Contacts of the strand formed by residues 268 - 280 (chain B) in PDB entry 3FEO
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 ASN 268 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B ASP* 2.9 28.1 + - + +
267B LEU* 1.3 81.5 - - - +
269B LEU* 1.3 59.9 + - - +
270B SER* 2.9 29.6 + - - -
271B THR* 3.1 34.3 + - - +
375B MET* 3.9 10.6 - - - +
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Residues in contact with LEU 269 (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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264B ILE* 3.6 24.4 - - + +
265B ASP 3.7 9.6 - - - +
266B PRO* 3.9 21.8 - - + +
268B ASN* 1.3 72.1 + - - +
270B SER* 1.3 56.7 + - - +
271B THR 3.2 3.7 + - - -
304B TYR* 5.2 2.5 - - - +
310B SER* 6.2 0.4 - - - +
374B LEU* 3.5 50.7 - - + +
375B MET* 3.8 14.1 - - + -
406B GLN* 4.0 21.8 - - + -
407B TRP* 2.8 38.7 + - - +
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASN* 2.9 17.4 + - - -
269B LEU* 1.3 76.8 - - - +
271B THR* 1.3 58.7 + - - +
375B MET* 6.1 1.4 - - - +
394B ARG* 3.1 23.9 + - - +
403B GLU 3.3 20.7 + - - -
404B TYR* 3.7 9.2 + - - -
405B ASP 2.6 25.7 + - - -
406B GLN* 4.6 1.2 - - - +
407B TRP* 3.6 6.0 + - - -
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Residues in contact with THR 271 (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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264B ILE* 3.4 10.2 - - - +
265B ASP* 3.3 20.1 + - - -
268B ASN* 3.4 30.8 + - - +
269B LEU 3.2 0.6 - - - -
270B SER* 1.3 79.5 + - - +
272B ILE* 1.3 62.6 + - - +
273B CYS* 4.1 14.8 - - - -
323B GLU 5.7 0.9 - - - -
325B THR* 3.5 22.5 + - - +
407B TRP* 4.3 1.5 - - - -
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Residues in contact with ILE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLU* 3.8 19.5 - - + -
263B ALA 3.3 10.1 - - - +
264B ILE* 4.0 14.1 - - + -
271B THR* 1.3 77.2 - - - +
273B CYS* 1.3 62.2 + - - +
312B PHE* 4.2 18.2 - - + -
316B PHE* 5.3 0.7 - - + -
317B CYS* 3.4 26.2 - - - -
322B ILE* 3.8 25.1 - - + -
323B GLU 4.0 7.2 + - - +
324B LEU* 3.5 4.0 - - + +
325B THR* 2.9 26.3 + - - -
392B LEU* 4.2 12.1 - - + -
407B TRP* 3.8 26.9 - - + +
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Residues in contact with CYS 273 (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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262B GLU* 3.3 2.3 - - - -
263B ALA 2.6 33.7 + - - +
265B ASP* 4.0 28.7 - - - -
271B THR* 4.1 7.6 - - - -
272B ILE* 1.3 77.8 - - - +
274B VAL* 1.3 71.9 + - - +
275B ALA* 3.2 3.8 + - - +
290B ILE* 3.9 24.7 - - + -
324B LEU* 3.8 7.4 - - - -
325B THR* 3.6 27.4 - - - +
326B PRO 5.8 0.7 - - - +
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Residues in contact with VAL 274 (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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260B LYS* 5.2 0.2 - - + -
261B LEU 3.9 5.2 - - - -
273B CYS* 1.3 74.2 - - - +
275B ALA* 1.3 59.6 + - - +
290B ILE* 3.7 5.2 - - - +
291B ASP* 3.4 40.2 + - + +
324B LEU* 3.7 9.6 - - + +
325B THR 3.3 16.6 + - - +
326B PRO* 4.1 1.6 - - + -
327B PRO* 4.0 14.8 - - + -
335B PHE* 3.5 31.4 - - + -
337B TRP* 3.8 17.5 - - + -
340B TYR* 3.7 20.2 - - + +
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Residues in contact with ALA 275 (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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260B LYS* 3.2 9.2 - - - +
261B LEU* 2.9 39.1 + - + +
263B ALA* 4.0 13.9 - - + -
273B CYS 3.8 8.5 - - - +
274B VAL* 1.3 75.0 - - - +
276B THR* 1.3 64.0 + - - +
288B ILE* 3.7 17.5 - - + -
289B GLY 3.1 16.4 - - - +
290B ILE* 4.6 4.3 - - + -
291B ASP* 3.7 2.9 - - - -
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Residues in contact with THR 276 (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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258B GLY* 3.6 36.3 - - - +
259B MET 3.4 3.6 - - - +
260B LYS* 2.5 23.6 + - - +
261B LEU* 4.0 4.0 - - - -
275B ALA* 1.3 72.3 - - - +
277B ILE* 1.3 70.0 + - - +
278B ARG* 3.3 28.0 + - - +
288B ILE* 3.3 3.6 - - - -
289B GLY 2.9 31.9 + - - -
291B ASP* 2.5 27.0 + - - -
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Residues in contact with ILE 277 (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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255B PHE* 3.7 32.5 - - + -
256B LYS 3.6 26.5 - - - +
257B GLU* 3.6 10.5 - - - +
258B GLY 2.9 26.3 + - - -
259B MET* 2.9 23.8 + - + +
261B LEU* 3.8 23.3 - - + +
276B THR* 1.3 74.6 - - - +
278B ARG* 1.3 61.7 + - - +
279B LYS 4.2 12.3 - - - +
280B VAL* 4.2 13.5 - - + -
286B LEU* 4.2 11.0 - - + -
287B MET 3.8 2.5 - - - +
288B ILE* 4.2 13.0 - - + -
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Residues in contact with ARG 278 (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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257B GLU* 3.5 17.9 - - - +
258B GLY* 4.9 5.5 - - - +
260B LYS* 4.4 5.1 - - - +
276B THR* 3.6 47.6 + - - +
277B ILE* 1.3 79.3 + - - +
279B LYS* 1.4 60.7 + - - +
287B MET 2.7 14.8 + - - +
289B GLY 3.7 5.6 - - - +
291B ASP* 4.6 1.8 + - - -
294B GLU* 3.4 22.3 + - - +
301B TRP* 3.3 63.7 - - + +
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLU* 3.9 10.8 - - - +
277B ILE* 3.8 4.2 - - - +
278B ARG* 1.4 78.3 - - - +
280B VAL* 1.3 64.5 + - - +
281B LEU* 3.8 12.2 + - + -
286B LEU* 3.5 4.7 - - - -
287B MET* 2.8 51.9 + - + +
301B TRP* 4.9 8.7 - - + -
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Residues in contact with VAL 280 (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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254B TRP* 3.7 31.2 - - + +
255B PHE* 3.5 28.5 - - + +
256B LYS* 4.1 1.1 - - - -
257B GLU* 4.1 24.2 + - + +
277B ILE* 4.2 6.7 - - + -
279B LYS* 1.3 76.1 - - - +
281B LEU* 1.3 72.2 + - - +
285B PHE 4.1 2.0 - - - -
286B LEU* 4.4 4.3 - - + -
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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