Contacts of the strand formed by residues 164 - 180 (chain C) in PDB entry 5O67
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 TRP 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C PHE* 4.2 1.8 - - - -
159C ASN* 3.2 8.5 - - - +
160C LEU* 3.1 42.7 + - + -
163C ARG* 1.3 94.1 - - + +
165C GLN* 1.3 61.9 + - - +
166C PHE* 4.1 23.1 - + + -
210C ILE* 3.9 24.5 - - + -
211C ALA 3.4 18.8 - - - -
212C TYR* 3.6 36.1 - + + -
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Residues in contact with GLN 165 (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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101C GLY 3.2 26.1 + - - -
102C PHE* 3.8 18.0 - - + +
103C ALA* 3.1 35.5 + - - +
157C ARG* 3.5 25.9 - - + +
158C TYR 3.3 15.5 - - - +
159C ASN* 4.1 5.5 - - - +
164C TRP* 1.3 77.9 - - - +
166C PHE* 1.3 73.4 + - - +
167C ASP* 4.9 4.9 - - + +
209C GLY 3.7 0.5 - - - +
210C ILE* 3.3 5.9 - - - -
211C ALA* 3.0 38.9 + - + +
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Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C GLY 3.9 0.5 - - - +
157C ARG* 3.5 2.6 - - - -
158C TYR* 2.9 46.1 + + + +
160C LEU* 4.5 19.1 - - + -
164C TRP* 4.1 33.9 - + + -
165C GLN* 1.3 75.6 - - - +
167C ASP* 1.3 58.9 + - - +
209C GLY 3.4 4.9 - - - +
210C ILE* 3.7 37.2 - - + -
503C C8E 3.8 44.9 - - + -
504C C8E 4.1 32.5 - - + +
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Residues in contact with ASP 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C THR* 4.7 8.3 - - + -
156C GLY 3.2 11.4 - - - +
157C ARG* 4.1 17.9 - - + +
165C GLN* 4.3 4.9 - - - +
166C PHE* 1.3 74.7 - - - +
168C VAL* 1.3 63.1 + - - +
208C PHE* 3.4 5.8 - - - +
209C GLY 3.0 31.4 + - - +
229C ARG* 4.2 21.8 - - - +
504C C8E 4.3 4.3 - - - +
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Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C LEU 4.0 0.5 - - - +
155C THR* 3.4 5.0 - - - +
156C GLY* 3.0 30.0 + - - +
167C ASP* 1.3 75.3 - - - +
169C ASN* 1.3 70.7 + - - +
170C VAL* 4.7 9.8 - - + +
206C VAL* 5.2 6.7 - - + -
207C ASN 3.6 13.9 - - - +
208C PHE* 4.1 8.3 - - + +
504C C8E 3.7 40.6 - - + -
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Residues in contact with ASN 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ASP* 3.3 27.2 + - - +
154C LEU 3.2 8.6 + - - +
155C THR* 3.0 27.8 + - + +
167C ASP* 6.2 0.2 - - + -
168C VAL* 1.3 74.4 - - - +
170C VAL* 1.3 75.6 + - - +
171C PRO* 3.8 5.2 - - - +
206C VAL* 3.6 5.9 - - - +
207C ASN* 3.0 62.8 + - - +
229C ARG* 4.8 3.8 - - - +
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Residues in contact with VAL 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU 4.0 0.5 - - - +
153C ASP* 3.8 0.7 - - - -
154C LEU* 2.8 47.8 + - + +
168C VAL* 4.7 11.7 - - + -
169C ASN* 1.3 79.0 - - - +
171C PRO* 1.3 65.1 - - - +
172C VAL* 4.0 5.9 + - + -
203C ILE* 4.1 24.2 - - + -
206C VAL* 4.1 22.0 - - + -
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Residues in contact with PRO 171 (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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151C THR* 4.2 11.9 - - + -
152C LEU 3.6 5.4 - - - +
153C ASP* 3.5 16.2 - - - +
169C ASN* 3.8 15.9 - - - +
170C VAL* 1.3 88.2 - - + +
172C VAL* 1.3 61.3 + - - +
173C VAL* 4.5 6.5 - - + -
203C ILE* 3.6 6.4 - - - +
204C GLY* 2.9 27.1 + - - -
205C ASP* 3.6 34.8 - - + +
206C VAL* 4.1 5.8 - - - +
207C ASN* 5.0 0.7 - - - +
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Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C TRP 4.2 0.2 - - - +
151C THR* 3.3 4.9 - - - +
152C LEU* 2.7 55.3 + - + +
154C LEU* 4.5 20.4 - - + -
170C VAL* 4.7 4.5 - - + +
171C PRO* 1.3 77.9 - - - +
173C VAL* 1.3 65.0 + - - +
174C TYR 4.3 0.3 + - - -
201C PRO* 4.1 14.6 - - + -
202C THR* 3.6 25.8 - - - +
203C ILE* 4.7 11.4 - - + +
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Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASN* 5.9 2.0 - - + -
