Contacts of the helix formed by residues 286 - 299 (chain C) in PDB entry 2POZ
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 GLY 286 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C SER* 3.2 11.9 + - - -
97C GLU* 3.3 11.2 - - - -
98C GLN* 4.9 0.4 - - - -
281C ILE* 3.4 19.0 + - - -
284C ALA 3.8 0.4 - - - -
285C GLY* 1.3 80.5 - - - +
287C LEU* 1.3 61.0 + - - -
288C MSE 3.6 1.8 - - - -
289C GLU* 4.1 0.7 - - - -
290C THR* 2.8 33.3 + - - -
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Residues in contact with LEU 287 (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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97C GLU* 2.7 15.8 + - - +
98C GLN* 4.4 16.9 - - + +
101C TRP* 4.2 11.9 - - + -
112C VAL* 4.2 19.1 - - + -
116C PHE* 4.0 14.2 - - + -
281C ILE* 3.9 22.4 - - + +
286C GLY* 1.3 69.0 - - - +
288C MSE 1.3 59.1 + - - +
290C THR* 3.4 4.6 + - - -
291C LYS* 3.0 26.9 + - - +
317C ALA* 3.8 20.6 - - + +
320C GLN* 4.5 2.7 - - + -
321C LEU* 3.9 22.2 - - + +
366C LEU* 3.4 31.6 - - + -
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Residues in contact with MSE 288 (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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69C GLU* 3.9 10.8 - - - +
97C GLU* 2.8 17.4 + - - +
101C TRP* 3.6 30.1 - - + +
115C LEU 5.9 0.2 - - - +
116C PHE* 3.7 31.8 - - + -
287C LEU* 1.3 72.2 - - - +
289C GLU* 1.3 61.7 + - - +
291C LYS* 3.0 19.8 + - + +
292C LYS* 2.8 59.4 + - - +
115H LEU 4.8 0.7 - - - +
116H PHE* 3.9 17.5 - - - +
288H MSE 4.7 11.2 - - + +
291H LYS* 4.0 12.1 - - - -
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Residues in contact with GLU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TRP* 3.7 23.1 - - + +
97C GLU* 3.9 2.8 + - - +
261C THR* 3.6 6.2 - - - -
262C ARG* 2.7 66.6 + - - +
263C PHE* 5.3 0.2 - - - -
284C ALA 3.4 23.6 - - - +
285C GLY* 3.8 25.1 - - - +
286C GLY 3.8 0.2 + - - -
287C LEU 3.4 0.4 - - - -
288C MSE 1.3 78.4 - - - +
290C THR* 1.3 58.3 + - - +
292C LYS* 3.2 12.1 + - - +
293C ILE* 2.9 31.9 + - + +
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Residues in contact with THR 290 (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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279C PRO* 3.8 28.5 - - + +
281C ILE* 3.7 18.1 - - + +
284C ALA* 3.6 19.8 - - - +
286C GLY 2.8 24.0 + - - -
287C LEU 3.8 3.6 - - - -
289C GLU* 1.3 75.6 - - - +
291C LYS* 1.3 59.3 + - - +
293C ILE* 3.1 9.0 + - - +
294C CYS* 2.8 28.7 + - - -
321C LEU* 3.3 28.0 - - + -
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Residues in contact with LYS 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C PHE* 3.4 44.5 + - + -
287C LEU 3.0 15.3 + - - +
288C MSE 3.0 22.2 + - - +
290C THR* 1.3 76.4 - - - +
292C LYS* 1.3 58.0 + - - +
294C CYS* 3.2 5.0 + - - +
295C ALA* 2.9 27.5 + - - +
321C LEU* 3.7 17.2 - - + +
324C ASN* 2.7 22.7 + - - +
325C ILE* 4.7 6.6 - - + +
69H GLU* 2.7 28.0 + - - -
288H MSE 3.8 17.5 - - - -
292H LYS* 4.1 12.3 - - - +
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Residues in contact with LYS 292 (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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69C GLU* 3.0 35.9 + - - -
262C ARG* 3.9 38.5 - - - +
288C MSE 2.8 35.7 + - + +
289C GLU* 3.4 14.3 + - - +
291C LYS* 1.3 77.7 - - + +
293C ILE* 1.3 60.7 + - - +
295C ALA* 3.3 7.7 + - - +
296C MSE 3.0 27.0 + - - +
291H LYS* 4.0 12.9 - - - +
292H LYS* 5.7 7.9 - - + +
295H ALA* 3.7 28.2 - - + +
298H GLU* 4.6 4.2 + - - -
326H THR* 5.6 0.2 + - - -
