Contacts of the strand formed by residues 316 - 328 (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 THR 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A GLU* 2.9 26.5 + - + +
287A VAL 3.3 11.4 - - - +
288A LEU* 4.0 17.0 - - + -
289A ALA 4.1 0.7 - - - +
314A LYS* 3.2 27.4 + - - -
315A LYS* 1.4 88.2 + - + +
317A ARG* 1.3 74.2 + - - +
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Residues in contact with ARG 317 (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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286A GLU* 3.3 7.2 - - - +
287A VAL* 2.8 34.0 + - - +
289A ALA* 3.7 32.2 - - - +
292A ALA* 4.4 5.8 - - + -
306A VAL* 3.9 24.5 - - + -
307A GLU* 3.3 32.6 + - + +
309A THR* 3.5 29.7 + - - +
311A ASP 4.8 3.4 + - - -
312A PRO* 6.2 0.2 - - - +
314A LYS* 3.0 32.7 + - - +
316A THR* 1.3 86.7 + - - +
318A THR* 1.3 61.6 + - - +
319A VAL* 3.7 1.1 + - - +
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Residues in contact with THR 318 (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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284A THR* 3.7 27.1 - - + -
285A GLU 3.8 5.4 - - - +
286A GLU* 2.4 21.1 + - + +
305A LYS 4.0 1.0 - - - +
306A VAL* 3.8 0.5 - - - -
307A GLU* 3.0 48.2 + - - +
317A ARG* 1.3 69.9 - - - +
319A VAL* 1.3 62.9 + - - +
320A GLU* 5.3 5.6 - - + +
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TYR 3.7 1.7 - - - +
284A THR* 3.3 6.9 - - - +
285A GLU* 3.0 36.5 + - + +
287A VAL* 4.0 17.9 - - + -
292A ALA* 3.8 29.8 - - + -
295A MET* 4.4 12.8 - - + -
304A VAL* 3.6 28.9 - - + -
305A LYS 3.4 3.4 - - - +
306A VAL* 3.8 13.5 - - + -
317A ARG 4.2 2.2 - - - +
318A THR* 1.3 76.8 - - - +
320A GLU* 1.4 63.0 + - - +
321A LYS* 4.3 13.4 - - + +
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Residues in contact with GLU 320 (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* 4.0 14.1 - - + -
283A TYR 3.6 3.4 - - - -
284A THR* 3.4 27.4 + - + +
303A SER 4.0 0.5 - - - +
304A VAL* 3.3 3.1 - - - -
305A LYS* 2.8 51.7 + - + +
318A THR* 5.3 4.9 - - + +
319A VAL* 1.4 73.2 - - - +
321A LYS* 1.3 62.8 + - - +
322A LYS* 3.9 22.3 + - - +
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Residues in contact with LYS 321 (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 3.7 1.2 - - - +
282A VAL* 3.5 3.5 - - - -
283A TYR* 2.9 50.0 + - + +
285A GLU* 4.2 16.9 + - + +
295A MET* 3.7 40.1 - - - +
298A ASP* 4.0 10.1 + - - -
301A TYR* 3.5 56.6 + - + +
303A SER 3.7 4.7 - - - -
304A VAL* 4.2 9.9 - - + -
319A VAL* 4.3 10.8 - - + -
320A GLU* 1.3 72.3 - - - +
322A LYS* 1.3 60.0 + - - +
323A VAL 4.2 0.2 + - - -
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Residues in contact with LYS 322 (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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280A GLU* 3.3 30.7 + - + +
281A ASN 3.4 3.4 - - - +
282A VAL* 3.9 26.2 - - + -
301A TYR* 3.7 2.3 - - - +
302A ASP* 2.9 27.4 + - + +
303A SER* 2.8 37.3 + - - +
305A LYS* 5.1 9.6 - - + +
320A GLU* 4.2 28.0 + - - +
321A LYS* 1.3 74.2 - - - +
323A VAL* 1.3 60.3 + - - +
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Residues in contact with VAL 323 (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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280A GLU* 4.5 2.2 - - - +
281A ASN* 2.9 33.7 + - + +
283A TYR* 3.6 36.8 - - + +
300A ASN 3.6 18.8 - - - +
301A TYR* 3.8 16.6 - - + -
302A ASP* 3.4 12.3 - - - +
322A LYS* 1.3 73.7 - - - +
324A LYS* 1.3 70.9 + - - +
325A LYS* 4.2 20.9 - - + +
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Residues in contact with LYS 324 (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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137A ALA 2.8 29.1 + - - +
138A ASN* 4.6 5.1 - - - +
139A LYS* 5.2 3.0 - - - +
278A LEU* 3.7 47.6 - - + +
279A HIS* 3.4 5.8 - - - +
280A GLU* 4.2 19.1 - - + +
302A ASP* 3.0 23.3 + - - +
323A VAL* 1.3 78.4 - - - +
325A LYS* 1.3 67.5 + - - +
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Residues in contact with LYS 325 (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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277A LEU 3.2 2.3 - - - +
278A LEU* 3.8 7.2 - - - -
279A HIS* 2.8 35.1 + - - +
281A ASN* 3.6 20.2 - - - +
283A TYR* 4.4 14.4 + - - +
300A ASN 5.8 0.2 + - - -
323A VAL* 3.7 29.1 + - + +
324A LYS* 1.3 78.8 - - - +
326A TRP* 1.3 64.5 + - - +
327A THR* 4.5 2.2 - - - +
300B ASN* 3.8 26.2 - - - +
325B LYS* 4.5 17.3 - - - +
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Residues in contact with TRP 326 (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 3.8 18.6 - - - -
134A ARG* 3.6 40.4 - - + -
135A ILE 3.6 9.2 - - - -
136A SER* 4.1 10.1 - - - -
276A TYR* 3.7 19.4 - - + -
277A LEU 3.3 8.1 - - - -
278A LEU* 3.5 58.3 - - + +
325A LYS* 1.3 73.1 - - - +
327A THR* 1.3 63.0 + - - +
299B PRO* 3.5 42.1 + - + -
300B ASN* 2.8 50.6 + - - +
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Residues in contact with THR 327 (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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261A MET* 5.8 1.6 - - + -
276A TYR* 3.4 4.7 - - - -
277A LEU 2.9 29.9 + - - -
279A HIS* 2.8 35.4 + - - +
281A ASN* 5.1 1.2 + - - -
325A LYS* 4.1 1.9 + - - +
326A TRP* 1.3 76.6 + - - +
328A LEU* 1.3 74.2 + - - +
329A MET* 3.4 12.8 + - - +
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Residues in contact with LEU 328 (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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274A PRO* 3.6 23.1 - - + -
275A ILE 3.4 10.3 - - - +
276A TYR* 3.8 28.5 - - + +
327A THR* 1.3 79.3 - - - +
329A MET* 1.3 60.9 + - - +
330A ASN* 3.4 44.1 - - - +
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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