Contacts of the helix formed by residues 193 - 211 (chain F) in PDB entry 5ZCS
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 GLU 193 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192F CYS* 1.3 78.0 - - + +
194F LEU* 1.3 60.9 + - - +
195F ALA 3.3 0.2 - - - -
196F LEU* 3.4 6.4 + - - +
197F GLN* 2.9 29.2 + - - +
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Residues in contact with LEU 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F CYS 3.4 3.6 - - - +
193F GLU* 1.3 76.5 - - - +
195F ALA* 1.3 61.1 + - - +
197F GLN* 3.8 6.1 - - - +
198F ASN* 2.9 31.7 + - - +
234F LEU* 4.9 17.3 - - + -
237F HIS* 3.7 22.8 - - + +
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Residues in contact with ALA 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F CYS* 3.9 17.8 + - - +
193F GLU 3.3 0.2 - - - -
194F LEU* 1.3 77.7 - - - +
196F LEU* 1.3 61.4 + - - +
198F ASN* 4.5 4.6 - - - +
199F PRO* 3.5 21.8 - - - +
237F HIS* 4.5 6.4 - - + +
238F PRO* 5.7 7.9 - - + -
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Residues in contact with LEU 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F CYS 3.5 14.5 + - - +
193F GLU* 3.4 5.9 + - - +
194F LEU 3.2 0.6 - - - -
195F ALA* 1.3 77.1 - - - +
197F GLN* 1.3 60.7 + - - +
199F PRO* 3.8 5.0 - - - +
200F GLU* 3.2 25.5 + - - +
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Residues in contact with GLN 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F GLU 2.9 17.7 + - - +
194F LEU* 3.3 7.6 + - - +
196F LEU* 1.3 76.6 - - - +
198F ASN* 1.3 58.3 + - - +
200F GLU* 3.6 5.7 + - - +
201F VAL* 3.1 26.7 + - - +
230F THR* 5.2 16.5 - - - -
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Residues in contact with ASN 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F LEU 2.9 17.2 + - - +
195F ALA* 4.5 4.9 - - - +
197F GLN* 1.3 75.2 - - - +
199F PRO* 1.3 59.0 - - - +
201F VAL* 3.3 6.9 + - - +
202F VAL* 2.9 28.2 + - - +
237F HIS 3.9 24.5 - - - +
238F PRO* 4.7 4.5 - - + -
242F GLN* 5.6 10.4 - - + +
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Residues in contact with PRO 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F ALA 3.5 18.1 - - - +
196F LEU* 4.0 6.1 - - - +
197F GLN 3.4 0.4 - - - -
198F ASN* 1.3 77.4 - - - +
200F GLU* 1.3 60.3 + - - +
202F VAL* 3.3 6.9 + - + +
203F ALA* 2.9 28.9 + - - +
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Residues in contact with GLU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F LEU 3.2 16.8 + - - +
197F GLN* 3.9 6.5 - - - +
198F ASN 3.3 0.2 - - - -
199F PRO* 1.3 77.8 - - - +
201F VAL* 1.3 59.8 + - - +
203F ALA* 3.4 6.8 + - - +
204F LEU* 2.9 28.4 + - - +
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Residues in contact with VAL 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F GLN 3.1 18.3 + - - +
198F ASN* 3.7 7.4 - - - +
199F PRO 3.3 0.2 - - - -
200F GLU* 1.3 72.4 - - - +
202F VAL* 1.3 61.6 + - - +
204F LEU* 3.4 6.7 + - - +
205F ARG* 2.9 28.4 + - - +
227F LEU* 4.2 27.1 - - + +
230F THR* 6.1 2.7 - - - -
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Residues in contact with VAL 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F ASN 2.9 16.8 + - - +
199F PRO* 3.7 8.1 - - + +
200F GLU 3.3 0.2 - - - -
201F VAL* 1.3 76.8 - - - +
203F ALA* 1.3 56.3 + - - +
205F ARG* 3.4 6.6 + - - +
206F GLY* 2.9 24.9 + - - -
242F GLN* 6.2 4.5 - - + -
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Residues in contact with ALA 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F PRO 2.9 17.0 + - - +
200F GLU* 3.7 7.4 - - - +
202F VAL* 1.3 77.7 - - - +
204F LEU* 1.3 57.4 + - - +
206F GLY* 3.4 1.8 + - - -
207F GLY* 2.9 24.9 + - - -
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Residues in contact with LEU 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F GLU 2.9 17.2 + - - +
201F VAL* 3.7 7.6 - - - +
203F ALA* 1.3 75.7 - - - +
205F ARG* 1.3 58.7 + - - +
207F GLY* 3.4 1.8 + - - -
208F LEU* 2.9 29.5 + - - +
223F ILE* 4.5 25.4 - - + +
227F LEU* 6.3 1.6 - - + -
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Residues in contact with ARG 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F VAL 2.9 17.0 + - - +
202F VAL* 3.7 7.6 - - - +
203F ALA 3.3 0.2 - - - -
204F LEU* 1.3 76.1 - - - +
206F GLY* 1.3 59.1 + - - +
208F LEU* 3.4 6.6 + - - +
209F ASN* 2.9 28.9 + - - +
245F ARG* 5.7 6.7 - - + +
246F ALA* 6.2 1.6 - - - -
249F GLU* 4.9 19.0 - - + +
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Residues in contact with GLY 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F VAL 2.9 16.4 + - - -
203F ALA* 3.8 2.7 - - - -
205F ARG* 1.3 77.4 - - - +
207F GLY* 1.3 56.2 + - - +
209F ASN* 3.4 6.2 + - - +
210F THR* 2.9 29.6 + - - -
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Residues in contact with GLY 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F ALA 2.9 16.8 + - - -
204F LEU* 3.8 2.7 - - - -
206F GLY* 1.3 73.8 - - - +
208F LEU* 1.3 60.1 + - - +
210F THR* 3.9 5.8 - - - -
211F ILE* 3.1 27.9 + - - +
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Residues in contact with LEU 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F LEU 2.9 17.4 + - - +
205F ARG* 3.8 6.7 - - - +
206F GLY 3.3 0.2 - - - -
207F GLY* 1.3 75.3 - - - +
209F ASN* 1.3 62.0 + - - +
211F ILE* 3.5 20.6 + - - +
212F LEU 5.5 0.2 - - - -
213F LYS* 4.9 5.1 + - - +
220F LEU* 4.4 23.8 - - + +
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Residues in contact with ASN 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F ARG 2.9 17.7 + - - +
206F GLY* 3.8 7.0 - - - +
208F LEU* 1.3 75.7 - - - +
210F THR* 1.3 61.5 + - - +
211F ILE 3.5 6.6 - - - +
249F GLU* 5.8 7.2 - - + -
252F ARG* 6.0 7.0 - - + -
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Residues in contact with THR 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F GLY 2.9 18.5 + - - -
207F GLY* 4.0 7.2 - - - -
209F ASN* 1.3 75.7 - - - +
211F ILE* 1.3 60.5 + - - +
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Residues in contact with ILE 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F GLY 3.1 18.3 + - - +
208F LEU* 3.6 11.3 - - - +
209F ASN 3.3 10.3 - - - +
210F THR* 1.3 80.7 - - - +
212F LEU* 1.3 68.4 + - - +
213F LYS* 3.7 18.4 - - + -
216F ILE* 5.1 8.1 - - + -
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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