Contacts of the strand formed by residues 176 - 189 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A THR* 5.8 0.2 + - - -
128A ASN* 4.4 10.5 + - - -
129A GLU* 4.0 33.5 + - - +
172A TYR* 3.3 8.8 - - - -
173A ASP 2.9 32.5 + - - +
174A ASP* 3.1 10.9 - - + +
175A GLY* 1.3 92.3 + - - +
177A ILE* 1.3 72.0 + - - +
178A VAL* 4.0 1.5 - - + +
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Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLU* 3.8 34.3 - - + +
136A ALA* 4.6 7.6 - - + -
170A PHE* 3.5 30.7 - - + -
171A GLN 3.4 7.9 - - - +
172A TYR* 3.7 22.9 - - + +
176A LYS* 1.3 85.4 - - + +
178A VAL* 1.3 64.9 + - - +
179A GLY* 3.7 14.6 - - - +
215A TRP* 4.2 32.0 + - + -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 4.9 8.7 - - + +
171A GLN* 2.9 46.9 + - + +
173A ASP* 3.5 38.4 - - + +
176A LYS* 4.0 5.4 - - + +
177A ILE* 1.3 77.5 - - - +
179A GLY* 1.3 58.4 + - - +
214A GLU 5.0 2.1 - - - +
215A TRP* 4.0 12.8 - - - -
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PHE* 3.4 2.6 - - - -
171A GLN* 2.7 38.6 + - - -
177A ILE* 3.6 7.6 - - - +
178A VAL* 1.3 86.1 - - - +
180A ILE* 1.3 63.7 + - - +
215A TRP* 3.7 22.7 - - - -
217A THR* 5.9 1.8 - - - -
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A VAL* 3.3 21.3 - - + -
169A THR 2.9 21.1 - - - +
170A PHE* 4.0 20.6 - - + -
171A GLN* 3.7 7.3 + - - +
179A GLY* 1.3 79.1 - - - +
181A ASP* 1.3 59.9 + - - +
182A ALA 3.9 8.7 - - - +
183A VAL* 4.4 8.3 - - + -
211A LEU* 4.0 28.0 - - + -
212A PRO* 4.9 0.2 - - + -
215A TRP* 3.0 43.2 + - + +
216A LEU* 4.9 3.6 - - + -
217A THR* 5.9 0.2 - - - +
220A THR* 2.9 28.7 + - + +
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Residues in contact with ASP 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 3.8 21.8 - - + +
169A THR* 3.1 17.2 + - - +
171A GLN* 2.6 39.6 + - + +
180A ILE* 1.3 71.6 - - - +
182A ALA* 1.3 56.3 + - + +
219A ALA* 4.1 9.3 - - - +
220A THR* 2.9 8.1 - - - +
221A LYS* 2.7 42.8 + - + +
308B THR 5.7 1.3 - - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN 4.1 0.2 - - - +
168A VAL* 3.7 2.3 - - - -
169A THR* 3.2 42.8 + - + +
180A ILE* 3.9 2.6 - - - +
181A ASP* 1.3 82.7 - - + +
183A VAL* 1.3 65.0 + - - +
184A VAL* 5.8 0.7 - - + -
221A LYS* 3.2 12.6 - - + +
223A PHE* 3.5 26.7 - - + -
308B THR* 4.5 14.8 - - + +
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 5.3 4.9 - - + -
167A GLN 3.6 2.9 - - - +
168A VAL* 4.4 5.6 - - + -
180A ILE* 4.4 9.0 - - + -
182A ALA* 1.3 77.9 - - - +
184A VAL* 1.3 64.4 + - - +
185A LEU* 4.8 0.7 - - + +
207A ILE* 3.5 34.3 - - + -
211A LEU* 3.5 28.0 - - + -
216A LEU* 4.8 0.7 - - + -
220A THR* 4.3 8.5 - - + -
221A LYS 2.6 8.9 + - - -
