Contacts of the strand formed by residues 176 - 189 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B THR* 5.8 0.2 + - - -
128B ASN* 4.4 10.9 + - - -
129B GLU* 4.0 33.8 + - - +
172B TYR* 3.3 8.4 - - - -
173B ASP 2.9 32.4 + - - +
174B ASP* 3.2 10.4 - - + +
175B GLY* 1.3 92.8 + - - +
177B ILE* 1.3 72.9 + - - +
178B VAL* 4.0 1.0 - - + +
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU* 3.7 34.8 - - + +
136B ALA* 4.5 7.2 - - + -
170B PHE* 3.5 31.0 - - + -
171B GLN 3.4 7.0 - - - +
172B TYR* 3.7 21.8 - - + +
176B LYS* 1.3 86.5 - - + +
178B VAL* 1.3 63.5 + - - +
179B GLY* 3.7 14.8 - - - +
215B TRP* 4.2 31.9 + - + -
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 4.9 9.2 - - + +
171B GLN* 2.9 45.9 + - + +
172B TYR 4.6 0.4 - - - +
173B ASP* 3.5 38.1 - - + +
176B LYS 4.0 4.5 - - - +
177B ILE* 1.3 78.0 - - - +
179B GLY* 1.3 58.2 + - - +
214B GLU 5.0 1.9 - - - +
215B TRP* 4.1 12.7 - - - -
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Residues in contact with GLY 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B PHE* 3.4 4.9 - - - -
171B GLN* 2.6 39.4 + - - -
177B ILE* 3.6 7.6 - - - +
178B VAL* 1.3 85.5 - - - +
180B ILE* 1.3 61.8 + - - +
215B TRP* 3.7 22.0 - - - -
217B THR* 6.0 1.8 - - - -
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Residues in contact with ILE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL* 3.3 21.5 - - + -
169B THR 2.9 20.9 - - - +
170B PHE* 4.0 21.1 - - + -
171B GLN* 3.6 8.2 + - - +
179B GLY* 1.3 79.5 - - - +
181B ASP* 1.3 60.1 + - - +
182B ALA 3.8 9.0 - - - +
183B VAL* 4.3 8.1 - - + -
211B LEU* 4.1 28.0 - - + -
212B PRO* 4.8 0.2 - - + -
215B TRP* 3.0 44.7 + - + +
216B LEU* 4.9 3.4 - - + -
217B THR* 5.8 0.2 - - - +
220B THR* 2.8 29.3 + - + +
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Residues in contact with ASP 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A THR 5.6 1.6 - - - +
4B LEU* 3.9 22.6 - - + +
169B THR* 3.1 16.7 + - - +
171B GLN* 2.6 37.8 + - + +
180B ILE* 1.3 72.1 - - - +
182B ALA* 1.3 55.0 + - + +
219B ALA* 4.1 9.4 - - - +
220B THR* 2.9 8.7 - - - +
221B LYS* 2.6 43.9 + - + +
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A THR* 4.4 15.3 - - + +
168B VAL* 3.7 2.4 - - - -
169B THR* 3.1 43.6 + - + +
180B ILE* 3.8 2.5 - - - +
181B ASP* 1.3 81.4 - - + +
183B VAL* 1.3 65.8 + - - +
184B VAL* 5.7 0.9 - - + -
220B THR* 4.6 0.2 - - - -
221B LYS* 3.2 12.6 - - + +
223B PHE* 3.5 26.2 - - + -
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 5.4 4.0 - - + -
167B GLN 3.6 3.4 - - - +
168B VAL* 4.4 6.3 - - + -
180B ILE* 4.3 12.3 - - + -
182B ALA* 1.3 79.1 - - - +
184B VAL* 1.3 64.8 + - - +
185B LEU* 4.8 0.7 - - + +
207B ILE* 3.6 25.1 - - + -
211B LEU* 3.4 29.2 - - + -
216B LEU* 4.8 0.7 - - + -
220B THR* 4.4 5.4 - - + -
221B LYS 2.7 8.1 + - - +
222B PHE* 3.5 34.1 - - + -
