Contacts of the strand formed by residues 316 - 328 (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 THR 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286B GLU* 2.9 26.6 + - + +
287B VAL 3.3 11.7 - - - +
288B LEU* 4.0 17.0 - - + -
289B ALA 4.1 0.2 - - - +
314B LYS* 3.2 27.3 + - - -
315B LYS* 1.3 87.7 + - + +
317B ARG* 1.3 74.8 + - - +
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Residues in contact with ARG 317 (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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286B GLU* 3.3 7.6 - - - +
287B VAL* 2.8 35.6 + - - +
289B ALA* 3.7 32.3 - - - +
292B ALA* 4.3 5.6 - - + -
306B VAL* 4.0 22.2 - - + -
307B GLU* 3.3 34.4 + - + +
308B GLU* 5.4 0.4 - - - +
309B THR* 3.6 27.5 + - - +
311B ASP 4.8 2.4 + - - -
312B PRO* 6.0 1.0 - - - +
314B LYS* 3.0 33.3 + - - +
316B THR* 1.3 88.3 + - - +
318B THR* 1.4 60.7 + - - +
319B VAL* 3.7 1.1 + - - -
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B THR* 3.8 26.7 - - + -
285B GLU 3.8 6.7 - - - +
286B GLU* 2.4 21.8 + - + +
305B LYS 4.0 0.9 - - - +
306B VAL* 3.9 0.2 - - - -
307B GLU* 2.8 53.5 + - - +
317B ARG* 1.4 70.5 - - - +
319B VAL* 1.3 61.7 + - - +
320B GLU* 4.4 6.4 + - + +
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Residues in contact with VAL 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B TYR 3.7 1.6 - - - +
284B THR* 3.3 6.9 - - - +
285B GLU* 3.0 38.2 + - + +
287B VAL* 4.0 17.7 - - + -
292B ALA* 3.8 30.3 - - + -
295B MET* 4.4 12.1 - - + -
304B VAL* 3.6 29.2 - - + -
305B LYS 3.4 3.6 - - - +
306B VAL* 3.8 12.8 - - + -
317B ARG 4.2 2.0 - - - +
318B THR* 1.3 78.7 - - - +
320B GLU* 1.3 63.6 + - - +
321B LYS* 4.2 13.2 - - + +
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Residues in contact with GLU 320 (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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282B VAL* 4.0 15.4 - - + +
283B TYR 3.6 3.4 - - - -
284B THR* 3.4 26.9 + - + +
303B SER 4.0 0.3 - - - +
304B VAL* 3.3 2.8 - - - -
305B LYS* 2.8 53.9 + - + +
318B THR* 5.3 5.0 - - + +
319B VAL* 1.3 74.2 - - - +
321B LYS* 1.3 63.0 + - - +
322B LYS* 3.9 9.9 + - + +
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ASN 3.7 1.0 - - - +
282B VAL* 3.4 3.6 - - - -
283B TYR* 2.8 49.5 + - + +
285B GLU* 4.1 18.1 + - + +
295B MET* 3.7 40.3 - - - +
298B ASP* 3.9 10.1 + - - -
301B TYR* 3.5 56.8 + - + +
303B SER 3.8 4.7 - - - -
304B VAL* 4.2 10.3 - - + -
319B VAL* 4.2 10.5 - - + +
320B GLU* 1.3 73.6 - - - +
322B LYS* 1.3 61.0 + - - +
323B VAL 4.2 0.2 + - - -
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Residues in contact with LYS 322 (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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280B GLU* 3.3 29.2 - - + +
281B ASN 3.4 4.0 - - - +
282B VAL* 3.9 25.6 - - + -
301B TYR* 3.7 1.5 - - - +
302B ASP* 2.9 27.9 + - + +
303B SER* 2.8 38.0 + - - +
305B LYS* 5.5 7.0 - - + -
320B GLU* 3.9 13.0 + - + +
321B LYS* 1.3 75.5 - - - +
323B VAL* 1.3 60.7 + - - +
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLU* 4.5 1.9 - - - +
281B ASN* 2.9 34.1 + - + +
283B TYR* 3.6 36.8 - - + +
300B ASN 3.6 19.3 - - - +
301B TYR* 3.8 15.9 - - + -
302B ASP* 3.4 12.6 - - - +
321B LYS 4.2 0.2 + - - -
322B LYS* 1.3 73.7 - - - +
324B LYS* 1.3 71.6 + - - +
325B LYS* 4.2 20.4 - - + +
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Residues in contact with LYS 324 (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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3B SO4 2.9 33.6 + - - +
137B ALA 2.8 28.9 + - - +
138B ASN* 4.6 1.8 - - - +
278B LEU* 3.7 47.0 - - + +
279B HIS* 3.4 6.1 - - - +
280B GLU* 4.2 19.1 - - + +
302B ASP* 3.0 21.6 + - + +
323B VAL* 1.3 79.2 - - - +
325B LYS* 1.3 64.3 + - - +
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Residues in contact with LYS 325 (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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300A ASN* 3.8 20.0 - - + +
325A LYS* 4.5 19.0 - - - +
277B LEU 3.2 2.4 - - - +
278B LEU* 3.8 7.0 - - - -
279B HIS* 2.8 35.8 + - - +
281B ASN* 3.6 19.7 - - - +
283B TYR* 3.6 22.0 - - - +
300B ASN 5.8 0.6 + - - -
323B VAL* 3.7 25.9 + - + +
324B LYS* 1.3 78.1 + - - +
326B TRP* 1.3 63.8 + - - +
327B THR* 4.5 2.0 - - - +
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Residues in contact with TRP 326 (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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299A PRO* 3.4 42.5 + - + +
300A ASN* 2.8 41.5 + - - +
2B SO4 3.8 19.7 - - - -
134B ARG* 3.6 41.3 - - + -
135B ILE 3.6 9.0 - - - -
136B SER* 4.1 9.6 - - - -
276B TYR* 3.7 19.6 - - + -
277B LEU 3.3 8.5 - - - -
278B LEU* 3.5 58.7 - - + +
325B LYS* 1.3 74.3 - - - +
327B THR* 1.3 60.5 + - - +
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Residues in contact with THR 327 (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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261B MET* 5.7 1.8 - - + -
276B TYR* 3.4 5.2 - - - -
277B LEU 2.9 30.5 + - - +
279B HIS* 2.8 36.3 + - - +
281B ASN* 5.1 1.6 + - - -
325B LYS* 4.1 2.3 + - - +
326B TRP* 1.3 75.8 + - - +
328B LEU* 1.4 74.4 + - - +
329B MET* 3.4 11.8 + - - +
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Residues in contact with LEU 328 (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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274B PRO* 3.6 23.3 - - + -
275B ILE 3.4 10.5 - - - +
276B TYR* 3.8 28.9 - - + +
327B THR* 1.4 80.9 - - - +
329B MET* 1.3 60.6 + - - +
330B ASN* 3.4 43.2 - - - +
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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