Contacts of the helix formed by residues 182 - 191 (chain A) in PDB entry 3ZS4
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 ASN 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ILE* 3.6 21.6 - - - +
171A ASP* 2.8 38.4 + - + +
174A LYS* 4.6 11.2 - - + +
180A GLY 4.0 0.2 + - - -
181A PRO* 1.3 70.1 - - - +
183A LEU* 1.3 61.4 + - - +
184A ASP* 3.3 12.3 + - - +
185A LEU* 2.9 27.8 + - + +
186A LEU* 3.1 28.1 + - - +
201A GLY 5.0 0.6 + - - -
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Residues in contact with LEU 183 (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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181A PRO* 3.5 18.2 + - + +
182A ASN* 1.3 72.8 + - - +
184A ASP* 1.3 59.8 + - - +
186A LEU* 3.5 6.0 + - + -
187A ALA* 3.0 30.5 + - - +
211A ALA* 3.7 26.5 - - + +
212A ILE* 3.9 39.7 - - + +
214A THR* 5.8 0.7 - - - +
215A LEU* 3.7 18.1 - - + +
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Residues in contact with ASP 184 (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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182A ASN* 3.3 8.1 + - - +
183A LEU* 1.3 77.8 - - - +
185A LEU* 1.3 60.3 + - - +
187A ALA* 4.0 4.8 - - - +
188A GLY* 2.9 26.2 + - - -
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Residues in contact with LEU 185 (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 VAL* 4.1 16.2 - - + -
133A ILE* 4.5 3.8 - - + -
138A HIS* 3.9 19.3 - - + -
152A LEU* 3.7 30.7 - - + -
153A TRP* 4.6 3.1 - - + -
169A VAL* 3.9 21.8 - - + -
171A ASP* 3.8 34.1 - - + +
182A ASN* 2.9 28.4 + - + +
184A ASP* 1.3 76.7 - - - +
186A LEU* 1.3 65.6 + - + +
188A GLY* 3.3 2.5 + - - -
189A VAL* 3.0 34.0 + - + +
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Residues in contact with LEU 186 (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* 4.2 25.4 - - + +
181A PRO* 4.6 7.0 - - + -
182A ASN 3.1 25.4 + - - +
183A LEU* 3.8 11.4 - - + +
184A ASP 3.3 0.2 - - - -
185A LEU* 1.3 78.2 - - + +
187A ALA* 1.3 56.6 + - - +
189A VAL* 3.4 4.4 + - - +
190A ALA* 3.0 31.2 + - - +
197A VAL* 4.3 11.7 - - + +
199A ALA* 3.6 42.0 - - + -
200A SER 4.9 0.2 - - - +
212A ILE* 4.3 19.5 - - + -
215A LEU* 3.9 12.6 - - + -
220A VAL* 4.3 8.5 - - + +
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Residues in contact with ALA 187 (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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183A LEU 3.0 17.7 + - - +
184A ASP* 4.0 5.4 - - - +
186A LEU* 1.3 73.5 - - - +
188A GLY* 1.3 60.7 + - - +
190A ALA* 3.7 5.5 - - - -
191A ASP* 2.9 38.7 + - - -
215A LEU* 4.1 13.8 - - + +
218A ARG* 3.7 31.4 - - - +
220A VAL* 5.5 0.2 - - - -
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Residues in contact with GLY 188 (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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153A TRP* 3.7 12.8 - - - -
184A ASP 2.9 19.1 + - - -
185A LEU 3.7 1.8 - - - -
187A ALA* 1.3 77.8 - - - +
189A VAL* 1.3 61.2 + - - +
191A ASP* 3.8 1.5 + - - -
192A ARG* 2.8 45.4 + - - +
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Residues in contact with VAL 189 (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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129A LEU* 4.8 2.2 - - + -
152A LEU* 4.4 11.9 - - + -
153A TRP* 4.1 17.3 - - + -
156A LEU* 4.0 24.4 - - + +
167A PHE* 4.9 1.3 - - + -
169A VAL* 3.8 33.7 - - + -
185A LEU* 3.0 30.4 + - + +
186A LEU* 3.9 3.1 - - - +
188A GLY* 1.3 73.2 - - - +
190A ALA* 1.3 62.3 + - - +
192A ARG* 2.9 20.8 + - - +
193A THR* 3.4 11.8 + - + +
197A VAL* 3.8 13.7 - - + -
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Residues in contact with ALA 190 (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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186A LEU 3.0 18.6 + - - +
187A ALA* 3.8 5.6 - - - +
189A VAL* 1.3 75.9 - - - +
191A ASP* 1.3 57.6 + - - +
192A ARG 3.2 0.2 - - - -
193A THR* 3.0 24.7 - - - +
195A ALA 5.4 0.8 - - - +
197A VAL* 4.0 16.1 - - + +
215A LEU* 6.2 0.2 - - + -
218A ARG* 3.5 35.1 - - + +
219A GLY* 4.4 3.4 - - - -
220A VAL* 4.1 16.2 - - + -
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Residues in contact with ASP 191 (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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187A ALA 2.9 20.9 + - - +
188A GLY* 4.0 5.6 - - - +
189A VAL 3.2 0.2 - - - -
190A ALA* 1.3 77.4 - - - +
192A ARG* 1.3 67.1 + - + +
193A THR 3.5 0.8 + - - -
218A ARG* 2.5 51.0 + - - +
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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