Contacts of the strand formed by residues 306 - 313 (chain A) in PDB entry 2PI8
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 HIS 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A VAL* 4.4 1.8 - - - +
97A GLN* 3.1 49.2 + - + +
99A THR* 3.4 31.3 - - + +
260A SER* 4.2 2.6 - - - -
261A ASP 4.6 0.3 + - - -
265A ILE* 5.5 0.2 - - - +
301A ALA 3.6 23.4 + - - -
302A ILE* 3.4 29.3 - - + +
303A LYS 3.5 17.3 - - - +
304A GLY 2.8 10.4 + - - +
305A GLN* 1.3 75.1 - - - +
307A PHE* 1.3 96.5 + - - +
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Residues in contact with PHE 307 (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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87A MSE 3.5 39.9 - - + -
96A VAL* 3.4 26.9 - - + -
97A GLN 2.9 7.6 + - - +
98A PHE* 3.5 28.0 - + + -
99A THR 2.8 25.1 + - - -
258A VAL* 4.0 18.4 - - + -
259A ALA 3.4 4.5 - - - +
260A SER* 3.4 30.7 - - - -
265A ILE* 3.8 15.3 - - + -
271A LEU* 3.6 27.8 - - + -
302A ILE* 4.7 0.9 - - - -
306A HIS* 1.3 87.1 + - - +
308A ALA* 1.3 60.5 + - - +
309A ILE 3.9 0.7 - - - -
330A VAL* 3.9 7.2 - - + -
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Residues in contact with ALA 308 (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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99A THR* 3.5 20.9 - - + -
101A TYR* 3.1 24.4 - - + -
258A VAL* 3.2 3.3 - - - -
259A ALA* 2.8 51.4 + - + -
302A ILE* 3.7 13.0 - - + -
307A PHE* 1.3 72.4 - - - +
309A ILE* 1.3 61.1 + - - +
3E NAG 4.6 2.9 - - - +
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Residues in contact with ILE 309 (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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98A PHE* 3.9 29.2 - - + -
99A THR 2.8 17.4 + - - +
100A GLY* 3.4 3.5 - - - -
101A TYR* 3.3 18.1 + - - -
255A ARG* 4.2 13.2 - - + -
258A VAL* 3.7 17.0 - - + -
275A VAL* 3.7 41.5 - - + -
291A ARG* 6.1 0.4 - - - -
293A MSE 4.0 17.9 - - - -
308A ALA* 1.3 68.1 - - - +
310A TYR* 1.3 68.3 + - - +
311A GLN* 3.2 29.4 + - - +
324A TYR* 5.0 4.9 - - + -
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Residues in contact with TYR 310 (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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101A TYR* 3.5 42.6 - + - +
102A TYR* 4.2 1.3 - - - -
103A THR* 3.0 31.9 + - - -
244A VAL* 3.5 21.2 - - + +
252A LEU* 3.6 35.9 + - + -
253A VAL 3.5 15.3 - - - -
254A GLY* 4.0 5.2 - - - -
255A ARG* 2.6 35.7 + - - -
257A SER* 3.1 23.6 + - - +
308A ALA 3.3 2.6 + - - -
309A ILE* 1.3 69.4 - - - +
311A GLN* 1.3 52.5 + - - +
312A GLY* 3.3 28.8 + - - -
313A ILE* 3.5 16.1 - - + +
4E NAG 5.5 0.9 - - + -
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Residues in contact with GLN 311 (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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100A GLY* 4.8 1.2 - - - -
101A TYR 3.0 10.3 + - - +
102A TYR* 4.4 0.2 - - + -
254A GLY* 3.5 14.4 - - - -
255A ARG* 3.4 17.5 + - - +
275A VAL* 6.1 0.2 - - - +
309A ILE* 3.6 34.2 + - - +
310A TYR* 1.3 72.5 - - - +
312A GLY* 1.3 58.3 + - - +
317A ALA* 3.3 21.1 - - + +
320A ARG* 2.7 57.0 + - - +
321A ALA* 3.4 28.4 - - + +
324A TYR* 3.5 26.4 - - - -
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Residues in contact with GLY 312 (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 TYR* 3.4 3.8 - - - +
103A THR 2.8 26.0 + - - -
254A GLY* 4.3 5.2 - - - -
310A TYR* 3.3 24.2 + - - -
311A GLN* 1.3 82.7 - - - +
313A ILE* 1.3 64.8 + - - -
317A ALA* 3.7 7.6 - - - +
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Residues in contact with ILE 313 (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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103A THR* 3.4 15.7 - - - +
105A VAL* 3.8 10.5 - - + -
166A TYR* 3.5 43.7 - - + +
244A VAL* 3.9 7.6 - - + -
252A LEU 6.1 0.4 - - - +
310A TYR* 3.5 12.6 - - - +
312A GLY* 1.3 78.6 - - - +
314A GLY* 1.3 62.9 + - - +
317A ALA* 3.7 7.3 + - - +
171B ASP* 3.1 28.8 - - - +
172B GLY* 4.4 6.1 - - - -
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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