Contacts of the helix formed by residues 288 - 306 (chain B) in PDB entry 4OE4
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 SER 288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285B PHE* 3.6 4.9 - - - -
287B GLY* 1.3 75.8 - - - +
289B THR* 1.3 64.8 + - - +
290B ASN* 4.0 6.8 + - - +
291B VAL* 3.3 17.3 + - - +
292B PHE 3.0 18.0 + - - -
318B THR* 4.3 0.7 - - - -
319B GLY 5.3 2.0 - - - +
458B GLU* 5.8 2.5 - - - -
1000B NAD 2.5 36.0 + - - -
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Residues in contact with THR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A TYR* 5.5 7.0 - - + +
287B GLY 3.8 1.2 + - - -
288B SER* 1.3 72.6 - - - +
290B ASN* 1.3 68.4 + - - +
292B PHE* 3.2 4.8 + - + +
293B LYS* 2.9 32.2 + - + +
318B THR* 3.5 29.7 + - + +
319B GLY 4.5 7.0 + - - +
458B GLU* 4.9 8.8 + - - -
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Residues in contact with ASN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B SER* 3.3 7.0 + - - +
289B THR* 1.3 86.3 - - - +
291B VAL* 1.3 63.3 + - + +
293B LYS* 3.3 8.0 + - - +
294B SER* 3.1 21.3 + - - -
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PHE* 3.6 22.0 - - + -
288B SER* 3.3 9.1 + - - +
290B ASN* 1.3 75.5 - - + +
292B PHE* 1.3 66.5 + - - +
294B SER* 3.2 8.0 + - - -
295B LEU* 2.9 23.6 + - + +
1000B NAD 3.1 82.8 - - + +
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Residues in contact with PHE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A TYR* 3.5 42.0 - + - -
283B LEU* 4.7 4.9 - - + -
285B PHE* 3.7 32.0 - + + -
288B SER 3.0 14.0 + - - +
289B THR* 3.4 8.5 - - + +
291B VAL* 1.3 76.7 - - - +
293B LYS* 1.3 52.3 + - - +
295B LEU* 3.1 5.8 + - - +
296B TYR* 2.7 53.0 + + - +
314B ILE* 3.4 35.0 - - + -
316B GLY* 3.7 24.0 - - - -
318B THR* 3.9 16.4 - - + -
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Residues in contact with LYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A VAL* 5.7 0.5 - - - +
311A TYR* 4.1 15.0 - - - +
289B THR* 2.9 19.7 + - + +
290B ASN* 3.6 7.9 - - - +
292B PHE* 1.3 76.5 - - - +
294B SER* 1.3 53.4 + - - +
296B TYR* 3.4 6.9 - - - +
297B GLY* 2.7 32.9 + - - -
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ASN 3.1 13.4 + - - -
291B VAL* 3.4 11.4 - - - -
293B LYS* 1.3 73.8 - - - +
295B LEU* 1.3 59.6 + - - +
297B GLY* 3.2 1.9 + - - -
298B LYS* 2.8 51.2 + - - +
1000B NAD 4.8 15.0 + - - -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B TYR* 4.9 8.3 - - + -
208B VAL* 4.7 2.9 - - + -
271B THR* 3.5 33.2 - - + +
275B LEU* 4.8 3.8 - - + -
283B LEU* 3.8 26.2 - - + -
285B PHE* 3.4 41.3 - - + -
291B VAL* 2.9 19.3 + - + +
292B PHE* 3.5 5.8 - - - +
294B SER* 1.3 74.6 - - - +
296B TYR* 1.3 54.3 + - - +
298B LYS* 3.1 8.5 + - + +
299B ILE* 2.8 42.9 + - + +
1000B NAD 3.6 18.8 - - + +
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Residues in contact with TYR 296 (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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300A GLN* 2.5 38.3 + - - -
303A VAL* 3.5 28.8 - - + +
304A VAL* 4.6 4.9 - - + -
311A TYR* 4.0 23.0 - + + +
312A PRO* 5.2 5.5 + - - +
283B LEU* 5.1 0.6 - - - +
292B PHE* 2.7 45.8 + + + +
293B LYS* 3.4 10.5 - - - +
295B LEU* 1.3 72.1 - - - +
297B GLY* 1.3 65.7 + - - +
299B ILE* 3.2 7.2 + - - +
300B GLN* 2.9 46.8 + - + +
314B ILE* 3.7 21.3 - - + -
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Residues in contact with GLY 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A VAL* 3.9 25.1 - - - +
293B LYS 2.7 18.7 + - - -
294B SER* 3.6 2.9 - - - -
296B TYR* 1.3 73.2 - - - +
298B LYS* 1.3 55.9 + - - +
