Contacts of the strand formed by residues 176 - 189 (chain C) in PDB entry 1P7L
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 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C ASN* 4.4 9.7 + - - -
129C GLU* 3.9 34.6 + - - +
172C TYR* 3.3 8.6 - - - -
173C ASP 2.8 32.1 + - - +
174C ASP* 3.1 10.2 - - + +
175C GLY* 1.3 92.8 + - - +
177C ILE* 1.3 69.9 + - + +
178C VAL* 3.6 1.4 + - + +
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Residues in contact with ILE 177 (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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129C GLU* 3.7 34.8 - - + +
136C ALA* 4.5 8.1 - - + -
170C PHE* 3.5 30.3 - - + -
171C GLN 3.4 7.0 - - - +
172C TYR* 3.7 21.8 - - + +
176C LYS* 1.3 84.5 - - - +
178C VAL* 1.3 63.8 + - - +
179C GLY 3.7 13.7 - - - +
215C TRP* 4.1 33.5 + - + -
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Residues in contact with VAL 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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2C LYS* 5.0 8.3 - - + +
171C GLN* 3.0 46.3 + - + +
173C ASP* 3.5 37.7 - - + +
176C LYS* 3.9 5.2 - - + +
177C ILE* 1.3 78.2 - - - +
179C GLY* 1.3 59.6 + - - +
214C GLU 5.0 2.1 - - - +
215C TRP* 4.1 11.9 - - - -
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Residues in contact with GLY 179 (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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170C PHE* 3.4 6.6 - - - +
171C GLN* 2.6 39.6 + - - -
177C ILE* 3.6 5.1 - - - +
178C VAL* 1.3 85.3 - - - +
180C ILE* 1.3 63.9 + - - +
215C TRP* 3.6 22.4 - - - -
217C THR* 5.9 1.6 - - - -
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Residues in contact with ILE 180 (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 VAL* 3.3 22.0 - - + -
169C THR 3.0 20.2 - - - +
170C PHE* 4.0 22.0 - - + -
171C GLN* 3.7 7.5 + - - +
179C GLY* 1.3 80.2 - - - +
181C ASP* 1.3 59.9 + - - +
182C ALA 3.8 8.7 - - - +
183C VAL* 4.3 8.3 - - + -
211C LEU* 4.1 28.0 - - + -
212C PRO* 4.9 0.2 - - + -
215C TRP* 2.9 43.6 + - + +
216C LEU* 4.8 5.6 - - + -
217C THR* 5.8 0.2 - - - +
220C THR* 2.8 27.9 + - + +
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Residues in contact with ASP 181 (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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4C LEU* 3.9 21.6 - - + +
169C THR* 3.2 17.4 + - - +
171C GLN* 2.5 41.4 + - + +
180C ILE* 1.3 71.9 - - - +
182C ALA* 1.3 55.3 + - + +
219C ALA* 5.1 7.4 - - - +
220C THR* 2.8 9.9 - - - +
221C LYS* 2.7 43.1 + - + +
308D THR 5.6 1.8 - - - +
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Residues in contact with ALA 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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168C VAL* 3.6 2.3 - - - -
169C THR* 3.1 44.1 + - + +
180C ILE* 3.8 2.0 - - - +
181C ASP* 1.3 79.7 - - + +
183C VAL* 1.3 65.7 + - - +
184C VAL* 5.7 1.1 - - + -
220C THR* 4.6 0.2 - - - -
221C LYS* 3.2 11.9 - - + +
223C PHE* 3.5 26.0 - - + -
308D THR* 4.2 16.4 - - - +
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Residues in contact with VAL 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 5.3 4.5 - - + -
167C GLN 3.6 3.8 - - - +
168C VAL* 4.3 6.1 - - + -
180C ILE* 4.3 12.6 - - + -
182C ALA* 1.3 79.0 - - - +
184C VAL* 1.3 62.8 + - - +
185C LEU* 4.8 0.7 - - + +
207C ILE* 3.5 33.9 - - + -
211C LEU* 3.4 29.2 - - + -
216C LEU* 4.8 0.9 - - + -
