Contacts of the helix formed by residues 184 - 203 (chain A) in PDB entry 5ZCJ
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 PRO 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 5.5 5.2 - - - +
182A MET 4.8 0.9 - - - +
183A MET* 1.3 90.0 - - + +
185A GLU* 1.3 66.5 + - - +
186A GLU* 3.2 26.0 - - + +
187A LYS* 3.1 35.8 + - + +
188A LEU* 3.1 11.7 + - - +
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Residues in contact with GLU 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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6A VAL* 5.4 8.9 - - + +
8A GLU* 5.7 0.7 - - - +
178A LYS* 3.3 42.5 - - + +
183A MET 3.6 1.8 + - - -
184A PRO* 1.3 71.9 - - - +
186A GLU* 1.3 68.5 + - - +
188A LEU* 3.1 15.5 + - + +
189A VAL* 2.9 34.4 + - + +
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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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184A PRO* 3.8 16.8 - - + +
185A GLU* 1.3 87.8 + - - +
187A LYS* 1.3 69.8 + - + +
189A VAL* 3.4 9.0 + - - +
190A GLU* 3.0 40.6 + - - +
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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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183A MET* 4.1 18.9 - - + +
184A PRO* 3.1 33.4 + - + +
186A GLU* 1.3 82.3 - - + +
188A LEU* 1.3 61.3 + - - +
190A GLU* 3.9 17.5 + - - +
191A ALA* 2.9 31.4 + - - +
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Residues in contact with LEU 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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6A VAL* 4.6 8.4 - - + +
157A PHE* 3.7 29.8 - - + -
161A LEU* 4.9 1.9 - - - +
174A LEU* 3.6 39.5 - - + +
177A LEU* 4.1 9.2 - - + -
178A LYS* 3.9 26.5 - - + +
183A MET* 3.8 20.6 - - + +
184A PRO 3.1 18.1 + - - +
185A GLU* 3.1 11.6 + - + +
187A LYS* 1.3 74.6 - - - +
189A VAL* 1.3 59.3 + - - +
191A ALA* 3.4 3.8 + - - +
192A LEU* 3.0 30.7 + - - +
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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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6A VAL* 3.7 30.7 - - + +
185A GLU* 2.9 30.0 + - + +
186A GLU* 3.7 9.4 - - - +
188A LEU* 1.3 74.4 - - - +
190A GLU* 1.3 60.8 + - + +
192A LEU* 3.3 3.7 + - - +
193A ALA* 2.9 29.7 + - + +
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Residues in contact with GLU 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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153A ARG* 5.2 7.9 + - - -
186A GLU* 3.0 27.7 + - - +
187A LYS* 3.9 17.9 + - - +
188A LEU 3.3 0.2 - - - -
189A VAL* 1.3 79.8 - - + +
191A ALA* 1.3 61.5 + - - +
193A ALA* 3.3 7.8 + - - +
194A ALA* 3.0 23.7 + - - +
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Residues in contact with ALA 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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149A THR* 5.3 2.2 - - - +
157A PHE* 3.6 33.2 - - + -
158A PRO* 3.8 26.3 - - + +
161A LEU* 4.0 5.6 - - + -
183A MET* 5.5 0.2 - - + -
187A LYS 2.9 18.9 + - - +
188A LEU 3.9 2.9 - - - +
190A GLU* 1.3 75.0 - - - +
192A LEU* 1.3 58.3 + - - +
194A ALA* 3.4 1.0 + - - -
195A ALA* 3.0 28.2 + - - +
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Residues in contact with LEU 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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6A VAL* 3.9 20.2 - - + +
7A PRO* 3.5 31.4 - - + -
161A LEU* 4.0 14.3 - - + +
170A LYS* 3.7 34.5 - - - +
174A LEU* 4.2 13.2 - - + -
188A LEU 3.0 18.1 + - - +
189A VAL* 3.8 4.5 - - - +
191A ALA* 1.3 74.6 - - - +
193A ALA* 1.3 61.0 + - - +
195A ALA* 3.7 2.8 - - + +
196A THR* 2.9 41.5 + - - +
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Residues in contact with ALA 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 VAL* 2.9 19.3 + - + +
190A GLU* 3.7 7.6 - - - +
191A ALA 3.3 0.2 - - - -
192A LEU* 1.3 75.2 - - - +
194A ALA* 1.3 60.7 + - - +
196A THR* 3.5 5.4 + - - -
197A GLU* 2.9 28.8 + - - +
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Residues in contact with ALA 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 ARG* 3.9 22.9 - - + +
