Contacts of the helix formed by residues 286 - 299 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B SER* 3.1 13.0 + - - -
97B GLU* 3.2 12.1 - - - -
98B GLN* 4.8 0.7 - - - -
281B ILE* 3.4 19.8 + - - -
285B GLY* 1.3 79.5 - - - +
287B LEU* 1.3 58.4 + - - -
288B MSE 3.5 2.0 - - - -
289B GLU 4.0 0.7 - - - -
290B THR* 2.8 32.6 + - - -
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU* 2.7 13.3 + - - +
98B GLN* 4.3 18.1 - - + +
101B TRP* 4.2 18.4 - - + -
112B VAL* 4.4 9.4 - - + -
116B PHE* 3.9 16.4 - - + -
281B ILE* 3.8 16.1 + - + -
286B GLY* 1.3 71.6 - - - +
288B MSE 1.3 58.1 + - - +
290B THR* 3.4 2.4 + - - -
291B LYS* 2.9 26.5 + - - +
317B ALA* 3.5 23.3 - - + +
320B GLN* 4.4 2.7 - - + -
321B LEU* 3.7 29.3 - - + +
366B LEU* 3.5 31.6 - - + -
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Residues in contact with MSE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 6.1 0.2 - - + -
69B GLU* 4.1 11.2 - - - +
97B GLU* 2.7 18.7 + - - +
101B TRP* 3.7 29.8 - - + +
116B PHE* 3.8 20.7 - - + -
287B LEU* 1.3 72.2 - - - +
289B GLU* 1.3 59.1 + - - +
291B LYS* 3.1 20.8 + - + +
292B LYS* 2.8 61.7 + - - +
115F LEU 4.9 0.4 - - - +
116F PHE* 3.7 26.0 - - - +
288F MSE 4.7 13.0 - - + +
291F LYS* 3.9 11.4 - - - -
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TRP* 3.7 23.8 - - + +
97B GLU* 3.8 2.2 + - - -
261B THR* 3.6 5.8 - - - -
262B ARG* 2.8 67.7 + - - +
263B PHE* 5.4 0.2 - - - -
284B ALA 3.4 24.0 - - - +
285B GLY* 3.7 26.7 - - - +
287B LEU 3.3 0.4 - - - -
288B MSE 1.3 77.9 - - - +
290B THR* 1.3 57.6 + - - +
292B LYS* 3.2 12.3 + - - +
293B ILE* 2.8 32.1 + - + +
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B PRO* 3.8 28.9 - - + +
281B ILE* 3.6 24.0 - - + -
284B ALA* 3.7 13.5 - - - +
286B GLY 2.8 23.3 + - - -
287B LEU 3.8 3.4 - - - -
289B GLU* 1.3 74.0 - - - +
291B LYS* 1.3 60.6 + - - +
293B ILE* 3.1 8.4 + - - +
294B CYS* 2.8 30.7 + - - -
321B LEU* 3.5 26.5 - - + -
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Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B PHE* 3.4 42.6 - - + -
287B LEU 2.9 14.5 + - - +
288B MSE 3.1 22.2 + - - +
290B THR* 1.3 74.5 - - - +
292B LYS* 1.3 58.7 + - + +
294B CYS* 3.2 7.3 + - - +
295B ALA* 2.9 27.8 + - + +
321B LEU* 3.7 13.6 - - + +
324B ASN* 2.6 24.3 + - - +
325B ILE* 4.7 8.7 - - + +
69F GLU* 2.6 27.9 + - - -
288F MSE 4.0 16.4 - - + -
292F LYS* 4.2 13.8 - - - +
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU* 2.9 33.1 + - - -
262B ARG* 3.9 36.2 - - - +
288B MSE 2.8 42.3 + - + +
289B GLU* 3.4 13.6 + - - +
291B LYS* 1.3 77.7 - - + +
293B ILE* 1.3 60.7 + - - +
295B ALA* 3.3 8.1 + - - +
296B MSE 3.0 29.8 + - + +
291F LYS* 4.1 11.3 - - - +
292F LYS* 5.8 7.0 - - + +
295F ALA* 3.7 27.2 - - + +
296F MSE 5.6 0.3 - - - +
298F GLU* 5.0 3.6 + - - -
326F THR* 5.6 2.6 + - - -
