Contacts of the strand formed by residues 290 - 298 (chain B) in PDB entry 3O4O
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 GLU 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B TYR* 4.1 0.7 - - - -
250B PHE* 3.0 32.6 + - + +
252B PHE* 6.0 0.9 - - + +
256B SER 5.3 3.3 - - - +
258B ASN* 2.7 31.9 + - - +
282B ILE* 5.3 4.4 - - + +
283B SER 3.4 7.4 - - - +
284B HIS* 4.3 19.1 - - + +
288B GLU 3.5 9.0 + - - +
289B ASP* 1.3 75.9 - - - +
291B THR* 1.3 62.7 + - - +
292B ARG* 3.2 34.0 + - + -
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Residues in contact with THR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL 3.2 12.8 - - - -
249B TYR* 4.0 19.5 - - + -
282B ILE* 3.8 2.8 - - - -
283B SER* 2.7 45.8 + - - +
284B HIS* 5.2 0.2 - - - -
285B SER* 5.3 2.0 - - - +
289B ASP 3.5 10.5 - - - +
290B GLU* 1.3 80.9 - - - +
292B ARG* 1.3 64.7 + - - +
293B THR* 4.3 5.2 + - - -
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B CYS 3.8 1.0 - - - +
247B THR* 4.4 0.2 - - - -
248B VAL* 2.8 33.0 + - - +
250B PHE* 3.8 15.2 - - + -
258B ASN* 2.7 35.9 + - - +
259B GLU* 4.5 3.0 - - - +
260B VAL* 3.9 31.8 - - + +
280B GLU* 4.6 15.5 + - + +
281B SER 4.0 5.4 - - - +
282B ILE* 3.7 30.3 - - + +
290B GLU* 3.2 30.0 + - + +
291B THR* 1.3 73.9 - - - +
293B THR* 1.3 68.2 + - - +
294B GLN* 5.9 1.1 - - + +
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Residues in contact with THR 293 (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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245B PRO* 4.9 4.5 - - + -
246B CYS 3.3 8.7 - - - +
247B THR* 3.5 32.0 - - + +
280B GLU* 3.5 3.5 - - - +
281B SER* 3.1 50.2 + - - +
291B THR* 4.3 5.7 + - - -
292B ARG* 1.3 81.9 + - - +
294B GLN* 1.3 82.0 + - - +
295B ILE* 4.7 9.6 - - + -
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Residues in contact with GLN 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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244B ILE 3.4 1.3 - - - +
245B PRO* 3.1 4.5 - - - +
246B CYS* 2.6 37.0 + - - +
260B VAL* 2.8 53.9 + - + +
261B TRP* 4.0 5.2 - - - -
262B TRP* 3.9 21.3 - - + +
278B ILE* 3.4 30.8 - - + +
279B ASN 3.3 8.1 - - - +
280B GLU* 4.1 24.1 + - + -
292B ARG* 5.9 1.5 - - + +
293B THR* 1.3 84.6 - - - +
295B ILE* 1.3 64.4 + - - +
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Residues in contact with ILE 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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243B LEU* 5.2 6.1 - - + -
244B ILE 3.1 9.2 - - - +
245B PRO* 3.3 39.7 - - + -
278B ILE* 3.4 22.2 - - - +
279B ASN* 3.2 49.2 + - + +
281B SER* 4.9 4.9 - - - +
293B THR* 4.7 11.4 - - + -
294B GLN* 1.3 74.1 - - - +
296B LEU* 1.3 74.6 + - - +
297B SER 4.2 0.4 - - - -
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Residues in contact with LEU 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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242B LEU* 3.2 18.3 - - + +
243B LEU* 3.4 12.2 - - - -
244B ILE* 3.4 39.9 + - + +
262B TRP* 3.5 41.3 - - + +
269B PRO* 6.6 0.2 - - + -
276B VAL* 4.3 19.1 - - + -
277B THR 3.7 3.6 - - - -
278B ILE* 4.1 11.0 - - + -
295B ILE* 1.3 96.6 - - - +
297B SER* 1.3 64.9 + - - +
298B ILE* 3.6 8.2 - - + +
310B TYR* 5.1 14.6 - - + -
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Residues in contact with SER 297 (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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241B GLU 5.8 0.2 - - - -
242B LEU 4.5 0.7 - - - -
243B LEU* 5.5 2.2 - - - +
276B VAL* 3.7 16.3 - - - +
277B THR* 3.5 17.7 + - - -
295B ILE 4.2 0.4 - - - -
296B LEU* 1.3 72.9 - - - +
298B ILE* 1.3 73.2 + - - +
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Residues in contact with ILE 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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241B GLU* 3.4 21.7 + - - +
242B LEU* 3.1 50.8 + - + +
275B ASP 4.4 5.6 - - - +
276B VAL* 3.9 22.0 - - + -
296B LEU* 3.6 12.3 + - + +
297B SER* 1.3 88.1 + - - +
299B LYS* 1.3 79.0 + - - +
300B LYS 4.7 2.7 - - - +
301B VAL* 4.5 11.4 - - + -
305B ASP* 6.0 0.7 - - - +
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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