300B GLN* 3.3 1.6 + - - +
301B SER* 2.7 35.7 + - - -
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 3.8 22.0 + - - +
271B THR* 4.5 15.2 - - + +
272B ASP* 2.5 35.5 + - - +
275B LEU* 3.9 14.8 - - + +
294B SER* 2.8 33.3 + - - +
295B LEU* 3.5 8.5 - - + +
297B GLY* 1.3 71.8 - - - +
299B ILE* 1.3 63.0 + - - +
301B SER* 3.4 9.8 - - - -
302B GLY* 3.4 15.9 + - - -
307B LYS* 5.0 3.8 + - - -
308B TYR* 4.6 2.8 + - - -
1000B NAD 5.2 3.4 + - - +
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Residues in contact with ILE 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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275B LEU* 3.9 22.9 - - + -
280B PHE* 3.7 26.0 - - + -
283B LEU* 3.8 29.2 - - + -
295B LEU* 2.8 25.4 + - + +
296B TYR 3.2 4.0 + - - +
298B LYS* 1.3 73.3 - - - +
300B GLN* 1.3 59.2 + - - +
302B GLY* 3.1 5.0 + - - -
303B VAL* 2.9 26.9 + - + +
308B TYR* 3.6 8.9 - - + -
312B PRO* 3.8 28.3 - - + -
314B ILE* 4.0 25.4 - - + -
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Residues in contact with GLN 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TYR* 2.7 34.3 + - - -
300A GLN* 3.3 47.3 + - + +
304A VAL* 5.1 4.9 - - + -
296B TYR* 2.9 43.3 + - + +
297B GLY* 3.9 4.7 - - - +
299B ILE* 1.3 73.2 - - - +
301B SER* 1.3 68.7 + - - +
303B VAL* 3.5 6.7 - - - +
304B VAL* 3.0 27.6 + - + +
314B ILE* 3.4 20.3 - - - +
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLY 2.7 23.7 + - - -
298B LYS* 3.4 11.7 + - - -
300B GLN* 1.3 76.7 - - - +
302B GLY* 1.3 63.3 + - - -
304B VAL* 3.3 3.9 + - - +
305B GLU* 2.9 26.1 + - - +
307B LYS* 6.1 0.4 - - - -
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Residues in contact with GLY 302 (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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298B LYS 3.4 3.6 + - - -
299B ILE 3.1 8.0 + - - -
301B SER* 1.3 80.0 - - - +
303B VAL* 1.3 51.3 + - - +
305B GLU* 3.3 3.2 + - - -
306B GLY 2.8 30.3 + - - -
307B LYS* 2.8 36.1 + - - +
308B TYR* 3.8 15.7 - - - -
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LYS* 6.0 0.3 + - - -
296A TYR* 3.4 28.5 - - + +
299B ILE* 2.9 21.6 + - + +
300B GLN* 3.2 21.1 + - - +
302B GLY* 1.3 74.4 - - - +
304B VAL* 1.3 59.2 + - - +
306B GLY* 2.9 20.7 + - - -
308B TYR* 3.7 8.9 - - + -
310B ASP 5.9 0.2 - - - +
311B TYR* 3.6 25.5 - - + -
312B PRO* 3.7 33.0 - - + -
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LYS 5.7 1.6 - - - +
296A TYR* 4.7 12.3 - - + -
297A GLY* 4.0 31.4 - - - +
300A GLN* 5.0 6.1 - - + -
300B GLN 3.0 16.8 + - - +
301B SER* 4.0 3.4 - - - +
303B VAL* 1.3 70.6 - - - +
305B GLU* 1.3 58.7 + - - +
306B GLY* 3.0 9.4 + - - -
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Residues in contact with GLU 305 (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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301B SER 2.9 18.5 + - - +
302B GLY* 3.8 5.8 - - - +
304B VAL* 1.3 74.7 - - - +
306B GLY* 1.3 61.5 + - - +
307B LYS* 3.4 9.2 + - + +
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Residues in contact with GLY 306 (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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293A LYS* 5.9 5.4 - - - -
302B GLY 2.8 6.1 + - - -
303B VAL 2.9 14.6 + - - -
304B VAL 3.0 2.6 - - - -
305B GLU* 1.3 79.2 - - - +
307B LYS* 1.3 62.0 + - - -
308B TYR 3.1 10.8 + - - +
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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
------------------------------------------------------------
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