Contacts of the strand formed by residues 180 - 187 (chain R) in PDB entry 4DOH
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 180 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178R ASN 3.2 14.3 + - - +
179R LEU* 1.3 74.2 - - - +
181R TYR* 1.3 67.0 + - - +
197R CYS* 4.6 16.9 - - + +
198R VAL 3.7 6.7 - - - +
199R THR* 3.6 26.9 - - + -
220R SER* 3.7 2.9 - - - -
221R PHE* 2.9 73.8 + - + +
223R PRO* 5.1 7.0 - - - -
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Residues in contact with TYR 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140R PRO* 3.5 26.9 - - + -
155R LEU* 4.2 20.2 - - + -
157R ALA* 2.9 25.4 - - - +
158R PRO* 3.9 5.2 - - + -
173R GLN* 2.7 37.0 + - - -
179R LEU* 3.3 12.2 - - + +
180R LYS* 1.3 74.8 - - - +
182R ASN* 1.3 61.0 + - - +
183R VAL* 3.8 1.5 + - + -
197R CYS* 3.4 5.6 - - - +
198R VAL* 2.9 47.3 + - + +
199R THR* 4.2 11.0 - - - -
201R HIS* 3.9 8.5 + + - -
218R VAL* 3.6 14.4 - - + -
219R GLU 3.4 2.9 - - - -
220R SER* 3.2 28.0 - - - -
221R PHE* 5.1 0.4 - - - -
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Residues in contact with ASN 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180R LYS 4.3 0.6 - - - -
181R TYR* 1.3 71.4 - - - +
183R VAL* 1.3 62.8 + - - +
184R SER* 3.7 2.8 + - - -
195R SER* 3.9 14.0 + - - -
196R GLN 3.7 6.2 + - - +
197R CYS* 4.3 14.4 - - - -
217R HIS 3.7 1.2 - - - +
218R VAL* 3.6 3.6 - - - -
219R GLU* 2.9 53.2 + - + +
221R PHE* 4.7 4.9 - - + -
302R NAG 2.3 61.8 + - + +
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Residues in contact with VAL 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153R VAL* 5.4 5.2 - - + -
155R LEU* 4.6 5.8 - - + -
181R TYR 4.3 1.6 - - - +
182R ASN* 1.3 74.3 + - - +
184R SER* 1.3 60.6 + - - +
185R VAL* 4.0 11.6 + - + +
194R TRP 3.8 1.4 - - - +
195R SER* 3.3 2.3 - - - -
196R GLN* 2.6 45.4 + - + +
198R VAL* 3.9 28.0 - - + -
203R LEU* 4.2 24.0 - - + -
216R VAL* 3.9 25.1 - - + -
217R HIS 4.0 2.2 - - - -
218R VAL* 4.2 20.2 - - + -
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Residues in contact with SER 184 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182R ASN* 3.7 2.2 + - - -
183R VAL* 1.3 71.7 - - - +
185R VAL* 1.3 61.6 + - - +
193R THR* 5.1 6.2 + - - -
194R TRP 3.9 3.4 + - - -
195R SER* 2.9 13.7 + - - -
215R CYS 3.5 1.2 - - - +
216R VAL* 3.2 8.7 - - - +
217R HIS* 3.0 65.2 + - - -
219R GLU* 6.0 0.4 - - - -
302R NAG 2.7 30.3 + - - -
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Residues in contact with VAL 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183R VAL* 4.4 15.3 - - + +
184R SER* 1.3 77.6 - - - +
186R LEU* 1.3 63.0 + - - +
187R ASN 4.1 0.7 + - - +
192R ARG 4.1 0.3 - - - +
193R THR* 3.1 6.2 + - - -
194R TRP* 3.0 79.4 + - + +
196R GLN* 5.4 0.7 - - - +
205R LEU* 4.1 27.1 - - + -
208R LEU* 6.0 0.2 - - + -
214R TYR* 4.0 27.6 - - + -
215R CYS 3.7 3.1 - - - +
216R VAL* 4.8 5.2 - - + -
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Residues in contact with LEU 186 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184R SER 4.1 0.4 - - - -
185R VAL* 1.3 73.0 - - - +
187R ASN* 1.3 62.4 + - - +
188R THR* 3.6 24.2 + - + +
191R ASN* 4.0 24.7 - - - +
192R ARG 3.1 24.5 - - - +
193R THR* 3.6 17.9 - - - +
214R TYR* 3.4 7.6 - - - +
215R CYS* 2.7 52.0 + - + +
217R HIS* 5.8 5.8 - - - +
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Residues in contact with ASN 187 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ASP* 3.5 23.6 + - - +
185R VAL* 4.1 1.8 + - - +
186R LEU* 1.3 69.9 - - - +
188R THR* 1.3 57.7 + - - +
189R LYS* 2.8 24.6 + - - +
190R SER* 3.1 24.8 + - - +
191R ASN* 2.9 30.1 + - - -
192R ARG 2.8 13.2 + - - +
194R TRP* 6.0 2.0 - - - +
209R GLU* 4.8 7.5 - - - +
212R THR* 3.5 9.4 - - - +
213R LEU 4.3 0.9 - - - -
214R TYR* 3.5 35.1 + - + -
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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