220C THR* 4.4 4.0 - - + +
221C LYS 2.7 8.7 + - - +
222C PHE* 3.5 24.2 - - + -
223C PHE* 2.7 34.6 + - - +
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Residues in contact with VAL 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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144C LEU* 5.0 1.4 - - - +
166C SER* 3.3 4.9 - - - -
167C GLN* 2.5 61.6 + - + +
182C ALA 5.7 0.7 - - - -
183C VAL* 1.3 74.6 - - - +
185C LEU* 1.3 67.6 + - - +
186C SER* 4.4 6.7 - - - +
223C PHE* 3.3 37.2 - - + +
226C PRO* 5.8 1.6 - - + -
119D GLN* 3.4 32.1 - - + +
301D ALA* 3.6 20.0 - - + -
302D ILE 5.7 0.7 - - - +
308D THR* 4.5 3.4 - - + -
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Residues in contact with LEU 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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144C LEU* 4.1 27.8 - - + +
145C VAL* 5.5 1.6 - - + -
148C GLN* 5.2 4.3 - - + -
164C ALA* 5.5 1.3 - - + -
165C LYS 3.6 2.7 - - - +
166C SER* 3.8 24.7 - - - -
183C VAL 4.3 0.2 - - - -
184C VAL* 1.3 75.7 - - - +
186C SER* 1.3 74.5 + - - +
187C THR* 4.3 14.6 - - + -
202C VAL* 3.9 24.7 - - + -
206C ILE* 4.6 16.4 - - + -
207C ILE* 4.1 20.4 - - + -
223C PHE 2.9 10.1 + - - +
224C ILE* 3.4 10.1 - - + +
225C ASN* 3.3 20.1 + - - +
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Residues in contact with SER 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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164C ALA* 3.0 4.5 - - - +
165C LYS* 2.7 46.3 + - - +
184C VAL* 4.4 3.1 - - - +
185C LEU* 1.3 75.9 - - - +
187C THR* 1.3 61.1 + - - +
225C ASN* 3.1 5.2 - - - -
226C PRO* 4.1 7.6 - - - +
230C PHE* 4.0 3.1 - - - -
685C SAM 3.7 34.1 - - - -
119D GLN* 3.7 14.2 + - - -
302D ILE* 3.9 12.6 - - - +
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Residues in contact with THR 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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148C GLN* 3.3 23.6 + - + -
160C LEU* 3.7 19.1 - - + +
163C ASP 3.6 4.9 - - - -
164C ALA* 4.0 7.6 - - - -
185C LEU* 4.3 10.1 - - + +
186C SER* 1.3 75.9 - - - +
188C GLN* 1.3 74.1 + - - +
189C HIS* 3.7 1.7 + - - -
198C LEU* 4.7 5.2 - - + -
202C VAL* 4.2 21.1 - - + -
206C ILE* 5.6 0.2 - - + -
225C ASN* 2.8 36.2 + - - +
230C PHE* 3.3 7.9 - - - -
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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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77C TYR* 3.0 26.3 + - - -
82C MET* 3.4 21.0 + - - +
160C LEU* 3.9 2.1 - - - -
161C ARG* 3.0 40.5 + - + +
163C ASP* 2.7 27.3 + - + +
187C THR* 1.3 85.8 + - - +
189C HIS* 1.3 64.4 + - - +
230C PHE* 3.4 22.9 - - + +
231C VAL 3.2 18.8 + - - +
232C ILE* 4.0 0.4 - - - +
233C GLY* 2.7 32.0 - - - +
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Residues in contact with HIS 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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159C TRP* 3.3 20.4 - - + +
161C ARG* 3.5 15.2 + - - +
187C THR 3.9 0.2 - - - -
188C GLN* 1.3 75.9 - - - +
190C SER* 1.3 81.9 + - - +
191C GLU* 5.5 0.7 - - - -
193C ILE* 4.4 12.5 - - + +
194C ASP 6.2 0.2 - - - -
195C GLN* 4.4 9.8 + - + +
198C LEU* 3.3 35.0 - - + +
225C ASN* 3.6 13.9 + - - -
229C ARG* 4.5 3.4 - - + -
230C PHE 3.0 34.4 + - - -
231C VAL* 3.3 45.6 - - + +
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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