Contacts of the helix formed by residues 181 - 191 (chain J) in PDB entry 5ANC
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 181 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180J VAL* 1.3 77.6 - - - +
182J GLU* 1.3 63.7 + - + +
183J GLY 3.2 3.0 + - - -
184J LYS* 3.6 43.2 + - + +
185J LYS* 3.9 4.0 + - - +
203J GLY* 4.1 20.2 - - - +
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Residues in contact with GLU 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180J VAL* 3.4 10.3 - - + +
181J ASN* 1.3 74.6 - - + +
183J GLY* 1.3 59.6 + - - +
184J LYS 3.2 0.9 - - - -
185J LYS* 3.2 23.9 + - + +
186J LEU* 2.9 28.8 + - - +
229J LYS* 3.0 51.3 + - + +
230J GLY* 4.6 1.0 - - - -
231J LYS* 4.3 11.8 + - - +
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Residues in contact with GLY 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J LEU* 4.0 25.4 - - - +
179J PRO 3.9 3.4 + - - -
180J VAL 3.7 5.0 + - - -
181J ASN 3.2 1.6 - - - -
182J GLU* 1.3 77.1 - - - +
184J LYS* 1.3 56.6 + - - +
186J LEU* 3.2 5.0 + - - +
187J LYS* 2.9 28.6 + - - +
207J GLU* 3.3 22.4 - - - -
229J LYS* 4.2 5.7 - - - +
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Residues in contact with LYS 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181J ASN* 3.7 36.3 - - + +
183J GLY* 1.3 73.9 - - - +
185J LYS* 1.3 63.7 + - - +
187J LYS* 3.2 10.7 + - - +
188J GLU* 3.0 28.1 + - + +
201J ASP* 3.5 32.2 - - - +
202J TYR* 3.2 41.8 - - - +
203J GLY 4.0 1.9 - - - +
207J GLU* 3.1 11.5 + - - +
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Residues in contact with LYS 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181J ASN 3.9 2.6 + - - +
182J GLU* 3.2 29.8 + - + +
184J LYS* 1.3 79.1 - - - +
186J LEU* 1.3 58.3 + - - +
188J GLU* 3.2 10.7 + - + +
189J LYS* 2.9 49.9 + - - +
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Residues in contact with LEU 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J PHE* 3.7 21.8 - - + -
178J LEU* 3.5 33.0 - - + -
182J GLU 2.9 13.6 + - - +
183J GLY* 3.2 9.6 + - - +
185J LYS* 1.3 76.8 - - - +
187J LYS* 1.3 56.5 + - - +
189J LYS* 3.2 10.2 + - + +
190J LEU* 2.9 52.9 + - + +
225J LYS* 3.9 17.9 - - - +
228J THR* 4.5 17.7 - - + -
229J LYS* 4.2 19.5 - - + +
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Residues in contact with LYS 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J LEU* 5.3 1.7 - - - +
183J GLY 2.9 12.5 + - - +
184J LYS* 3.3 13.0 - - - +
186J LEU* 1.3 76.9 - - - +
188J GLU* 1.3 71.7 + - - +
190J LEU* 3.4 4.8 + - - +
191J LYS* 3.3 26.2 + - + +
196J VAL* 4.2 20.0 - - + +
199J SER* 3.9 32.6 - - - +
200J GLU 4.0 6.5 + - - +
201J ASP* 3.1 35.9 + - - -
207J GLU* 5.5 1.1 - - - +
209J VAL* 4.2 27.1 - - + -
211J LEU* 6.4 0.7 - - - -
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Residues in contact with GLU 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184J LYS* 3.0 19.7 + - + +
185J LYS* 3.2 11.0 + - + +
187J LYS* 1.3 88.6 - - + +
189J LYS* 1.3 64.3 + - - +
190J LEU 3.5 0.2 + - - -
191J LYS* 3.6 36.0 + - - +
192J PRO* 3.9 4.9 - - - +
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Residues in contact with LYS 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185J LYS* 2.9 36.3 + - - +
186J LEU* 3.2 14.6 + - + +
188J GLU* 1.3 77.4 - - - +
190J LEU* 1.3 64.9 + - + +
191J LYS 3.3 0.2 - - - -
192J PRO* 3.4 21.3 - - - +
193J LEU* 4.8 1.6 + - - +
228J THR* 3.4 33.7 + - + +
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Residues in contact with LEU 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J PHE* 5.3 2.9 - - + -
186J LEU* 2.9 48.0 + - + +
187J LYS* 3.4 4.4 + - - +
189J LYS* 1.3 82.2 - - + +
191J LYS* 1.3 62.3 + - - +
192J PRO 3.5 1.3 - - - -
193J LEU* 3.3 33.6 + - + +
194J ILE* 3.2 32.2 + - + +
196J VAL* 4.4 3.1 - - - +
211J LEU* 5.6 13.5 - - + -
225J LYS* 3.9 37.2 - - + +
228J THR* 6.2 1.8 - - + +
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Residues in contact with LYS 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J LYS* 3.3 15.8 + - + +
188J GLU* 3.8 28.8 + - - +
190J LEU* 1.3 78.0 - - - +
192J PRO* 1.4 67.4 - - + +
194J ILE 2.9 15.9 - - - +
195J LYS* 5.0 0.7 - - - -
196J VAL* 3.7 27.6 - - + +
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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