223B PHE* 2.7 35.4 + - - +
224B ILE* 6.0 0.2 - - + -
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.4 30.7 - - + +
301A ALA* 3.7 20.0 - - + -
302A ILE* 5.8 1.3 - - + +
308A THR* 4.7 2.5 - - + -
144B LEU* 5.2 1.4 - - - +
166B SER* 3.3 4.5 - - - -
167B GLN* 2.5 60.4 + - + +
182B ALA* 5.7 1.1 - - + -
183B VAL* 1.3 75.1 - - - +
185B LEU* 1.3 67.9 - - - +
186B SER* 4.4 7.2 - - - +
223B PHE* 3.3 35.9 - - + +
226B PRO* 5.7 2.7 - - + -
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 4.2 25.8 - - + -
145B VAL* 5.5 1.8 - - + -
148B GLN* 5.3 4.7 - - + -
164B ALA* 5.5 0.9 - - + -
165B LYS 3.6 2.9 - - - +
166B SER* 3.7 24.9 - - - -
183B VAL* 4.8 0.6 - - + +
184B VAL* 1.3 75.8 - - - +
186B SER* 1.3 73.6 + - - +
187B THR* 4.2 14.5 - - + +
202B VAL* 4.0 24.2 - - + -
206B ILE* 4.7 15.3 - - + -
207B ILE* 4.1 21.1 - - + -
223B PHE 2.8 10.9 + - - +
224B ILE* 3.4 8.3 - - + +
225B ASN* 3.3 20.6 + - - +
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 4.0 13.1 + - - -
302A ILE* 4.1 10.2 - - - +
164B ALA* 3.1 4.0 - - - +
165B LYS* 2.6 47.6 + - - +
184B VAL* 4.3 3.7 - - - +
185B LEU* 1.3 76.3 - - - +
187B THR* 1.3 60.1 + - - +
225B ASN* 3.2 4.7 - - - -
226B PRO* 4.2 9.0 - - - +
230B PHE* 4.1 3.4 - - - -
484B ANP 3.5 36.6 + - - -
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Residues in contact with THR 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLN* 3.2 24.3 + - + -
160B LEU* 3.7 20.1 - - + +
163B ASP 3.6 5.4 - - - -
164B ALA* 3.9 7.4 - - - -
185B LEU* 4.2 15.7 - - + +
186B SER* 1.3 75.0 - - - +
188B GLN* 1.3 74.4 + - - +
189B HIS* 3.9 0.5 - - - -
198B LEU* 4.8 5.2 - - + -
202B VAL* 4.2 15.3 - - + -
206B ILE* 5.5 0.4 - - + -
224B ILE* 5.8 0.2 - - + -
225B ASN* 2.9 39.2 + - - +
230B PHE* 3.2 9.0 - - - +
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Residues in contact with GLN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B TYR* 3.1 25.1 + - - -
82B MET 3.3 24.0 + - - -
160B LEU* 3.9 2.3 - - - +
161B ARG* 3.0 43.6 + - + +
163B ASP* 2.8 22.8 + - + +
187B THR* 1.3 80.8 + - - +
189B HIS* 1.3 63.4 + - - +
230B PHE* 3.3 25.6 - - + +
231B VAL 3.2 20.6 + - - +
232B ILE* 4.1 0.4 - - - +
233B GLY* 2.9 29.2 - - - +
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Residues in contact with HIS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B TRP* 3.3 22.2 - - + +
161B ARG* 3.5 15.9 + - - +
187B THR* 3.9 1.1 - - + -
188B GLN* 1.3 75.9 - - - +
190B SER* 1.3 80.6 + - - +
191B GLU* 5.5 0.4 - - - -
193B ILE* 4.4 12.2 - - + +
194B ASP 6.2 0.7 - - - -
195B GLN* 4.4 7.8 + - + -
198B LEU* 3.3 35.1 - - + +
225B ASN* 3.6 12.6 + - - -
229B ARG* 4.4 3.7 - - - -
230B PHE 3.0 36.9 + - - -
231B VAL* 3.3 45.7 - - + +
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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