Contacts of the strand formed by residues 270 - 278 (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 THR 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE* 3.6 28.1 - - + -
57A GLN* 4.6 2.2 - - - +
60A VAL* 3.4 26.6 + - - +
61A TYR* 3.5 22.2 - - - -
64A VAL* 4.6 6.7 - - + -
268A GLY 3.5 1.2 + - - -
269A THR* 1.3 75.5 - - - +
271A LEU* 1.3 68.3 + - - +
292A LEU* 4.4 5.2 - - + -
293A MSE 3.7 2.7 - - - -
294A VAL* 4.7 3.3 - - - +
332A VAL* 3.6 1.4 - - - -
333A LEU* 3.2 48.8 + - + -
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Residues in contact with LEU 271 (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 4.5 0.2 - - - -
258A VAL* 3.9 21.3 - - + -
265A ILE* 4.3 10.8 - - + -
269A THR* 3.7 19.5 - - + +
270A THR* 1.3 83.3 - - - +
272A ILE* 1.3 60.1 + - - +
273A ALA* 3.8 1.3 + - + -
291A ARG 3.6 1.0 - - - +
292A LEU* 3.6 3.9 - - - -
293A MSE 2.7 49.3 + - + +
295A ALA* 4.6 3.1 - - + +
307A PHE* 3.6 35.0 - - + -
330A VAL* 3.7 19.1 - - + -
331A TRP 3.5 2.7 - - - -
332A VAL* 3.6 28.3 - - + -
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Residues in contact with ILE 272 (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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27A PRO* 5.6 2.9 - - + -
29A ALA* 5.2 1.6 - - + -
33A PRO* 4.7 1.1 - - + -
67A TRP* 3.7 33.2 - - + -
74A THR* 4.2 11.9 - - + -
77A MSE 4.9 5.6 - - + -
270A THR 4.3 0.2 - - - -
271A LEU* 1.3 72.3 - - - +
273A ALA* 1.3 62.6 + - - +
290A LEU* 3.7 28.9 - - + -
291A ARG 3.3 8.5 - - - +
292A LEU* 3.6 16.8 - - + +
330A VAL* 3.2 1.0 - - - -
331A TRP* 2.8 66.7 + - + +
333A LEU* 3.8 16.7 - - + +
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Residues in contact with ALA 273 (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* 3.6 26.2 - - + -
271A LEU 3.8 0.4 + - - -
272A ILE* 1.3 76.5 - - - +
274A GLU* 1.3 61.7 + - - +
275A VAL* 3.4 2.7 + - + +
289A GLU 3.1 4.5 - - - +
290A LEU* 3.5 5.4 - - - +
291A ARG* 2.9 33.3 + - - +
293A MSE 3.8 17.0 - - + -
329A ARG 3.2 12.3 - - - +
330A VAL* 3.6 10.3 - - + -
331A TRP* 4.8 1.6 - - - -
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Residues in contact with GLU 274 (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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29A ALA* 4.0 9.9 - - + -
30A VAL* 3.6 28.5 + - - +
98A PHE* 4.1 1.5 - - - -
273A ALA* 1.3 69.4 - - - +
275A VAL* 1.3 63.3 + - - +
276A PRO* 3.4 8.7 - - - +
288A TYR* 3.4 33.0 - - + +
289A GLU 3.5 1.8 + - - -
290A LEU* 3.4 31.4 + - - +
328A GLY* 3.5 11.6 - - - -
329A ARG* 2.8 53.9 + - - +
331A TRP* 4.2 8.0 - - + -
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Residues in contact with VAL 275 (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* 4.4 7.4 - - + -
273A ALA* 4.3 4.5 - - + +
274A GLU* 1.3 71.7 - - - +
276A PRO* 1.3 69.0 - - + +
277A LEU* 4.3 0.2 - - - +
288A TYR* 4.2 0.2 - - - -
289A GLU* 2.8 55.7 + - + +
291A ARG* 4.7 10.5 - - + -
293A MSE 3.8 31.0 - - + -
309A ILE* 3.7 28.3 - - + -
311A GLN* 6.1 0.2 - - - +
324A TYR* 3.5 25.1 - - + +
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Residues in contact with PRO 276 (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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8A ARG 4.6 0.9 - - - +
98A PHE* 3.9 11.2 - - + -
274A GLU 3.4 7.1 - - - +
275A VAL* 1.3 85.3 - - + +
277A LEU* 1.3 62.6 + - - +
278A LEU* 4.4 1.3 - - - +
284A PHE* 3.6 23.1 - - + -
287A GLN 4.0 0.9 - - - +
288A TYR* 3.8 14.1 - - + -
324A TYR* 2.9 33.9 + - + -
326A HIS* 3.5 25.6 - - + -
327A TYR 3.2 28.0 - - - +
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Residues in contact with LEU 277 (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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275A VAL 3.4 0.6 + - - +
276A PRO* 1.3 71.0 - - - +
278A LEU* 1.3 63.2 + - - +
284A PHE* 3.2 25.3 - - - -
285A ASN* 3.3 19.4 - - - +
287A GLN* 3.0 36.9 + - + +
288A TYR 3.4 26.9 - - - +
289A GLU* 3.7 37.2 - - + +
324A TYR* 4.1 9.2 - - - +
69C ARG* 4.1 18.8 - - + +
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Residues in contact with LEU 278 (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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276A PRO 4.7 0.2 - - - +
277A LEU* 1.3 80.9 - - - +
279A ASP* 1.3 76.9 + - - +
282A GLY* 3.8 11.2 - - - +
283A LYS 3.4 17.0 - - - +
284A PHE* 4.4 0.9 - - - +
285A ASN* 4.1 5.4 - - - +
320A ARG* 4.6 8.7 - - + +
323A TRP* 4.0 28.5 - - + +
324A TYR* 4.1 35.8 + - + -
326A HIS* 3.5 35.9 - - + +
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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