Contacts of the strand formed by residues 186 - 199 (chain C) in PDB entry 6D6U
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 PHE 186 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C VAL* 3.5 43.1 - - + -
52C GLU* 3.7 9.4 - - - -
146C ASP* 5.3 0.4 - - - -
148C GLN* 4.2 15.9 - - + -
183C LEU* 3.6 40.3 + - + +
185C GLN* 1.3 93.0 - - + +
187C SER* 1.3 63.9 + - - +
214C LEU* 3.7 29.6 - - + -
215C LYS 3.6 10.8 - - - -
216C ARG* 3.4 55.0 - - + +
217C ASN* 4.7 1.9 + - - -
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C LEU* 5.2 2.2 - - - +
186C PHE* 1.3 80.3 - - - +
188C ILE* 1.3 71.8 + - - +
189C VAL* 3.6 5.9 + - - +
214C LEU* 4.0 3.9 - - - -
215C LYS* 3.2 35.5 + - - +
216C ARG 5.4 0.5 + - - -
217C ASN* 5.1 8.7 + - - -
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Residues in contact with ILE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ILE* 4.9 3.6 - - + -
178C VAL* 3.8 26.2 - - + +
181C ILE* 3.7 31.9 - - + +
183C LEU* 4.5 11.2 - - + -
187C SER* 1.3 76.0 - - - +
189C VAL* 1.3 66.6 + - - +
190C ASP* 4.3 9.2 - - - +
191C TYR* 5.3 1.8 - - + -
212C PHE* 3.9 26.9 - - + -
213C LYS 4.2 3.6 - - - +
214C LEU* 3.6 25.1 - - + -
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Residues in contact with VAL 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C SER* 3.6 12.5 + - - +
188C ILE* 1.3 83.4 - - - +
190C ASP* 1.3 70.7 + - + +
213C LYS* 3.8 26.0 + - + +
214C LEU 5.1 0.2 - - - -
215C LYS* 4.2 24.2 - - + +
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Residues in contact with ASP 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ILE* 4.3 2.8 - - - +
189C VAL* 1.3 90.2 - - + +
191C TYR* 1.3 92.7 + - - +
192C LYS* 4.6 17.2 - - - +
212C PHE* 3.2 21.4 - - - +
213C LYS* 3.3 9.7 + - + +
1H NAG 4.4 10.5 - - + +
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Residues in contact with TYR 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ASP 6.0 0.7 - - - -
172C ASP 4.5 9.8 + - - -
175C VAL* 3.6 38.9 + - + -
178C VAL* 3.9 36.2 - - + +
179C THR* 5.6 10.1 - - + +
188C ILE* 5.3 1.6 - - + -
190C ASP* 1.3 93.3 + - - +
192C LYS* 1.3 65.2 + - - +
193C LEU* 4.9 12.6 - - + -
210C LEU* 4.9 9.6 - - + -
211C SER 3.2 6.5 - - - +
212C PHE* 3.5 22.0 - - + -
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Residues in contact with LYS 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C ASP* 4.6 15.0 - - - +
191C TYR* 1.3 78.6 - - - +
193C LEU* 1.3 74.3 + - - +
194C ILE* 4.9 9.5 - - + +
209C SER 4.1 0.5 - - - +
210C LEU* 4.1 2.4 - - - +
211C SER* 2.9 28.7 + - - -
1H NAG 4.3 41.3 + - + +
2H NAG 3.9 25.0 + - - +
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Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C TRP* 4.1 29.8 - - + +
171C ASP* 3.4 33.9 - - + +
174C ALA* 3.6 22.2 - - + -
175C VAL* 3.9 15.3 - - + +
191C TYR* 4.9 11.7 - - + -
192C LYS* 1.3 83.3 - - - +
194C ILE* 1.3 65.6 + - - +
209C SER 3.9 1.8 - - - +
210C LEU* 3.6 24.5 - - + -
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Residues in contact with ILE 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C TRP* 3.4 9.1 + - - -
192C LYS* 4.9 7.9 - - + +
193C LEU* 1.3 83.5 - - - +
195C THR* 1.3 71.9 + - - +
196C LYS* 3.7 30.3 - - + +
208C LEU* 3.6 2.0 - - - +
209C SER* 3.4 46.4 + - - +
211C SER* 4.7 9.0 - - - +
1H NAG 3.2 32.5 - - - +
2H NAG 3.7 22.9 - - - +
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Residues in contact with THR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C PHE 4.2 12.1 - - - +
167C TYR* 5.0 5.3 - - + +
168C TRP* 4.0 10.0 + - - -
194C ILE* 1.3 79.8 + - - +
196C LYS* 1.3 73.5 + - - +
197C LYS* 6.3 0.2 - - + -
207C ARG 3.9 0.4 - - - +
208C LEU* 3.3 23.8 - - + +
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Residues in contact with LYS 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLU* 4.6 7.5 + - - -
194C ILE* 3.7 22.8 - - + +
195C THR* 1.3 85.0 - - - +
197C LYS* 1.3 76.1 + - - +
198C VAL* 5.0 4.6 - - + +
206C PRO* 4.2 1.9 - - - +
207C ARG* 3.2 64.4 + - + +
209C SER* 5.0 9.9 - - - -
1H NAG 6.0 1.2 - - - -
2H NAG 4.1 29.0 + - - +
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Residues in contact with LYS 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C THR* 4.1 24.0 + - + +
165C GLU* 4.7 13.2 + - - -
196C LYS* 1.3 83.2 - - - +
198C VAL* 1.3 65.0 + - - +
199C VAL* 4.2 5.4 + - + +
204C SER* 4.2 15.3 - - - +
205C TYR 3.7 7.0 - - - +
206C PRO* 5.0 6.5 - - + -
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Residues in contact with VAL 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C GLU* 4.7 3.4 - - - +
196C LYS* 5.0 7.6 - - + +
197C LYS* 1.3 76.9 - - - +
199C VAL* 1.3 65.0 + - - +
200C PHE* 3.6 31.9 + - + -
204C SER 3.3 2.1 - - - -
205C TYR* 2.6 45.5 + - + +
207C ARG* 3.3 51.6 - - + +
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Residues in contact with VAL 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C LYS* 4.2 5.4 + - + +
198C VAL* 1.3 81.1 - - - +
200C PHE* 1.3 76.3 + - - +
203C GLY 3.3 11.0 - - - +
204C SER* 3.7 21.5 - - - +
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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