Contacts of the strand formed by residues 181 - 193 (chain C) in PDB entry 5IXM
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 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C ASP* 3.4 1.9 + - - -
178C VAL* 2.9 39.2 + - - +
179C GLY 3.2 0.2 - - - -
180C PRO* 1.3 107.4 - - + +
182C ASP* 1.3 68.4 - - - +
183C MET* 4.2 12.1 - - + -
211C VAL* 3.7 31.2 - - + -
212C ASN 3.2 15.5 - - - +
213C LEU* 4.1 26.0 - - + -
608C C8E 3.6 30.1 - - - -
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Residues in contact with ASP 182 (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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175C LYS 3.7 3.4 - - - -
176C ASN* 3.4 16.7 - - - +
177C ASP* 3.1 23.6 + - - -
180C PRO 4.3 0.2 + - - -
181C PHE* 1.3 73.2 - - - +
183C MET* 1.3 63.1 + - - +
210C THR 3.9 0.5 - - - +
211C VAL* 3.8 1.0 - - - -
212C ASN* 2.9 47.1 + - + +
214C PRO* 3.6 16.7 - - - +
37D ARG* 2.6 34.6 + - - -
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Residues in contact with MET 183 (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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173C TYR* 4.7 1.1 - - + -
174C TYR* 3.7 1.6 - - - +
175C LYS* 2.8 42.7 + - + +
176C ASN* 5.3 0.7 - - - +
178C VAL* 3.6 39.9 - - + -
181C PHE* 4.6 11.7 - - + -
182C ASP* 1.3 79.6 - - - +
184C HIS* 1.3 64.3 + - - +
185C VAL* 5.8 3.1 - - + -
210C THR 3.3 4.7 - - - +
211C VAL* 4.3 33.4 - - + -
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Residues in contact with HIS 184 (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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172C ASN* 2.9 29.7 + - - -
173C TYR* 3.3 13.0 - - - -
174C TYR* 3.2 34.4 - + + -
183C MET* 1.3 78.1 - - - +
185C VAL* 1.3 72.2 + - - +
186C TYR* 4.0 13.9 - - + -
208C GLU* 3.7 3.4 - - - +
209C PRO* 3.7 0.9 - - - +
210C THR* 2.9 53.8 + - + +
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Residues in contact with VAL 185 (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 MET 3.9 0.3 - - - +
172C ASN* 3.5 3.8 - - - -
173C TYR* 2.9 53.0 + - + +
183C MET* 6.0 2.5 - - + -
184C HIS* 1.3 82.5 - - - +
186C TYR* 1.3 63.5 + - - +
207C ILE* 3.7 29.8 - - + -
208C GLU 3.6 8.1 - - - +
209C PRO* 4.4 15.0 - - + -
210C THR 5.2 0.2 - - - +
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Residues in contact with TYR 186 (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 GLN* 5.0 0.2 + - - -
170C ASP* 2.8 31.8 + - + -
171C MET 3.3 12.8 - - - -
172C ASN* 3.4 26.9 - - - +
184C HIS* 4.0 12.3 + + + +
185C VAL* 1.3 76.2 - - - +
187C GLY* 1.3 72.2 + - - +
188C GLN* 2.9 19.5 + - + -
206C HIS* 4.0 18.8 - + - +
207C ILE* 3.5 6.0 - - - +
208C GLU* 2.9 60.3 + - + +
324C LEU* 4.9 4.0 - - + -
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Residues in contact with GLY 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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169C LEU 4.3 0.2 - - - -
170C ASP* 3.6 2.3 - - - -
171C MET* 2.9 41.8 + - - +
186C TYR* 1.3 82.7 - - - +
188C GLN* 1.3 63.5 + - - +
206C HIS 3.2 9.9 - - - -
207C ILE* 4.2 8.7 - - - -
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Residues in contact with GLN 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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168C GLN* 3.3 32.8 + - + +
169C LEU 3.0 7.6 - - - +
170C ASP* 3.3 11.8 + - - +
186C TYR* 2.9 24.2 + - + +
187C GLY* 1.3 76.2 - - - +
189C ALA* 1.3 66.3 + - - +
190C ALA* 3.7 6.6 - - - +
204C ARG* 2.7 30.3 + - - +
205C PHE* 3.5 3.5 - - - +
206C HIS* 2.9 41.2 + - + +
304C ASP* 5.5 0.4 + - - -
324C LEU* 3.5 19.8 - - - +
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Residues in contact with ALA 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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167C PRO* 3.8 2.4 - - - +
168C GLN* 3.6 1.7 - - - -
169C LEU* 2.9 51.8 + - + +
188C GLN* 1.3 76.0 - - - +
190C ALA* 1.3 59.7 + - - +
204C ARG 3.4 4.9 - - - -
205C PHE* 3.8 26.0 - - + -
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Residues in contact with ALA 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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165C ALA* 5.5 0.4 - - + -
167C PRO 3.4 5.4 - - - +
168C GLN* 4.0 12.3 - - + -
188C GLN* 3.7 17.0 - - - +
189C ALA* 1.3 74.4 - - - +
191C LYS* 1.3 61.3 + - - +
192C PHE* 3.7 32.3 - - + -
202C ALA 3.9 0.3 - - - +
203C SER* 3.4 4.3 - - - -
204C ARG* 2.9 37.0 + - - +
205C PHE* 5.4 1.5 - - - -
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Residues in contact with LYS 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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164C ARG 3.4 2.9 - - - +
165C ALA* 3.6 0.3 - - - -
166C GLN* 2.7 53.7 + - + +
167C PRO* 3.0 13.1 + - + -
190C ALA* 1.3 72.9 - - - +
192C PHE* 1.3 61.9 + - - +
193C THR* 3.7 25.4 + - + -
201C GLU* 4.0 11.6 + - - -
202C ALA 3.4 22.3 + - - +
203C SER* 3.5 20.5 + - - +
236C ASP* 3.8 20.2 + - - -
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Residues in contact with PHE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C TYR* 4.1 5.9 - - + -
164C ARG 3.3 14.6 - - - +
165C ALA* 4.4 9.6 - - + -
168C GLN* 5.3 3.1 - - - -
188C GLN* 4.6 0.2 - - - -
190C ALA* 3.7 21.3 - - + -
191C LYS* 1.3 71.4 - - - +
193C THR* 1.3 65.8 + - - +
201C GLU* 3.5 3.6 - - - -
202C ALA* 2.9 45.4 + - + +
204C ARG* 3.4 59.2 - - + -
303C TYR* 3.7 40.4 - + + -
304C ASP* 4.0 11.2 - - + -
114D LEU* 3.8 24.0 - - + -
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Residues in contact with THR 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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163C TYR* 3.6 5.1 - - - -
164C ARG* 2.8 42.9 + - - +
166C GLN* 4.7 11.0 - - + +
191C LYS* 3.7 24.1 + - + -
192C PHE* 1.3 80.1 - - - +
194C SER* 1.3 62.6 + - - +
201C GLU* 3.5 35.4 - - - +
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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
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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