Contacts of the helix formed by residues 184 - 201 (chain A) in PDB entry 4ZDR
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 SER 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A TYR* 2.9 17.0 + - - +
179A TYR* 4.6 0.2 - - - -
182A LEU* 3.5 20.3 + - - +
183A ASN* 1.3 76.1 + - - +
185A PRO* 1.3 58.0 - - - +
186A GLU* 3.0 30.6 + - - -
187A LYS* 3.2 15.7 + - - -
188A ALA* 3.0 25.5 + - - +
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Residues in contact with PRO 185 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A TYR* 3.5 37.0 - - + -
183A ASN* 3.3 17.5 - - + +
184A SER* 1.3 83.4 - - - +
186A GLU* 1.3 63.6 + - - +
188A ALA* 3.7 1.7 - - + +
189A CYS* 3.1 36.9 + - - +
228A TRP 5.5 3.4 - - - +
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Residues in contact with GLU 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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183A ASN 4.5 0.7 - - - +
184A SER* 3.0 29.3 + - - -
185A PRO* 1.3 83.8 - - - +
187A LYS* 1.3 78.0 + - + +
189A CYS* 3.2 6.1 + - - +
190A SER* 3.1 22.5 + - - -
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Residues in contact with LYS 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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178A TYR* 3.7 30.9 - - + -
184A SER* 3.2 18.6 + - - -
186A GLU* 1.3 86.2 - - + +
188A ALA* 1.3 62.7 + - - +
190A SER* 3.4 7.2 + - - -
191A LEU* 3.2 22.9 + - - +
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Residues in contact with ALA 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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175A SER* 3.3 33.9 - - - +
178A TYR* 3.8 5.5 - - - +
179A TYR* 3.7 19.5 - - + +
184A SER 3.0 16.7 + - - +
185A PRO* 3.7 6.5 - - + +
187A LYS* 1.3 77.7 - - - +
189A CYS* 1.3 63.3 + - - +
191A LEU* 3.2 4.7 + - - +
192A ALA* 3.0 20.3 + - - +
228A TRP* 4.1 9.6 - - + -
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Residues in contact with CYS 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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185A PRO* 3.1 21.8 + - - +
186A GLU* 3.2 4.0 + - - +
188A ALA* 1.3 75.2 - - - +
190A SER* 1.3 65.9 + - - +
193A LYS* 3.0 28.1 + - - +
225A LEU* 3.7 20.8 - - + +
228A TRP* 3.6 42.6 - - - -
229A THR* 4.7 5.8 - - - -
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Residues in contact with SER 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 GLU 3.1 12.2 + - - -
187A LYS* 3.5 11.9 - - - -
189A CYS* 1.3 78.1 - - - +
191A LEU* 1.3 61.1 + - - +
193A LYS* 4.0 2.0 - - - +
194A THR* 2.8 37.9 + - - -
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Residues in contact with LEU 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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153A PHE* 4.3 27.5 - - + -
171A ALA* 3.2 44.4 - - + +
174A PHE* 3.7 37.7 - - + -
175A SER* 3.8 9.0 - - - +
178A TYR* 4.0 15.0 - - + -
187A LYS 3.2 9.1 + - - +
188A ALA 3.5 7.6 - - - +
190A SER* 1.3 79.4 - - - +
192A ALA* 1.3 63.6 + - - +
194A THR* 3.8 3.9 - - - -
195A ALA* 3.0 26.2 + - + +
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Residues in contact with ALA 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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175A SER* 4.1 4.0 - - - +
188A ALA 3.0 14.1 + - - +
191A LEU* 1.3 79.1 - - - +
193A LYS* 1.3 57.6 + - - +
195A ALA* 3.4 1.8 - - - +
196A PHE* 2.8 30.5 + - - +
221A LEU* 4.1 29.6 - - + +
225A LEU* 3.5 29.8 - - + -
228A TRP* 4.2 12.1 - - + -
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Residues in contact with LYS 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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189A CYS 3.0 16.7 + - - +
