Contacts of the strand formed by residues 306 - 313 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C MSE 5.2 0.8 - - - +
96C VAL* 4.0 2.4 - - - +
97C GLN* 2.7 48.0 + - + +
99C THR* 3.3 39.0 - - + +
260C SER* 4.2 2.4 - - - -
261C ASP 4.6 0.2 + - - -
265C ILE* 5.5 0.2 - - - +
301C ALA* 3.5 23.7 + - - +
302C ILE* 3.4 31.0 - - + +
303C LYS 3.5 16.6 - - - +
304C GLY 2.8 10.6 + - - +
305C GLN* 1.3 75.5 - - - +
307C PHE* 1.3 79.7 + - - +
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Residues in contact with PHE 307 (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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87C MSE 3.4 44.6 - - + -
96C VAL* 4.0 10.8 - - + -
97C GLN 3.3 4.8 + - - +
98C PHE* 3.8 30.7 - + + -
99C THR* 3.0 28.6 + - - +
258C VAL* 4.0 16.8 - - + -
259C ALA 3.4 5.2 - - - +
260C SER* 3.4 28.9 - - - -
265C ILE* 3.7 17.0 - - + -
271C LEU* 3.6 27.6 - - + -
302C ILE* 4.5 0.7 - - - -
306C HIS* 1.3 85.6 + - - +
308C ALA* 1.3 60.3 + - - +
309C ILE 3.9 0.7 - - - -
330C VAL* 4.0 11.4 - - + -
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Residues in contact with ALA 308 (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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99C THR* 3.5 22.0 - - + -
101C TYR* 3.0 24.7 - - + -
258C VAL* 3.2 2.2 - - - -
259C ALA* 2.8 50.2 + - + -
302C ILE* 3.7 13.2 - - + -
307C PHE* 1.3 72.9 - - - +
309C ILE* 1.3 60.6 + - - +
2G NAG 5.5 1.3 - - - +
3G NAG 4.5 2.9 - - - +
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Residues in contact with ILE 309 (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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98C PHE* 3.6 38.1 - - + -
99C THR 2.8 14.3 + - - +
100C GLY* 3.3 3.6 - - - -
101C TYR* 3.3 18.9 + - - -
255C ARG* 4.2 12.3 - - + -
257C SER 4.4 0.4 - - - +
258C VAL* 3.6 16.2 - - + -
275C VAL* 3.7 36.8 - - + -
291C ARG* 6.0 0.9 - - - -
293C MSE 4.0 17.7 - - - -
308C ALA* 1.3 69.6 - - - +
310C TYR* 1.3 70.3 + - - +
311C GLN* 3.2 27.4 + - - +
324C TYR* 5.0 4.0 - - + -
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Residues in contact with TYR 310 (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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101C TYR* 3.5 42.2 - + - +
102C TYR* 4.2 5.6 - - - -
103C THR* 2.9 28.1 + - - -
244C VAL* 3.4 27.8 - - + +
252C LEU* 3.6 33.6 + - + -
253C VAL 3.4 23.6 - - - -
254C GLY* 4.1 1.6 - - - -
255C ARG* 2.6 36.2 + - - -
257C SER* 3.0 23.3 + - - +
308C ALA 3.3 2.8 + - - -
309C ILE* 1.3 68.9 - - - +
311C GLN* 1.3 53.6 + - - +
312C GLY* 3.4 28.0 + - - -
313C ILE* 3.5 8.1 - - + +
4G NAG 5.5 0.4 - - + -
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Residues in contact with GLN 311 (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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100C GLY* 4.7 1.2 - - - -
101C TYR 3.0 11.4 + - - +
102C TYR* 4.4 0.4 - - + -
254C GLY* 3.6 13.7 - - - -
255C ARG* 3.4 16.8 + - - +
309C ILE* 3.4 36.1 + - - +
310C TYR* 1.3 71.5 - - - +
312C GLY* 1.3 57.9 + - - +
317C ALA* 3.4 18.8 - - - +
320C ARG* 2.7 59.0 + - - +
321C ALA* 3.4 28.9 - - + +
324C TYR* 3.6 25.6 - - - -
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Residues in contact with GLY 312 (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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102C TYR* 3.3 4.5 - - - +
103C THR 2.8 25.3 + - - -
254C GLY* 4.3 5.6 - - - -
310C TYR* 3.4 22.9 + - - -
311C GLN* 1.3 81.3 - - - +
313C ILE* 1.3 63.7 + - - -
317C ALA* 3.6 8.1 - - - -
320C ARG* 5.1 0.2 - - - -
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Residues in contact with ILE 313 (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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103C THR* 3.3 19.7 - - - +
105C VAL* 3.8 13.0 - - + -
166C TYR* 3.6 40.2 - - + +
244C VAL* 3.9 8.1 - - + +
252C LEU 6.2 0.4 - - - +
310C TYR* 3.5 18.6 - - + +
312C GLY* 1.3 74.3 - - - +
314C GLY* 1.3 63.2 + - - +
317C ALA* 3.8 6.7 + - - +
171D ASP 5.0 7.4 - - - +
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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