Contacts of the strand formed by residues 321 - 329 (chain B) in PDB entry 5E1T
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 HIS 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B ASN 3.4 3.6 - - - -
313B GLY* 3.1 29.8 + - - -
317B GLY 3.9 1.2 + - - -
320B THR* 1.3 116.0 + - - +
322B LEU* 1.3 68.5 + - - +
385B PRO 4.1 2.9 - - - +
386B LEU* 3.0 50.7 - - + +
388B PHE 3.0 13.0 - - - +
389B PRO* 3.2 37.0 - - + +
390B LEU* 3.9 7.2 - - - +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B CYS* 5.3 0.2 - - - -
309B LEU* 4.5 11.2 - - + -
310B TYR 3.5 4.0 - - - +
311B LEU* 3.5 46.2 - - + +
321B HIS* 1.3 81.2 - - - +
323B SER* 1.3 60.8 + - - +
349B LEU* 4.3 11.7 - - + -
387B PHE* 3.6 20.5 + - + +
388B PHE* 2.7 51.6 + - + +
390B LEU* 4.1 14.8 - - + +
393B LEU* 4.3 14.4 - - + -
406B MET* 4.6 12.8 - - + -
408B LEU* 5.5 1.3 - - + -
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Residues in contact with SER 323 (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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308B ARG 3.7 1.7 - - - +
309B LEU* 3.5 6.1 - - - +
310B TYR* 2.9 36.5 + - - -
313B GLY* 3.5 6.5 - - - -
314B ASP 3.2 29.0 + - - -
317B GLY 3.9 1.2 + - - -
321B HIS 3.7 0.6 + - - -
322B LEU* 1.3 73.0 - - - +
324B LEU* 1.3 59.5 + - - +
325B PHE* 3.7 21.3 - - - -
384B CYS 3.7 3.4 - - - -
385B PRO* 2.4 29.3 + - - +
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Residues in contact with LEU 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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271B TRP* 4.5 4.9 - - + -
307B LEU* 4.4 15.9 - - + -
308B ARG 3.7 9.0 - - - +
309B LEU* 4.2 20.6 - - + -
322B LEU 4.1 0.2 + - - -
323B SER* 1.3 73.6 - - - +
325B PHE* 1.3 70.9 + - - +
347B PHE* 3.4 49.5 - - + -
348B MET 5.3 0.9 - - - +
384B CYS* 3.1 30.9 + - - +
387B PHE* 3.8 34.8 - - + -
408B LEU* 4.7 17.9 - - + -
409B LYS 5.8 0.7 - - - +
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Residues in contact with PHE 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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307B LEU* 3.3 9.5 - - - +
308B ARG 2.9 37.4 + - - +
310B TYR* 3.2 42.8 - + - -
314B ASP* 4.1 12.1 - - - -
323B SER* 3.7 24.5 - - - -
324B LEU* 1.3 78.0 - - - +
326B ILE* 1.3 60.1 + - - +
347B PHE* 3.9 7.6 - - - -
381B ALA* 3.5 24.2 - - + -
382B SER* 3.4 11.0 - - - +
383B GLY* 3.5 19.7 - - - -
384B CYS 3.9 0.4 - - - -
385B PRO* 3.4 38.1 - - + -
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Residues in contact with ILE 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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296B PHE* 4.1 3.4 - - + -
305B LEU* 3.5 35.4 - - + -
306B CYS 3.5 15.5 - - - +
307B LEU* 4.1 13.5 - - + -
325B PHE* 1.3 73.9 - - - +
327B VAL* 1.3 66.8 + - - +
328B ILE* 4.3 11.5 + - + -
341B PHE* 5.4 0.9 - - + -
345B VAL* 4.7 11.4 - - + -
347B PHE* 3.9 10.3 - - + -
362B PHE* 3.5 23.8 - - + -
371B PHE* 4.5 14.9 - - + -
380B VAL 4.7 0.3 - - - +
381B ALA* 3.4 4.2 - - - -
382B SER 3.0 39.7 + - - +
410B CYS* 4.9 4.7 - - - -
412B VAL* 5.2 2.2 - - + -
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Residues in contact with VAL 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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292B PHE* 4.4 9.6 - - + -
305B LEU* 3.3 5.2 - - - -
306B CYS* 2.8 55.9 + - - +
308B ARG* 3.8 21.1 - - + -
326B ILE* 1.3 79.0 - - - +
328B ILE* 1.3 65.8 + - - +
329B MET* 3.4 1.4 + - + +
378B THR* 3.8 19.5 - - + -
379B ASN 3.3 25.4 - - - +
380B VAL 5.2 0.2 - - - -
381B ALA* 3.6 24.5 - - + +
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Residues in contact with ILE 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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303B TYR* 5.2 1.8 - - + -
304B LYS 3.9 4.3 - - - +
305B LEU* 3.5 24.5 - - + -
326B ILE* 4.1 7.7 + - + -
327B VAL* 1.3 73.1 - - - +
329B MET* 1.3 66.7 + - - +
339B TRP* 4.0 28.9 - - + -
341B PHE* 3.5 34.8 - - + -
370B SER 3.3 24.7 + - - +
371B PHE* 3.9 14.4 - - + -
372B GLN 4.9 0.2 - - - +
374B PRO* 4.2 7.2 - - + -
378B THR* 3.7 1.2 - - - -
379B ASN* 2.8 36.7 + - - +
380B VAL 5.4 0.8 + - - -
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Residues in contact with MET 329 (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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295B ALA* 4.0 11.0 - - + -
304B LYS* 2.8 58.8 + - + +
305B LEU 4.0 2.5 - - - +
306B CYS* 3.8 34.5 - - - +
327B VAL* 3.8 12.8 - - + +
328B ILE* 1.3 79.5 - - - +
330B ARG* 1.3 64.5 + - - +
331B GLY 3.4 2.9 + - - -
334B ASP* 4.2 2.3 - - - +
339B TRP* 5.2 0.9 - - - -
374B PRO* 3.6 8.4 - - - +
377B GLU* 3.5 16.2 - - + +
378B THR* 3.9 23.3 - - + +
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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