Contacts of the strand formed by residues 275 - 288 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ILE* 3.8 18.2 - - + -
133A ILE* 3.3 22.7 - - + +
135A ILE* 3.8 22.4 - - + -
264A ILE* 3.7 24.2 - - + -
268A SER* 3.5 30.3 - - - -
271A ILE* 3.7 19.7 - - + -
273A PHE 4.0 0.9 - - - +
274A PRO* 1.3 78.1 - - - +
276A TYR* 1.3 62.5 + - - +
328A LEU* 3.4 3.3 - - - +
329A MET* 2.7 36.3 + - + +
330A ASN* 2.8 18.8 + - - +
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Residues in contact with TYR 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLU* 3.3 35.2 - - + -
133A ILE 2.8 12.9 + - - +
134A ARG* 3.5 2.8 - - + -
135A ILE* 2.8 29.5 + - - +
274A PRO* 3.7 21.0 - - + +
275A ILE* 1.3 76.9 - - - +
277A LEU* 1.3 58.9 + - - +
326A TRP* 3.7 22.3 - - + -
327A THR 3.4 5.8 - - - -
328A LEU* 3.8 42.9 - - + +
329A MET* 4.5 1.8 - - - -
294B ASP 4.0 5.4 + - - -
297B ASN* 3.3 26.8 + - - +
298B ASP* 3.8 6.7 + - - -
299B PRO* 3.6 23.6 - - + -
300B ASN* 5.9 0.2 - - - -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 3.3 24.2 - - + +
136A SER* 5.1 0.4 - - - -
257A ASP* 4.3 3.4 - - - +
260A LEU* 4.0 20.2 - - + -
261A MET* 3.6 44.6 - - + +
264A ILE* 3.8 24.0 - - + -
276A TYR* 1.3 73.7 - - - +
278A LEU* 1.4 67.6 + - - +
279A HIS* 3.4 15.4 + - + -
325A LYS 3.2 4.2 - - - +
326A TRP* 3.6 3.6 - - - -
327A THR 2.9 33.2 + - - +
329A MET* 3.8 21.5 - - + +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SO4 5.7 1.3 - - - +
135A ILE 3.0 9.4 + - - +
136A SER* 3.7 27.0 - - - -
137A ALA 4.9 3.6 + - - -
277A LEU* 1.4 75.2 - - - +
279A HIS* 1.3 59.9 + - - +
324A LYS* 3.7 59.5 - - + +
325A LYS* 3.4 7.4 - - - +
326A TRP* 3.5 44.0 - - + +
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Residues in contact with HIS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ASP* 3.1 33.0 + - - +
261A MET* 3.4 20.5 - - + +
277A LEU* 3.8 17.9 - - + -
278A LEU* 1.3 74.8 - - - +
280A GLU* 1.4 79.5 + - - +
281A ASN* 3.6 12.1 + - - +
324A LYS* 4.0 5.6 - - - -
325A LYS 2.8 37.1 + - - +
327A THR* 2.8 36.5 + - - +
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ASP* 3.6 13.0 + - - +
279A HIS* 1.4 92.8 + - - +
281A ASN* 1.3 69.2 + - - +
282A VAL* 4.1 11.8 - - + +
303A SER* 5.1 0.7 + - - -
322A LYS* 3.3 40.9 + - + +
323A VAL 3.9 7.6 - - - +
324A LYS* 4.2 13.3 - - + +
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Residues in contact with ASN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A HIS* 3.6 24.2 + - - +
280A GLU* 1.3 73.7 - - - +
282A VAL* 1.3 63.6 + - - +
283A TYR* 3.8 32.4 + - + +
321A LYS 3.7 0.7 - - - +
322A LYS* 3.4 5.0 - - - -
323A VAL* 2.9 36.9 + - + +
325A LYS* 3.6 19.1 - - - +
327A THR* 5.1 0.7 + - - -
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLU* 4.1 16.6 - - + +
281A ASN* 1.3 78.7 - - - +
283A TYR* 1.3 69.6 + - - +
284A THR* 3.9 18.7 + - - +
320A GLU* 4.0 23.3 - - + -
321A LYS 3.5 8.1 - - - +
322A LYS* 3.9 23.1 - - + -
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Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ASN* 3.8 30.2 + - + +
282A VAL* 1.3 77.9 - - - +
284A THR* 1.3 60.1 + - - +
285A GLU* 5.7 0.8 - - - +
301A TYR* 3.5 30.7 - + - -
319A VAL 3.7 1.7 - - - +
320A GLU* 3.6 0.9 - - - -
321A LYS* 2.9 53.1 + - + +
323A VAL* 3.6 28.2 - - + +
325A LYS* 4.4 14.6 + - - +
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Residues in contact with THR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A VAL* 3.9 10.0 + - - +
283A TYR* 1.3 72.8 - - - +
285A GLU* 1.4 66.6 + - - +
318A THR* 3.7 26.2 - - + -
319A VAL 3.3 6.3 - - - +
320A GLU* 3.4 26.2 + - + +
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A TYR 5.7 1.3 - - - +
284A THR* 1.4 78.4 - - - +
286A GLU* 1.3 65.9 + - - +
287A VAL* 3.7 20.2 + - + +
295A MET* 4.1 16.1 - - - +
318A THR* 3.8 5.3 - - - -
319A VAL* 3.0 35.6 + - + +
321A LYS* 4.2 19.3 + - + +
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A GLU* 1.3 81.3 - - - +
287A VAL* 1.3 62.7 + - - +
307A GLU* 4.3 1.2 - - - +
314A LYS* 4.6 3.8 + - - -
316A THR* 2.9 41.7 + - + +
317A ARG* 3.5 6.1 + - - +
318A THR* 2.4 39.0 + - + +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A GLU* 3.7 26.7 - - + +
286A GLU* 1.3 81.3 - - - +
288A LEU* 1.3 65.7 + - - +
291A ILE* 3.6 19.3 - - + -
292A ALA* 3.3 31.6 - - + +
295A MET* 3.7 23.6 - - + -
316A THR* 3.3 6.0 - - - -
317A ARG* 2.8 33.1 + - - +
319A VAL* 4.0 16.6 - - + -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A VAL* 1.3 73.9 - - - +
289A ALA* 1.3 66.5 + - - +
290A ASP* 3.3 5.8 - - - +
291A ILE* 2.9 43.3 + - + +
292A ALA* 3.0 9.8 + - - -
315A LYS* 3.5 22.7 - - + +
316A THR* 4.0 14.8 - - + +
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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
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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