190A SER* 4.1 2.5 - - - +
192A ALA* 1.3 77.4 - - - +
194A THR* 1.3 52.9 - - - +
196A PHE* 3.2 3.7 + - - +
197A ASP* 2.7 49.5 + - - +
225A LEU* 3.5 21.0 - - + +
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Residues in contact with THR 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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153A PHE* 6.5 0.7 - - + -
190A SER* 2.8 28.7 + - - -
191A LEU* 3.8 3.8 - - - -
193A LYS* 1.3 75.8 - - - +
195A ALA* 1.3 58.7 + - - +
197A ASP* 3.8 4.8 - - - +
198A GLU* 2.9 60.2 + - + +
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Residues in contact with ALA 195 (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 PHE* 6.0 3.4 - - + -
162A PRO* 4.8 2.1 - - - +
167A ARG* 5.8 4.7 - - - +
168A LEU* 4.1 10.5 - - + +
171A ALA* 3.7 28.5 - - + -
191A LEU* 3.0 20.4 + - + +
192A ALA* 3.4 4.0 - - - +
194A THR* 1.3 76.3 - - - +
196A PHE* 1.3 62.4 + - - +
198A GLU* 4.1 5.4 - - - +
199A ALA* 3.2 23.4 + - - +
221A LEU* 4.4 6.1 - - + -
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Residues in contact with PHE 196 (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 LEU* 5.4 0.2 - - - -
192A ALA 2.8 17.8 + - - +
193A LYS* 3.5 7.6 - - - +
195A ALA* 1.3 74.9 - - - +
197A ASP* 1.3 72.0 + - - +
199A ALA* 3.3 5.8 + - - +
200A ILE* 2.9 52.7 + - + +
218A MET* 3.5 40.8 - - + -
219A GLN* 5.3 0.4 - - - -
221A LEU* 4.4 11.8 - - + +
222A ARG* 3.4 46.9 - - + -
225A LEU* 4.9 3.6 - - + -
302A GOL 4.0 19.5 - - - -
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Residues in contact with ASP 197 (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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193A LYS* 2.7 33.2 + - - +
194A THR* 3.8 5.4 + - - +
196A PHE* 1.3 87.1 - - - +
198A GLU* 1.3 53.4 + - + +
200A ILE* 3.1 6.6 + - - +
201A ALA* 2.7 35.7 + - - +
302A GOL 4.1 9.9 - - - -
306A TME 4.0 31.9 - - + +
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Residues in contact with GLU 198 (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 PRO* 3.5 25.3 - - + +
167A ARG* 2.7 32.6 + - - +
194A THR* 2.9 42.3 + - + +
195A ALA* 4.1 2.7 - - - +
197A ASP* 1.3 78.5 - - + +
199A ALA* 1.3 62.7 + - - +
201A ALA* 3.3 17.6 - - - +
202A GLU* 3.6 5.0 - - - +
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Residues in contact with ALA 199 (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 PRO* 3.6 26.2 - - - +
163A THR* 3.8 9.1 - - + +
168A LEU* 4.0 6.3 - - + -
195A ALA 3.2 18.2 + - - +
196A PHE 3.5 4.5 - - - +
197A ASP 3.1 0.6 - - - -
198A GLU* 1.3 76.1 - - - +
200A ILE* 1.3 56.8 + - - +
202A GLU 2.7 25.1 + - - -
203A LEU* 3.3 10.0 + - - +
218A MET* 3.8 26.5 - - + -
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Residues in contact with ILE 200 (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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196A PHE* 2.9 46.7 + - + +
197A ASP* 3.1 10.7 + - - +
199A ALA* 1.3 74.2 - - - +
201A ALA* 1.3 66.0 + - - +
202A GLU 2.9 1.6 + - - -
203A LEU* 3.4 28.7 + - + +
218A MET* 3.6 19.9 - - + +
302A GOL 4.8 15.3 - - - +
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Residues in contact with ALA 201 (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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197A ASP 2.7 16.8 + - - +
198A GLU* 3.3 18.2 - - - +
200A ILE* 1.3 75.0 - - - +
202A GLU* 1.3 64.8 + - + +
203A LEU 3.7 0.6 + - - -
204A ASP* 5.3 4.2 - - - +
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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