Contacts of the strand formed by residues 275 - 288 (chain B) in PDB entry 3PEJ
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 ILE 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ILE* 3.8 17.3 - - + -
133B ILE* 3.3 22.4 - - + +
135B ILE* 3.8 20.9 - - + -
264B ILE* 3.7 24.2 - - + -
268B SER* 3.5 31.2 - - - -
271B ILE* 3.7 19.7 - - + -
273B PHE 4.0 1.3 - - - +
274B PRO* 1.3 77.8 - - - +
276B TYR* 1.3 63.6 + - - +
328B LEU* 3.4 3.3 - - - +
329B MET* 2.7 36.3 + - + +
330B ASN* 2.8 18.4 + - - +
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Residues in contact with TYR 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASP 4.1 5.0 + - - -
297A ASN* 3.4 25.7 - - - +
298A ASP* 4.0 5.9 + - - -
299A PRO* 3.7 23.3 - - + -
300A ASN* 5.9 0.7 - - - -
132B GLU* 3.3 35.2 - - + -
133B ILE 2.8 14.1 + - - +
134B ARG* 3.5 3.2 - - + -
135B ILE* 2.8 29.1 + - - +
274B PRO* 3.8 19.8 - - + +
275B ILE* 1.3 77.1 - - - +
277B LEU* 1.3 59.5 + - - +
326B TRP* 3.7 21.7 - - + -
327B THR 3.4 6.1 - - - +
328B LEU* 3.8 43.0 - - + +
329B MET* 4.5 0.9 - - - -
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 3.3 25.6 - - + +
136B SER* 5.1 0.4 - - - -
257B ASP* 4.5 3.1 - - - +
260B LEU* 4.0 19.3 - - + -
261B MET* 3.6 45.5 - - + +
264B ILE* 3.8 23.8 - - + -
276B TYR* 1.3 72.4 - - - +
278B LEU* 1.4 67.3 + - - +
279B HIS* 3.4 14.9 + - + -
325B LYS 3.2 4.7 - - - +
326B TRP* 3.6 4.0 - - - -
327B THR 2.9 30.5 + - - +
329B MET* 3.8 21.5 - - + +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE 3.0 9.4 + - - +
136B SER* 3.7 26.4 - - - -
137B ALA* 4.9 4.0 + - - +
277B LEU* 1.4 75.4 - - - +
279B HIS* 1.3 59.2 + - - +
324B LYS* 3.7 59.8 - - + +
325B LYS* 3.4 8.3 - - - -
326B TRP* 3.5 45.0 - - + +
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Residues in contact with HIS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASP* 3.3 33.1 + - - +
261B MET* 3.4 20.6 - - + +
277B LEU* 3.8 18.2 - - + -
278B LEU* 1.3 75.6 - - - +
280B GLU* 1.4 80.8 + - - +
281B ASN* 3.6 12.0 + - - +
324B LYS* 4.0 5.8 - - - -
325B LYS 2.8 36.9 + - - +
327B THR* 2.8 35.4 + - - +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASP* 4.2 11.7 + - - +
279B HIS* 1.4 91.6 + - - +
281B ASN* 1.3 69.7 + - - +
282B VAL* 4.1 11.8 - - + +
303B SER* 5.0 0.3 + - - -
322B LYS* 3.3 38.4 - - + +
323B VAL 3.9 7.6 - - - +
324B LYS* 4.2 13.5 - - + +
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Residues in contact with ASN 281 (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 HIS* 3.6 20.8 + - - +
280B GLU* 1.3 77.2 - - - +
282B VAL* 1.3 64.0 + - - +
283B TYR* 3.9 32.5 + - + +
321B LYS 3.7 1.0 - - - +
322B LYS* 3.4 4.9 - - - -
323B VAL* 2.9 39.1 + - + +
325B LYS* 3.6 19.6 - - - +
327B THR* 5.1 0.9 + - - -
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLU* 4.1 15.7 - - + +
281B ASN* 1.3 77.9 - - - +
283B TYR* 1.3 69.6 + - - +
284B THR* 3.9 19.2 + - - +
320B GLU* 4.0 25.4 - - + +
321B LYS 3.4 8.3 - - - +
322B LYS* 3.9 19.1 - - + -
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Residues in contact with TYR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ASN* 3.9 28.1 + - + +
282B VAL* 1.3 76.2 - - - +
284B THR* 1.3 60.4 + - - +
285B GLU* 4.3 0.9 + - - +
301B TYR* 3.5 31.4 - + - +
319B VAL 3.7 1.6 - - - +
320B GLU* 3.6 0.9 - - - -
321B LYS* 2.8 54.3 + - + +
323B VAL* 3.6 23.6 - - + +
325B LYS* 3.6 25.4 - - - -
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Residues in contact with THR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B VAL* 3.9 10.7 + - - +
283B TYR* 1.3 72.4 - - - +
285B GLU* 1.4 65.9 + - - +
318B THR* 3.8 26.9 - - + -
319B VAL 3.3 6.7 - - - +
320B GLU* 3.4 25.3 + - + +
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Residues in contact with GLU 285 (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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283B TYR 5.7 0.9 - - - +
284B THR* 1.4 76.9 - - - +
286B GLU* 1.3 68.0 + - - +
287B VAL* 3.7 20.5 + - + +
295B MET* 4.1 15.4 - - - +
318B THR* 4.7 4.5 - - - -
319B VAL* 3.0 35.2 + - + +
321B LYS* 4.1 21.0 + - + +
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU* 1.3 81.8 - - - +
287B VAL* 1.3 63.3 + - - +
307B GLU* 3.8 2.1 - - - +
314B LYS* 4.6 3.0 + - - -
316B THR* 2.9 42.1 + - + +
317B ARG 3.3 6.1 + - - +
318B THR* 2.4 38.6 + - + -
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU* 3.7 25.6 - - + +
286B GLU* 1.3 80.3 - - - +
288B LEU* 1.3 65.5 + - - +
291B ILE* 3.6 19.1 - - + -
292B ALA* 3.3 31.2 - - + +
295B MET* 3.7 23.8 - - + -
316B THR* 3.3 6.6 - - - -
317B ARG* 2.8 32.9 + - - +
319B VAL* 4.0 16.6 - - + -
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 1.3 73.0 - - - +
289B ALA* 1.3 66.0 + - - +
290B ASP* 3.3 4.9 - - - +
291B ILE* 2.9 44.2 + - + +
292B ALA 3.0 9.7 + - - -
315B LYS* 3.5 23.6 - - + +
316B THR* 4.0 14.1 - - + +
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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