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Residues in contact with ILE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C THR* 3.5 30.1 - - - +
262C ARG* 3.7 23.1 - - + +
265C PHE* 3.7 36.1 - - + -
269C PHE* 3.5 4.0 - - + -
277C ILE* 3.8 16.2 - - + -
279C PRO* 4.7 6.5 - - + -
284C ALA* 4.0 20.9 - - + +
289C GLU* 2.9 19.3 + - + +
290C THR* 3.1 11.0 + - - +
292C LYS* 1.3 77.9 - - - +
294C CYS* 1.3 56.2 + - - +
296C MSE 3.3 9.0 + - - +
297C ALA* 3.0 23.4 + - - +
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Residues in contact with CYS 294 (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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277C ILE* 5.0 0.2 - - - -
279C PRO* 4.6 3.4 - - - -
290C THR* 2.8 37.5 + - - +
291C LYS 3.2 4.9 + - - +
293C ILE* 1.3 74.3 - - - +
295C ALA* 1.3 66.1 + - - +
297C ALA* 3.2 6.0 + - - -
298C GLU* 3.2 8.0 + - - +
304C VAL* 3.7 33.0 - - + -
321C LEU* 4.3 1.3 - - - -
325C ILE* 3.9 30.3 - - + -
327C ASN* 3.0 33.0 + - - +
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Residues in contact with ALA 295 (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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291C LYS 2.9 16.1 + - - +
292C LYS* 3.6 6.7 - - - +
293C ILE 3.3 0.2 - - - -
294C CYS* 1.3 76.9 - - - +
296C MSE 1.3 64.2 + - + +
298C GLU* 3.3 13.2 + - - +
299C ALA* 3.7 2.3 + - - +
262H ARG* 2.9 44.5 + - - +
292H LYS* 3.8 34.1 - - + -
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Residues in contact with MSE 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ARG* 3.8 34.8 - - + +
266C ARG* 4.5 17.5 - - + -
269C PHE* 3.4 35.7 - - + -
292C LYS* 3.0 15.2 + - + +
293C ILE* 3.4 5.6 - - - +
295C ALA* 1.3 75.8 - - + +
297C ALA* 1.3 59.7 + - - +
299C ALA* 2.9 27.0 + - - +
300C TYR* 3.3 16.9 - - + -
295H ALA* 6.4 0.2 - - + -
296H MSE 3.2 49.8 - - + -
299H ALA* 4.9 3.4 - - + -
300H TYR* 4.8 13.7 - - + +
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Residues in contact with ALA 297 (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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269C PHE* 3.6 25.1 - - + -
277C ILE* 3.8 16.2 - - + -
293C ILE 3.0 14.1 + - - +
294C CYS 3.2 10.3 + - - +
296C MSE 1.3 77.6 - - - +
298C GLU* 1.3 56.6 + - - +
300C TYR* 2.9 18.0 + - - +
302C MSE 3.1 29.6 + - + +
304C VAL* 4.6 0.2 - - + -
327C ASN* 3.8 11.4 - - - +
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Residues in contact with GLU 298 (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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175B ARG* 2.8 35.4 + - - +
294C CYS 3.2 5.8 + - - +
295C ALA* 3.5 13.3 - - - +
296C MSE 3.1 1.0 - - - -
297C ALA* 1.3 76.5 - - - +
299C ALA* 1.3 61.3 + - - +
300C TYR 3.0 1.1 + - - -
301C ASN 3.3 1.9 + - - -
302C MSE 4.3 2.7 - - - -
326C THR* 2.6 33.4 + - - +
327C ASN* 3.3 30.2 - - + +
262H ARG* 3.0 30.1 + - - +
263H PHE* 3.8 14.1 - - + -
292H LYS* 5.0 4.2 + - - -
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Residues in contact with ALA 299 (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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238B ASP* 3.4 6.7 - - - +
295C ALA 3.7 3.5 + - - +
296C MSE 2.9 17.0 + - - +
298C GLU* 1.3 77.6 - - - +
300C TYR* 1.3 67.4 + - + +
301C ASN 3.5 0.7 - - - -
262H ARG* 4.4 17.5 - - + +
263H PHE* 3.7 27.0 - - + -
266H ARG* 2.9 30.6 + - + -
296H MSE 4.8 3.8 - - - -
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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