Contacts of the strand formed by residues 182 - 191 (chain A) in PDB entry 1PNG
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 ALA 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A LEU* 3.7 34.5 - - + -
179A THR* 3.8 9.8 - - + +
181A LYS* 1.3 77.0 - - - +
183A TYR* 1.3 67.5 + - - +
263A VAL* 3.9 5.2 - - - +
264A LEU* 3.1 36.4 + - + +
266A ASN* 5.0 4.1 - - - +
269A THR* 5.8 0.9 - - - +
299A VAL* 5.2 0.2 - - + -
300A ILE 3.2 11.2 - - - +
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Residues in contact with TYR 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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102A ASP* 2.6 38.2 + - - -
181A LYS* 4.3 24.7 - - + -
182A ALA* 1.3 82.2 - - - +
184A LEU* 1.3 67.7 + - - +
261A ILE* 3.9 28.3 - - + -
262A ASP 3.1 17.0 - - - +
263A VAL* 3.8 9.4 - - + -
264A LEU* 4.1 6.9 - - - +
299A VAL* 3.5 3.1 - - - +
300A ILE* 2.9 51.6 + - + -
302A LYS* 2.9 39.4 + - + -
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Residues in contact with LEU 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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148A VAL* 4.4 4.9 - - + -
173A ILE* 4.7 4.5 - - + -
183A TYR* 1.3 76.1 - - - +
185A ARG* 1.3 59.6 + - - +
186A THR* 4.1 9.6 - - - +
214A ILE* 4.0 20.9 - - + -
216A ILE* 4.4 2.0 - - + -
222A PHE* 4.2 17.9 - - + -
260A ARG 3.4 4.3 - - - +
261A ILE* 3.4 5.5 - - - +
262A ASP* 2.9 37.3 + - + +
264A LEU* 4.2 17.3 - - + -
273A PHE* 5.8 0.2 - - + -
275A TYR* 3.9 36.8 - - + -
297A SER* 4.7 1.6 - - - +
298A PHE 3.1 13.2 - - - +
299A VAL* 4.1 20.4 - - + -
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Residues in contact with ARG 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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77A GLU 5.3 0.8 + - - -
78A ILE 3.0 26.9 + - - -
98A ILE* 4.3 2.0 - - - +
99A ASP* 3.1 28.9 + - - +
100A VAL* 4.3 1.8 - - - +
101A THR 5.1 0.2 - - - +
102A ASP* 2.8 32.8 + - - +
103A PHE* 3.3 31.8 - - - -
183A TYR 4.1 0.2 + - - -
184A LEU* 1.3 72.3 - - - +
186A THR* 1.3 59.9 + - - +
187A THR* 5.2 5.3 + - - +
259A THR* 3.5 40.0 + - + +
260A ARG 3.4 3.6 - - - -
261A ILE* 4.1 7.7 - - + +
296A SER 3.8 0.5 - - - +
297A SER* 3.2 1.9 - - - -
298A PHE* 2.7 46.6 + - + +
300A ILE* 3.7 17.7 - - + -
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Residues in contact with THR 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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184A LEU* 4.7 2.8 - - - +
185A ARG* 1.3 75.5 + - - +
187A THR* 1.3 71.2 + - - +
188A ILE* 4.1 4.7 - - + -
214A ILE* 4.3 6.8 - - - +
224A HIS* 3.7 35.1 - - + +
259A THR* 3.8 0.7 - - - -
260A ARG* 2.9 38.9 + - - +
262A ASP* 4.9 0.3 + - - -
277A TYR* 4.2 3.6 - - + -
295A ILE* 4.0 24.0 - - + -
296A SER 3.2 11.9 - - - +
297A SER* 2.9 21.7 + - - +
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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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77A GLU* 4.5 2.6 - - - +
79A GLY* 6.0 2.0 - - - -
80A ARG* 2.8 55.0 + - + +
185A ARG* 5.2 6.1 + - - +
186A THR* 1.3 77.6 + - - +
188A ILE* 1.3 57.8 + - - +
257A VAL* 3.5 28.0 - - + +
258A PRO 3.6 11.9 + - - +
259A THR* 4.4 11.7 + - - +
295A ILE* 3.4 1.2 - - - +
296A SER* 2.9 31.4 + - - +
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Residues in contact with ILE 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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80A ARG* 4.0 0.7 - - - -
186A THR* 4.5 3.8 - - + -
187A THR* 1.3 76.9 - - - +
189A SER* 1.3 65.4 + - - +
212A HIS* 3.8 20.2 - - + -
226A LEU* 4.0 19.2 - - + +
250A GLY* 4.7 6.4 - - - +
257A VAL* 3.7 10.2 - - - +
258A PRO* 4.8 2.4 + - - +
260A ARG* 3.9 29.6 + - - +
277A TYR* 3.7 27.1 - - + +
279A PHE* 3.9 19.3 - - + -
293A TYR* 4.0 19.7 - - + -
294A ALA 3.3 9.9 - - - +
295A ILE* 4.2 13.5 - - + -
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Residues in contact with SER 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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62A TYR* 4.0 13.5 - - - -
80A ARG* 3.0 23.3 + - - -
82A ILE* 5.0 3.3 - - - +
188A ILE* 1.3 75.8 - - - +
190A GLY* 1.3 60.0 + - - +
226A LEU* 5.2 3.4 - - - -
249A ALA 5.3 0.4 - - - -
251A TRP* 4.0 22.0 - - - -
257A VAL* 4.0 18.2 - - - +
293A TYR* 3.5 6.4 - - - -
294A ALA* 2.9 29.9 + - - +
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Residues in contact with GLY 190 (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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189A SER* 1.3 76.6 - - - +
191A TRP* 1.3 61.2 + - - +
205A ALA 3.9 15.8 + - - -
206A GLU* 3.7 5.2 - - - -
226A LEU* 5.1 0.4 - - - +
249A ALA 4.9 3.2 + - - -
251A TRP* 3.1 30.3 + - - +
292A PHE 3.2 10.5 - - - -
293A TYR* 3.6 15.3 - - - -
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Residues in contact with TRP 191 (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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155A SER* 3.7 42.0 + - - +
156A ILE* 3.9 17.4 - - + +
190A GLY* 1.3 74.2 - - - +
192A GLY* 1.3 69.1 + - - +
193A HIS* 6.3 2.2 - + - -
205A ALA* 3.1 15.2 + - - +
206A GLU* 3.7 8.5 - - - +
251A TRP* 5.6 4.0 - + - -
290A ASP* 3.5 28.3 - - + -
291A ALA* 3.3 1.2 - - - -
292A PHE* 3.0 51.8 + + - +
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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