.3 5.9 + - - -
178A ASP* 2.6 69.2 + - - +
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Residues in contact with TYR 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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171A HIS* 2.9 41.8 + + + -
172A MSE 3.6 5.4 - - - +
174A GLN* 1.3 84.1 - - + +
176A VAL* 1.3 67.9 + - - +
178A ASP* 3.8 8.1 - - + -
179A ASN* 2.8 41.1 + - - +
181A LEU* 4.5 1.6 - - - -
105B ALA 3.1 30.7 + - - -
107B PRO* 3.5 39.8 - - + +
110B LEU* 3.6 13.2 - - + -
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Residues in contact with VAL 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 MSE 3.1 18.8 + - + +
173A LYS* 3.6 11.7 - - + +
175A TYR* 1.3 78.3 - - - +
177A SER* 1.3 58.9 + - - +
180A GLU* 3.1 4.2 + - - -
181A LEU* 2.7 62.4 + - + +
184A MSE 4.1 28.9 - - + -
185A GLU* 3.8 32.5 - - + +
188A ILE* 5.5 6.1 - - + -
110B LEU* 4.6 7.0 - - + -
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Residues in contact with SER 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 LYS 3.2 10.4 + - - -
174A GLN* 3.5 9.0 - - - -
175A TYR 3.1 0.4 - - - -
176A VAL* 1.3 80.5 - - - +
178A ASP* 1.3 67.5 + - - +
180A GLU* 3.2 17.5 + - - +
185A GLU* 5.1 8.5 - - - -
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Residues in contact with ASP 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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174A GLN* 2.6 64.1 + - - +
175A TYR* 3.7 11.0 + - + +
177A SER* 1.3 76.7 + - - +
179A ASN* 1.3 65.0 + - - +
180A GLU* 3.3 5.3 + - - +
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Residues in contact with ASN 179 (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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175A TYR* 2.8 48.8 + - - +
178A ASP* 1.3 81.7 - - - +
180A GLU* 1.3 75.6 + - - +
181A LEU* 3.3 23.8 + - + +
107B PRO* 4.2 10.1 - - - +
111B ARG* 3.4 28.4 + - - +
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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