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Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B THR* 3.6 19.7 - - - -
262B ARG* 3.7 23.1 - - + +
265B PHE* 3.5 49.6 - - + -
269B PHE* 3.6 1.7 - - + -
277B ILE* 3.8 16.8 - - + -
279B PRO* 4.6 6.1 - - + -
284B ALA* 3.9 18.6 - - + +
289B GLU 2.8 20.2 + - - +
290B THR* 3.1 10.5 + - - +
292B LYS* 1.3 74.8 - - - +
294B CYS* 1.3 58.8 + - - +
296B MSE 3.2 8.8 + - - +
297B ALA* 2.9 25.3 + - - +
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Residues in contact with CYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B ILE* 5.1 0.4 - - - -
279B PRO* 4.6 3.8 - - - -
290B THR* 2.8 37.6 + - - +
291B LYS 3.6 4.5 - - - +
293B ILE* 1.3 71.6 - - - +
295B ALA* 1.3 65.1 + - - +
297B ALA* 3.1 12.4 + - - -
298B GLU* 3.2 2.1 + - - +
304B VAL* 3.8 32.5 - - + -
321B LEU* 4.4 1.6 - - - -
325B ILE* 4.0 26.2 - - + -
327B ASN* 3.0 36.7 + - - +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B LYS* 2.9 13.6 + - + +
292B LYS* 3.6 9.6 - - - +
294B CYS* 1.3 76.1 - - - +
296B MSE 1.3 63.5 + - - +
298B GLU* 3.3 15.2 + - - +
299B ALA* 3.8 2.3 + - - +
262F ARG* 2.9 42.4 + - - +
292F LYS* 3.7 33.4 - - + -
296F MSE 6.4 0.2 - - + -
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Residues in contact with MSE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ARG* 3.1 57.0 - - + +
266B ARG* 5.1 3.6 - - - -
269B PHE* 3.7 27.1 - - + -
292B LYS* 3.0 12.9 + - + +
293B ILE* 3.4 8.7 - - - +
294B CYS 3.2 0.2 - - - -
295B ALA* 1.3 77.7 - - - +
297B ALA* 1.3 62.0 + - - +
299B ALA* 3.1 13.3 + - - +
300B TYR* 3.3 23.4 - - + -
295F ALA* 5.5 0.2 - - + -
296F MSE 3.8 48.4 - - + +
299F ALA* 4.7 7.6 - - + -
300F TYR* 5.6 4.5 - - - -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 3.7 17.9 - - + -
277B ILE* 3.6 25.6 - - + -
293B ILE 2.9 12.6 + - - +
294B CYS* 3.1 11.0 + - - +
296B MSE 1.3 77.4 - - - +
298B GLU* 1.3 56.2 + - - +
300B TYR* 3.0 17.0 + - - -
301B ASN 3.4 0.2 + - - -
302B MSE 3.1 28.5 + - + +
327B ASN* 3.8 10.8 - - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ARG* 2.7 41.4 + - - +
294B CYS 3.2 7.5 + - - +
295B ALA* 3.4 12.5 - - - +
296B MSE 3.1 0.8 - - - -
297B ALA* 1.3 71.8 - - - +
299B ALA* 1.3 60.2 + - - +
300B TYR 3.0 6.7 + - - -
301B ASN 3.3 1.7 + - - -
302B MSE 4.4 2.7 - - - -
326B THR* 3.3 39.6 + - - +
327B ASN* 3.3 29.8 + - + +
262F ARG* 2.8 28.7 + - - +
263F PHE* 3.7 10.3 - - + -
292F LYS* 4.9 3.6 + - - -
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ASP* 3.5 6.8 - - - +
295B ALA 3.8 1.2 + - - +
296B MSE 3.1 14.5 + - - +
298B GLU* 1.3 78.4 - - - +
300B TYR* 1.3 61.4 + - + +
301B ASN 3.5 0.4 - - - -
262F ARG* 4.4 18.6 - - + +
263F PHE* 3.5 29.0 - - + -
266F ARG* 2.7 38.5 + - + -
296F MSE 4.8 5.4 - - - -
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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