Contacts of the helix formed by residues 182 - 194 (chain A) in PDB entry 3SMZ
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 LYS 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ALA* 3.9 4.4 - - - +
157A SER* 5.0 6.1 - - - +
180A TYR* 3.6 6.2 - - - +
181A MET* 1.4 112.4 - - + +
183A LYS* 1.3 65.1 + - - +
184A ASP* 4.3 8.5 - - + +
185A SER* 3.1 34.4 + - - +
186A ALA 3.4 4.0 + - - -
188A ARG* 6.1 1.1 - - - +
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Residues in contact with LYS 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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131A ASP* 3.4 57.9 + - - +
132A ALA* 3.9 14.0 - - - +
181A MET 4.4 0.2 + - - -
182A LYS* 1.3 71.0 - - - +
184A ASP* 1.4 56.9 + - - +
186A ALA* 3.2 4.7 + - - +
187A ALA* 2.9 29.0 + - + +
207A TRP* 4.2 17.3 - - + -
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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 LYS* 3.2 6.8 - - + +
183A LYS* 1.4 73.9 - - - +
185A SER* 1.3 65.1 + - - +
187A ALA* 3.7 8.8 - - - +
188A ARG* 2.8 59.0 + - - +
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PHE* 3.3 29.3 + - - +
156A GLY* 3.6 10.0 - - - -
157A SER 4.7 0.7 + - - -
180A TYR* 3.7 23.1 - - - -
182A LYS* 3.1 32.0 + - - +
184A ASP* 1.3 79.4 - - - +
186A ALA* 1.4 57.1 + - - +
188A ARG* 3.4 10.5 + - - +
189A ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 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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132A ALA* 3.8 20.2 - - + +
134A LEU* 3.4 12.6 - - + +
180A TYR* 3.6 26.6 - - + -
182A LYS 3.4 1.4 + - - -
183A LYS 3.2 9.3 + - - +
185A SER* 1.4 76.7 - - - +
187A ALA* 1.3 58.8 + - - +
189A ALA 3.4 0.2 + - - -
190A LYS* 2.9 27.7 + - - +
207A TRP* 3.6 23.1 - - + -
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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
----------------------------------------------------------
183A LYS* 2.9 19.8 + - + +
184A ASP* 3.7 14.1 - - - +
185A SER 3.4 0.2 - - - -
186A ALA* 1.3 74.9 - - - +
188A ARG* 1.3 58.5 + - + +
190A LYS* 3.5 1.9 + - - +
191A SER* 3.1 29.1 + - - -
207A TRP* 3.7 19.4 - - + -
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Residues in contact with ARG 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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154A PRO 5.1 0.6 + - - -
155A PHE* 3.0 45.8 + - + +
182A LYS* 6.1 1.2 - - - +
184A ASP* 2.8 42.4 + - - +
185A SER* 3.8 14.4 + - - +
187A ALA* 1.3 73.3 - - + +
189A ALA* 1.3 66.0 + - - +
191A SER* 3.4 6.2 + - - -
192A ASP* 3.1 25.3 + - - +
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Residues in contact with ALA 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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134A LEU* 3.8 6.5 - - + -
155A PHE* 3.5 21.5 - - + -
180A TYR* 3.2 33.2 - - + +
185A SER 2.9 16.5 + - - +
186A ALA 3.4 4.9 + - - +
188A ARG* 1.3 77.6 - - - +
190A LYS* 1.3 56.8 + - - +
192A ASP* 3.4 0.7 + - - +
193A LEU* 3.0 40.8 + - + +
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Residues in contact with LYS 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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134A LEU* 3.8 18.3 - - + +
186A ALA 2.9 17.8 + - - +
187A ALA 3.9 4.0 - - - +
189A ALA* 1.3 74.8 - - - +
191A SER* 1.3 58.3 + - - +
194A LEU* 2.9 56.1 + - + +
205A VAL* 3.7 38.4 - - + +
206A HIS* 4.6 1.6 - - - +
207A TRP* 3.2 41.5 - - + +
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Residues in contact with SER 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 3.1 17.9 + - - -
188A ARG* 3.9 6.7 - - - -
189A ALA 3.4 0.2 - - - -
190A LYS* 1.3 77.6 - - - +
192A ASP* 1.3 63.0 + - - +
194A LEU* 4.3 9.9 - - - +
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Residues in contact with ASP 192 (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 PHE* 3.5 31.3 - - + -
188A ARG 3.1 16.8 + - - +
191A SER* 1.3 81.1 - - - +
193A LEU* 1.3 71.3 + - - +
194A LEU 3.7 4.0 + - - +
196A LYS* 3.9 19.2 + - - +
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Residues in contact with LEU 193 (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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134A LEU* 5.7 1.6 - - + -
136A VAL* 4.3 14.8 - - + -
151A LEU* 3.8 26.0 - - + +
152A VAL* 3.9 27.4 - - + -
155A PHE* 4.1 17.9 - - + -
189A ALA* 3.0 25.9 + - + +
192A ASP* 1.3 88.9 - - - +
194A LEU* 1.4 60.3 + - - +
195A GLY 3.1 0.7 + - - -
196A LYS* 2.9 43.6 + - + +
203A LEU* 3.4 17.3 - - + +
205A VAL* 3.8 14.4 - - + -
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Residues in contact with LEU 194 (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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190A LYS* 2.9 46.4 + - + +
191A SER* 4.3 7.5 - - - +
192A ASP 3.5 5.7 - - - +
193A LEU* 1.4 74.1 - - - +
195A GLY* 1.3 64.7 + - - +
196A LYS 3.5 0.3 + - - -
203A LEU 4.1 0.9 - - - +
204A TYR* 3.7 22.2 - - + -
205A VAL* 3.5 37.3 - - + +
313A ALA* 4.6 16.8 - - + +
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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