Contacts of the helix formed by residues 274 - 291 (chain A) in PDB entry 3PEI
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 MSE 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A LEU* 4.3 16.2 - - + +
173A GLN* 4.6 5.6 - - - +
175A LEU 6.0 1.1 - - - +
180A CYS* 4.5 19.5 - - + +
182A THR* 6.1 0.4 - - - -
185A MSE 3.7 31.2 - - + -
250A LYS 4.7 2.0 - - - -
251A GLY* 3.7 33.9 - - - +
252A LEU 3.8 15.5 - - - +
253A VAL* 4.0 20.2 - - + -
273A ASP* 1.3 76.7 - - - +
275A GLY* 1.3 53.1 + - - +
276A GLY 3.2 2.7 - - - -
277A VAL* 3.0 25.4 + - + +
278A ALA* 2.8 35.5 + - + -
302A LEU* 4.3 3.4 - - + -
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Residues in contact with GLY 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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173A GLN* 4.1 20.6 - - - +
273A ASP* 2.8 20.1 + - - -
274A MSE 1.3 76.0 - - - +
276A GLY* 1.3 56.3 + - - +
278A ALA* 4.1 0.4 - - - -
279A ALA* 2.9 33.1 + - - +
359A THR* 4.5 2.5 - - - -
449A ILE* 3.7 15.4 - - - +
453A ALA* 4.7 2.0 - - - -
465A ARG 4.8 0.9 - - - +
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLY* 3.9 6.7 - - - -
250A LYS 3.7 9.6 + - - -
273A ASP 4.8 0.8 + - - -
274A MSE 3.1 1.6 + - - -
275A GLY* 1.3 76.1 - - - +
277A VAL* 1.3 62.4 + - - +
280A VAL* 3.2 25.3 + - - +
357A LEU* 3.5 29.5 - - - +
358A ALA* 4.7 1.3 - - - -
359A THR 4.8 4.8 - - - +
449A ILE* 3.7 11.7 - - - +
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Residues in contact with VAL 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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185A MSE 4.5 11.0 - - + -
249A GLY 3.5 25.1 - - - +
250A LYS 3.5 2.0 + - - -
251A GLY* 3.6 17.5 - - - +
274A MSE 3.0 41.3 + - + +
276A GLY* 1.3 72.8 - - - +
278A ALA* 1.3 66.8 + - - +
280A VAL* 3.2 6.7 + - - +
281A MSE 3.0 28.2 + - - +
300A MSE 3.6 34.4 - - + +
302A LEU* 4.2 4.7 - - + -
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Residues in contact with ALA 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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169A ALA* 3.4 37.3 - - + +
172A LEU* 4.0 22.0 - - + -
173A GLN* 3.7 17.7 - - + +
274A MSE 2.8 18.3 + - + +
275A GLY 3.8 2.5 - - - +
276A GLY 3.3 0.2 - - - -
277A VAL* 1.3 79.5 - - - +
279A ALA* 1.3 57.2 + - - +
281A MSE 3.4 3.5 + - - +
282A GLY 2.9 23.0 + - - -
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Residues in contact with ALA 279 (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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169A ALA* 4.1 2.4 - - + +
275A GLY 2.9 17.9 + - - +
278A ALA* 1.3 75.0 - - - +
280A VAL* 1.3 59.8 + - - +
283A THR* 2.8 35.4 + - - -
357A LEU* 4.0 12.3 - - + -
464A GLY 5.0 0.2 - - - +
465A ARG 3.9 7.4 - - - +
466A PRO* 3.8 28.5 - - + -
467A VAL* 3.6 17.9 - - + +
470A LEU* 5.0 0.7 - - + -
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Residues in contact with VAL 280 (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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233A MSE 4.3 8.3 - - + -
247A LEU* 4.4 14.4 - - + +
248A VAL 4.3 3.1 - - - -
249A GLY* 3.8 22.2 - - - +
276A GLY 3.2 17.3 + - - +
277A VAL* 3.2 8.3 + - - +
279A ALA* 1.3 75.1 - - - +
281A MSE 1.3 57.7 + - - +
283A THR* 3.2 6.7 + - - -
284A MSE 2.9 33.7 + - + +
298A GLY* 3.7 34.3 - - - -
299A VAL 4.2 3.6 - - - +
300A MSE 4.6 2.2 - - + -
357A LEU* 3.8 15.7 - - + -
470A LEU* 5.7 0.2 - - - -
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Residues in contact with MSE 281 (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 TYR* 3.3 29.3 - - + +
172A LEU* 3.5 24.5 - - + -
185A MSE 3.7 11.7 - - + -
188A GLU* 3.7 23.3 - - + +
189A ALA* 4.0 2.9 - - - +
192A LEU* 3.4 32.9 - - + +
233A MSE 3.5 28.0 - - - +
277A VAL 3.0 17.5 + - - +
278A ALA 3.5 7.9 - - - +
280A VAL* 1.3 75.3 - - - +
282A GLY* 1.3 63.4 + - - +
284A MSE 3.3 5.1 + - - +
285A LYS* 3.0 24.4 + - - +
300A MSE 3.6 14.1 - - - +
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Residues in contact with GLY 282 (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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165A GLY* 3.3 39.7 - - - -
168A TYR* 4.2 7.6 - - - -
169A ALA 4.5 0.2 - - - -
278A ALA 2.9 16.6 + - - -
279A ALA 3.8 1.6 - - - -
280A VAL 3.2 0.2 - - - -
281A MSE 1.3 76.5 - - - +
283A THR* 1.3 57.8 + - - +
285A LYS* 3.5 0.7 + - - +
286A ALA* 3.1 23.6 + - - +
467A VAL* 4.2 6.3 - - - -
