Contacts of the strand formed by residues 285 - 294 (chain B) in PDB entry 5D3V
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 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A GLU* 5.6 0.4 - - - -
280B LYS* 4.4 3.1 - - - +
281B ILE* 3.3 6.3 - - - +
282B SER* 3.0 45.3 + - - +
283B ALA 3.2 15.8 - - - +
284B GLY* 1.3 85.2 + - - +
286B ILE* 1.3 63.0 + - - +
287B GLN* 4.1 24.7 - - - +
351B ASN* 3.7 3.6 + - - +
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Residues in contact with ILE 286 (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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279A LEU* 4.1 26.5 - - + -
286A ILE* 4.6 7.3 - - + +
287A GLN* 5.3 0.3 - - - -
288A GLU* 4.0 28.9 + - + +
279B LEU* 4.0 28.3 - - + -
280B LYS 3.5 3.4 - - - -
281B ILE* 4.0 23.6 - - + -
285B ASN* 1.3 76.4 - - - +
287B GLN* 1.3 71.8 + - - +
351B ASN* 4.1 6.3 - - - +
353B TYR* 3.9 38.8 - - + -
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Residues in contact with GLN 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ILE 4.8 5.4 - - - +
279B LEU* 3.8 6.5 - - - -
280B LYS* 2.7 55.3 + - + +
285B ASN* 4.1 24.2 - - - +
286B ILE* 1.3 89.7 - - - +
288B GLU* 1.3 59.2 + - - +
289B ARG* 3.3 42.4 + - + +
328B ARG* 5.2 3.6 - - - +
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Residues in contact with GLU 288 (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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284A GLY 3.8 8.1 - - - +
285A ASN* 5.2 0.2 - - - -
286A ILE* 4.4 19.2 + - + +
351A ASN* 3.8 20.3 + - - -
353A TYR* 3.2 34.9 + - - +
277B THR* 3.4 31.1 - - + +
278B LEU 3.5 8.3 - - - +
279B LEU* 3.9 10.8 - - + +
287B GLN* 1.3 72.9 - - - +
289B ARG* 1.3 79.1 + - - +
301B CYS 4.8 0.2 - - - +
302B LYS* 5.2 1.6 - - - +
303B ARG 5.7 0.5 + - - -
375B LYS* 4.5 4.7 + - - -
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Residues in contact with ARG 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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277B THR* 3.4 6.1 - - - -
278B LEU 2.9 32.2 + - - +
280B LYS* 4.2 26.9 - - + +
287B GLN* 3.3 46.1 + - + +
288B GLU* 1.3 90.8 + - - +
290B ALA* 1.3 60.0 + - - +
291B PHE* 3.5 21.0 - - + -
300B TYR* 4.4 8.8 - - + -
301B CYS 3.2 22.7 - - - +
302B LYS* 3.7 25.7 - - - +
303B ARG 5.9 0.2 - - - +
328B ARG* 3.5 42.1 - - - +
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Residues in contact with ALA 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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276B GLY 3.7 6.3 - - - +
277B THR* 4.4 10.1 - - - +
289B ARG* 1.3 71.4 - - - +
291B PHE* 1.3 59.2 + - - +
292B PHE* 3.8 23.6 - - + -
299B VAL 3.8 0.3 - - - +
300B TYR* 3.2 4.3 - - - -
301B CYS* 2.9 36.3 + - + +
303B ARG* 5.3 7.8 - - + +
325B TYR* 3.9 23.1 - - + -
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Residues in contact with PHE 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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275B GLN* 3.2 5.5 - - - +
276B GLY 2.8 34.9 + - - +
278B LEU* 3.8 34.1 - - + -
280B LYS* 4.0 23.8 - - + -
289B ARG* 3.5 27.6 - - + -
290B ALA* 1.3 75.3 - - - +
292B PHE* 1.3 63.5 + - - +
298B LEU* 4.2 23.6 - - + -
299B VAL 3.5 2.5 - - - -
300B TYR* 3.7 24.5 - + + -
361B ILE* 5.5 0.2 - - + -
370B PHE* 4.0 17.0 - + - -
372B CYS* 3.9 19.7 - - - -
383B TRP* 3.5 23.5 - + + -
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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
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253B LEU* 4.0 30.1 - - + -
257B ILE* 4.9 5.2 - - + -
272B LEU* 3.9 5.2 - - + -
274B LEU 3.6 3.4 - - - -
275B GLN* 3.4 37.7 - - + -
290B ALA* 3.8 28.9 - - + -
291B PHE* 1.3 75.1 - - - +
293B LEU* 1.3 59.8 + - - +
294B PHE* 3.6 25.6 - + + -
298B LEU* 3.4 5.9 - - - +
299B VAL* 2.8 46.1 + - + +
301B CYS* 4.1 20.4 - - + -
325B TYR* 3.8 32.3 - + - -
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Residues in contact with LEU 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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272B LEU* 3.5 3.5 - - - +
273B LEU* 2.8 41.5 + - + +
274B LEU* 2.8 20.7 + - + +
291B PHE 4.3 0.2 - - - -
292B PHE* 1.3 71.8 - - - +
294B PHE* 1.3 63.0 + - - +
297B LEU 3.7 11.2 - - - +
298B LEU* 4.0 13.0 - - + -
333B THR* 4.0 17.9 - - + -
336B MET* 5.2 2.0 - - + -
383B TRP* 4.1 15.4 - - + -
386B ALA* 3.6 44.0 - - + +
387B ILE* 4.0 17.7 - - + +
390B GLU* 4.3 8.3 - - + -
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Residues in contact with PHE 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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250B LEU* 3.6 29.6 - - + -
253B LEU* 3.6 26.2 - - + -
260B TRP* 5.4 0.9 - + - -
265B LEU* 3.8 28.0 - - + -
269B CYS* 3.6 22.4 - - + -
271B GLN 3.4 17.5 - - - +
272B LEU* 3.7 18.2 - - + -
273B LEU* 3.7 6.1 - - - -
292B PHE* 3.6 28.5 - - + -
293B LEU* 1.3 74.4 - - - +
295B ASP* 1.3 64.9 + - - +
296B ASN 3.1 3.3 + - - -
297B LEU* 2.8 31.5 + - + +
299B VAL* 4.0 13.7 - - + -
390B GLU* 3.8 10.6 - - - +
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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