150C TRP 3.7 7.6 - - - +
151C THR* 4.4 15.9 - - + +
171C PRO* 4.5 4.3 - - + -
172C VAL* 1.3 83.8 - - - +
174C TYR* 1.3 59.3 + - - +
175C ARG* 4.0 25.6 - - + -
199C ARG* 4.2 4.4 - - + +
200C ASP 3.8 4.5 - - - +
201C PRO* 3.7 4.6 - - - +
202C THR* 3.1 34.7 + - - +
204C GLY* 4.5 9.0 - - - -
260C THR* 4.0 31.4 - - - +
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Residues in contact with TYR 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ASP 4.2 0.4 - - - +
149C ASN* 3.6 0.3 - - - -
150C TRP* 3.1 62.2 + + + +
172C VAL 4.3 0.4 + - - -
173C VAL* 1.3 71.2 - - - +
175C ARG* 1.3 79.8 + - - +
176C GLU* 2.6 36.0 + - + +
198C SER* 4.8 4.9 - - - -
199C ARG 3.1 19.5 - - - -
200C ASP* 4.0 20.9 - - - -
201C PRO* 4.3 16.6 - - + -
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Residues in contact with ARG 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C TYR* 6.1 1.0 - - - -
147C ALA* 5.5 3.4 - - - +
148C ASP 3.8 4.7 - - - -
149C ASN* 3.5 30.8 + - - +
173C VAL* 4.0 18.4 - - + -
174C TYR* 1.3 82.4 - - - +
176C GLU* 1.3 64.2 + - - +
177C SER* 4.5 11.5 + - - +
198C SER* 3.3 7.3 - - - -
199C ARG* 3.1 36.9 + - + -
258C LEU* 3.6 30.5 - - + +
259C PRO* 3.0 51.3 + - - +
260C THR* 5.6 0.2 - - - +
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Residues in contact with GLU 176 (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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146C LYS 4.2 0.2 - - - +
147C ALA* 3.4 3.5 - - - +
148C ASP* 3.0 49.9 + - + +
174C TYR* 2.6 37.2 + - + +
175C ARG* 1.3 79.2 - - - +
177C SER* 1.3 60.8 + - - +
178C THR* 4.8 2.9 + - - +
196C SER* 6.6 0.2 - - - -
197C VAL 3.5 8.3 - - - +
198C SER* 4.2 7.9 - - - -
258C LEU* 4.7 0.4 - - - -
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Residues in contact with SER 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ILE* 6.1 2.2 - - - -
146C LYS 3.5 7.2 - - - -
147C ALA* 3.7 16.2 - - - +
149C ASN* 5.5 0.2 + - - -
175C ARG* 4.5 7.8 + - - +
176C GLU* 1.3 72.0 - - - +
178C THR* 1.3 67.2 + - - +
179C TYR* 3.7 28.1 + - - -
195C GLU 4.2 0.2 - - - +
196C SER* 3.4 2.9 - - - -
197C VAL* 3.0 33.4 + - - +
258C LEU* 3.8 23.9 - - - +
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Residues in contact with THR 178 (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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144C ARG 3.1 4.9 - - - +
145C ILE* 3.4 2.6 - - - -
146C LYS* 2.9 42.8 + - - +
176C GLU* 4.8 3.6 + - - +
177C SER* 1.3 82.1 + - - +
179C TYR* 1.3 62.3 + - - +
180C GLN* 5.2 4.6 - - + +
194C GLU* 4.2 21.8 - - + -
195C GLU 3.6 7.4 - - - +
196C SER* 3.4 20.7 + - - +
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Residues in contact with TYR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ARG 3.8 3.6 - - - -
145C ILE* 4.3 22.0 - - + -
177C SER* 3.7 26.1 + - - -
178C THR* 1.3 75.5 - - - +
180C GLN* 1.3 61.3 + - - +
193C SER 3.8 1.2 - - - +
194C GLU* 3.5 2.4 - - - -
195C GLU* 3.2 36.5 + - - +
197C VAL* 4.2 11.9 - - + -
253C TYR* 4.5 16.0 + + + -
254C VAL* 4.3 24.5 - - + -
255C PRO* 3.4 37.5 - - + +
258C LEU* 3.8 13.3 - - - +
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Residues in contact with GLN 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LYS* 5.5 2.0 - - - +
358B VAL* 4.0 11.2 - - - +
359B SER* 3.1 40.4 + - - +
361B ASP* 5.2 3.0 + - - -
143C ASP* 3.4 21.8 - - - +
144C ARG* 3.5 28.7 + - + +
178C THR* 5.2 4.9 - - + +
179C TYR* 1.3 79.5 - - - +
181C SER* 1.3 67.7 + - - +
192C THR* 4.7 8.2 - - + +
193C SER 3.6 7.0 - - - +
194C GLU* 3.5 27.1 - - + +
253C TYR* 4.6 7.5 - - - -
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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
------------------------------------------------------------
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