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Residues in contact with THR 283 (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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247A LEU* 3.7 26.5 - - + -
279A ALA 2.8 23.9 + - - -
280A VAL 3.6 4.7 - - - -
282A GLY* 1.3 75.2 - - - +
284A MSE 1.3 65.7 + - + +
286A ALA* 3.4 1.0 + - - +
287A ILE* 3.1 23.9 + - - +
467A VAL* 3.9 15.9 - - - +
470A LEU* 3.7 27.9 - - + +
471A VAL* 4.3 10.1 - - + -
474A LEU* 3.8 20.4 - - + -
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Residues in contact with MSE 284 (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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192A LEU* 4.0 9.2 - - + -
199A PHE* 3.7 24.7 - - + -
233A MSE 4.4 19.1 - - - +
235A TYR* 4.8 1.8 - - - -
247A LEU* 3.3 33.9 - - + -
280A VAL* 2.9 28.1 + - + +
281A MSE 3.7 4.7 - - - +
283A THR* 1.3 78.9 - - + +
285A LYS* 1.3 67.5 + - - +
287A ILE* 3.6 13.6 + - + +
288A ALA* 3.1 24.8 + - - +
296A VAL* 3.7 22.0 - - + -
298A GLY* 3.7 26.0 - - - -
474A LEU* 4.7 0.2 - - + -
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Residues in contact with LYS 285 (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 CYS* 3.9 30.2 + - - +
168A TYR* 3.9 44.1 - - + +
192A LEU* 4.1 22.3 - - + +
196A TYR* 4.5 4.9 + - + +
281A MSE 3.0 16.7 + - - +
282A GLY 3.7 3.8 - - - +
284A MSE 1.3 78.0 - - - +
286A ALA* 1.3 63.5 + - - +
288A ALA* 3.2 4.0 + - - +
289A MSE 3.0 36.3 + - + +
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Residues in contact with ALA 286 (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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161A ALA* 3.6 31.6 - - + +
162A ILE* 4.3 3.1 - - - -
165A GLY* 4.7 2.2 - - - -
282A GLY 3.1 16.9 + - - +
283A THR 3.9 0.7 - - - +
285A LYS* 1.3 77.3 - - - +
287A ILE* 1.3 63.0 + - - +
289A MSE 3.2 8.0 + - - +
290A LEU* 3.1 28.1 + - - +
467A VAL* 5.0 0.7 - - + -
471A VAL* 3.9 26.0 - - + -
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Residues in contact with ILE 287 (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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235A TYR* 3.4 33.5 + - + -
283A THR* 3.1 18.8 + - + +
284A MSE 3.7 19.1 - - + +
286A ALA* 1.3 76.7 - - - +
288A ALA* 1.3 60.0 + - - +
290A LEU* 3.4 2.2 + - - +
291A ASN 2.9 21.5 + - - -
292A LEU* 3.1 41.0 + - + -
294A VAL* 5.0 1.8 - - + -
296A VAL* 4.0 15.7 - - + -
471A VAL* 4.5 11.2 - - + -
474A LEU* 3.7 34.3 - - + -
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Residues in contact with ALA 288 (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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196A TYR* 3.6 35.2 - - + -
198A THR* 5.8 0.2 + - - -
199A PHE* 3.7 23.8 - - + -
235A TYR* 3.9 14.7 + - + -
284A MSE 3.1 18.8 + - - +
285A LYS 3.6 4.3 - - - +
287A ILE* 1.3 79.9 - - - +
289A MSE 1.3 60.4 + - - +
291A ASN* 3.2 14.0 + - - +
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Residues in contact with MSE 289 (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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0A MSE 5.2 14.1 - - + -
157A LYS* 4.3 11.8 + - - -
160A SER* 5.1 5.4 - - - +
161A ALA* 4.1 24.7 - - + +
164A CYS* 3.7 40.6 - - + -
196A TYR* 3.4 21.8 - - - +
285A LYS* 3.0 29.2 + - + +
286A ALA 3.6 5.8 - - - +
288A ALA* 1.3 77.5 - - - +
290A LEU* 1.3 60.8 + - - +
291A ASN* 3.1 2.4 + - - +
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Residues in contact with LEU 290 (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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157A LYS* 4.0 31.6 + - + +
158A ILE* 3.9 24.9 - - + +
161A ALA* 3.5 27.1 - - + -
286A ALA 3.1 20.5 + - - +
287A ILE* 3.4 4.7 + - - +
289A MSE 1.3 75.3 - - - +
291A ASN* 1.3 71.0 + - - +
292A LEU* 3.5 14.4 + - + +
471A VAL* 4.1 24.9 - - + -
475A ILE* 4.3 16.2 - - + -
491A EDO 3.5 22.2 + - - +
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Residues in contact with ASN 291 (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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157A LYS* 5.8 0.9 - - - +
198A THR* 4.6 12.8 + - - +
235A TYR* 3.3 15.9 + - - -
237A GLY* 5.9 0.7 - - - -
287A ILE 2.9 6.0 + - - -
288A ALA 3.6 8.3 - - - +
289A MSE 3.1 5.0 - - - +
290A LEU* 1.3 82.2 - - - +
292A LEU* 1.3 62.7 + - - +
293A PRO* 3.4 6.4 - - - +
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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