154A VAL* 4.4 11.3 - - + +
158A PRO* 4.1 9.0 - - + -
190A GLU 3.0 17.2 + - - +
191A ALA 3.8 3.4 - - - +
193A ALA* 1.3 73.2 - - - +
195A ALA* 1.3 61.2 + - - +
197A GLU* 3.4 8.0 + - - +
198A LYS* 3.0 27.9 + - - +
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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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158A PRO* 3.2 28.2 - - - +
161A LEU* 3.8 18.8 - - + +
162A SER* 3.9 11.7 - - - +
170A LYS* 5.5 0.9 - - - +
191A ALA 3.0 16.3 + - - +
192A LEU* 3.7 7.6 - - + +
193A ALA 3.3 0.2 - - - -
194A ALA* 1.3 77.0 - - - +
196A THR* 1.3 62.1 + - - +
198A LYS* 3.2 6.7 + - - +
199A GLN* 3.0 28.6 + - - +
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Residues in contact with THR 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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170A LYS* 5.5 1.6 + - - -
192A LEU* 2.9 29.0 + - - +
193A ALA* 3.9 5.8 - - - -
195A ALA* 1.3 75.4 - - - +
197A GLU* 1.3 57.3 + - - +
199A GLN* 3.2 15.4 + - - +
200A LYS* 2.8 39.0 + - - +
203B LEU* 3.8 14.4 - - + -
206B LEU* 3.8 28.5 - - + +
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Residues in contact with GLU 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 ALA 2.9 18.7 + - - +
194A ALA* 3.5 9.2 - - - +
196A THR* 1.3 76.1 - - - +
198A LYS* 1.3 63.1 + - - +
200A LYS* 3.0 18.4 + - - +
201A LYS* 3.0 60.6 + - + +
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Residues in contact with LYS 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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154A VAL* 5.3 11.0 - - + -
158A PRO 5.9 0.2 - - - -
159A ASN* 3.1 29.6 - - - +
162A SER* 2.9 27.8 + - - +
194A ALA 3.0 12.9 + - - +
195A ALA* 3.2 9.8 + - - +
197A GLU* 1.3 76.9 - - - +
199A GLN* 1.3 63.6 + - - +
201A LYS* 3.5 6.5 + - - +
202A ALA* 3.0 24.7 + - + +
59B LEU* 4.2 11.0 - - - -
164B ALA* 3.4 18.2 - - - +
165B PHE 5.5 3.0 + - - -
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Residues in contact with GLN 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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161A LEU 4.2 3.7 + - - -
162A SER* 3.1 41.8 + - - +
163A ASN 4.0 6.7 + - - -
170A LYS* 4.7 10.2 + - - +
195A ALA* 3.0 17.3 + - - +
196A THR* 3.2 21.1 + - - +
198A LYS* 1.3 78.1 - - + +
200A LYS* 1.3 62.6 + - - +
202A ALA* 3.5 12.5 + - - +
203A LEU* 3.5 12.5 + - - +
203B LEU* 3.6 29.7 - - + +
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Residues in contact with LYS 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 THR* 2.8 27.3 + - - +
197A GLU* 3.0 21.3 + - - +
199A GLN* 1.3 77.4 - - - +
201A LYS* 1.3 62.5 + - + +
202A ALA 3.4 0.7 + - - -
203A LEU* 3.4 12.3 + - - +
204A GLU* 3.5 21.1 + - - +
203B LEU* 3.9 20.0 - - + -
206B LEU* 5.1 13.3 - - - +
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Residues in contact with LYS 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 GLU* 3.0 48.4 + - + +
198A LYS* 4.2 4.9 - - - +
200A LYS* 1.3 74.2 - - + +
202A ALA* 1.3 63.9 + - - +
204A GLU* 3.2 38.3 + - - +
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Residues in contact with ALA 202 (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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198A LYS* 3.0 22.7 + - + +
199A GLN* 3.8 8.5 - - - +
200A LYS 3.2 0.6 - - - -
201A LYS* 1.3 78.4 - - - +
203A LEU* 1.3 60.9 + - + +
204A GLU 3.2 4.7 + - - -
199B GLN* 5.8 3.4 - - - +
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Residues in contact with LEU 203 (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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199A GLN 3.5 6.7 + - - +
200A LYS 3.4 9.2 + - - +
201A LYS 3.3 0.8 - - - -
202A ALA* 1.3 76.2 - - + +
204A GLU* 1.3 62.1 + - + +
196B THR* 4.0 22.7 - - + +
199B GLN* 3.4 52.7 - - + +
200B LYS* 3.9 25.3 + - + +
203B LEU* 3.7 27.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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