222A PHE* 3.5 24.9 - - + -
223A PHE* 2.7 34.7 + - - +
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 5.1 1.6 - - - +
166A SER* 3.3 4.7 - - - -
167A GLN* 2.5 64.2 + - + +
182A ALA* 5.8 1.1 - - + -
183A VAL* 1.3 75.5 - - - +
185A LEU* 1.3 67.0 - - - +
186A SER* 4.5 7.4 - - - +
223A PHE* 3.4 35.4 - - + +
226A PRO* 5.8 2.2 - - + -
119B GLN* 3.3 31.0 - - + +
301B ALA* 3.6 21.1 - - + -
302B ILE* 5.8 0.9 - - + +
308B THR* 4.7 2.5 - - + -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 4.1 26.5 - - + -
145A VAL* 5.5 1.8 - - + -
148A GLN* 5.2 4.5 - - + -
164A ALA* 5.5 1.3 - - + -
165A LYS 3.5 2.9 - - - +
166A SER* 3.7 24.7 - - - -
183A VAL* 4.8 0.4 - - + +
184A VAL* 1.3 75.0 - - - +
186A SER* 1.3 75.0 + - - +
187A THR* 4.3 14.1 - - + -
202A VAL* 4.0 24.7 - - + -
206A ILE* 4.7 15.7 - - + -
207A ILE* 4.1 20.4 - - + -
223A PHE 2.9 9.9 + - - +
224A ILE* 3.4 9.5 - - + +
225A ASN* 3.3 20.8 + - - +
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ALA* 3.1 3.6 - - - +
165A LYS* 2.7 47.0 + - - +
184A VAL* 4.3 3.9 - - - +
185A LEU* 1.3 76.5 + - - +
187A THR* 1.3 60.2 + - - +
225A ASN* 3.1 5.2 - - - -
226A PRO* 4.1 15.2 - - - +
230A PHE* 4.0 2.4 - - - -
384A ANP 3.5 36.1 - - - -
119B GLN* 4.1 12.1 + - - -
302B ILE* 4.1 4.9 - - - +
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLN* 3.3 24.0 + - + -
160A LEU* 3.7 19.2 - - + +
163A ASP 3.6 4.9 - - - -
164A ALA* 4.0 8.1 - - - -
185A LEU* 4.3 11.0 - - + +
186A SER* 1.3 74.3 - - - +
188A GLN* 1.3 76.1 + - - +
189A HIS* 3.9 0.7 - - - -
198A LEU* 4.8 5.8 - - + -
202A VAL* 4.2 20.4 - - + -
206A ILE* 5.5 0.4 - - + -
225A ASN* 2.9 39.5 + - - +
230A PHE* 3.2 8.2 - - - +
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Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TYR* 3.0 25.1 + - - -
82A MET* 3.4 23.4 + - - +
160A LEU* 3.9 2.4 - - - +
161A ARG* 3.0 39.9 + - + +
163A ASP* 2.7 25.9 + - + +
187A THR* 1.3 86.3 + - - +
189A HIS* 1.3 64.0 + - - +
230A PHE* 3.3 20.0 - - + +
231A VAL 3.2 21.1 + - - +
232A ILE* 4.1 0.2 - - - +
233A GLY* 2.9 29.8 - - - +
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Residues in contact with HIS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TRP* 3.3 21.1 - - + +
161A ARG* 3.5 19.4 + - - +
187A THR 3.9 0.4 - - - -
188A GLN* 1.3 76.0 - - - +
190A SER* 1.3 79.8 + - - +
191A GLU* 5.5 0.7 - - - -
193A ILE* 4.4 12.5 + - + -
194A ASP 6.3 0.2 - - - -
195A GLN* 4.4 8.1 + - + +
198A LEU* 3.3 35.4 - - + +
225A ASN* 3.6 13.5 + - - -
229A ARG* 4.5 3.7 - - + -
230A PHE 3.0 35.2 + - - -
231A VAL* 3.2 44.0 - - + +
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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