Contacts of the helix formed by residues 312 - 328 (chain B) in PDB entry 3SZ9
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 GLU 312 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B GLN* 1.3 87.7 + - - +
313B ASP* 1.3 72.7 + - - +
314B ILE 3.1 1.2 + - - -
315B TYR* 3.3 13.9 + - - +
316B ASP* 4.7 2.1 + - - -
409B LYS* 3.7 30.3 - - + +
410B PHE 2.8 14.9 + - - +
411B LYS* 3.6 39.5 + - - +
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Residues in contact with ASP 313 (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 SER* 4.5 11.8 + - - -
311B GLN* 2.8 27.4 + - - +
312B GLU* 1.3 85.4 - - - +
314B ILE* 1.3 60.7 + - + +
315B TYR 3.6 0.2 - - - -
316B ASP 5.5 0.2 - - - -
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Residues in contact with ILE 314 (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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277B ILE* 3.8 21.1 - - + +
278B MET 3.5 25.6 - - - +
279B SER* 3.7 29.6 - - - +
281B ALA* 5.2 2.9 - - + +
283B MET* 3.7 26.8 - - + +
310B VAL* 3.8 11.9 - - + -
311B GLN 3.4 12.6 - - - +
313B ASP* 1.3 82.6 - - + +
315B TYR* 1.3 66.7 + - - +
316B ASP 3.4 2.0 - - - -
317B GLU* 3.4 8.7 + - - +
318B PHE* 2.9 24.2 + - + +
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Residues in contact with TYR 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL* 3.8 20.9 - - + -
311B GLN 3.2 8.9 + - - +
312B GLU* 3.3 20.6 + - - +
314B ILE* 1.3 77.1 - - - +
316B ASP* 1.3 81.6 + - - +
318B PHE* 3.2 0.7 + - - +
319B VAL* 2.9 46.3 + - + +
387B GLY* 3.8 5.4 - - - -
388B ASP* 2.8 44.8 + - - -
407B ILE* 3.8 20.7 + - + -
408B LEU 4.0 0.7 - - - -
409B LYS* 3.5 53.6 - - + -
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Residues in contact with ASP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B GLU 4.7 1.9 + - - -
313B ASP 5.5 0.2 - - - -
314B ILE 3.4 0.6 - - - -
315B TYR* 1.3 96.7 - - - +
317B GLU* 1.3 64.2 + - - +
319B VAL* 3.3 4.3 + - - +
320B GLU* 2.9 38.2 + - + +
409B LYS* 5.2 2.6 + - - -
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Residues in contact with GLU 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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283B MET* 3.8 18.4 - - + +
314B ILE* 3.4 10.1 + - - +
315B TYR 3.3 0.4 - - - -
316B ASP* 1.3 80.2 - - - +
318B PHE* 1.3 63.5 + - - +
320B GLU* 3.2 11.1 + - + +
321B ARG* 2.8 67.0 + - + +
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Residues in contact with PHE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 3.9 33.7 - - + -
283B MET* 3.9 18.5 - - + +
286B ALA* 3.9 4.5 - - + -
287B VAL* 3.8 32.4 - - + +
290B ALA* 3.6 26.7 - - + -
308B THR* 3.8 10.5 - - + -
310B VAL* 3.5 30.1 - - + -
314B ILE* 2.9 19.0 + - + +
315B TYR 3.6 2.9 - - - +
317B GLU* 1.3 77.0 - - - +
319B VAL* 1.3 55.0 + - - +
321B ARG* 3.7 1.7 - - - +
322B SER* 2.7 57.5 + - - -
405B MET* 5.4 0.9 - - + -
407B ILE* 4.6 8.7 - - + -
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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
----------------------------------------------------------
315B TYR* 2.9 56.5 + - + +
316B ASP* 3.6 5.6 - - - +
318B PHE* 1.3 76.9 - - + +
320B GLU* 1.3 60.4 + - + +
322B SER* 3.1 6.6 + - - -
323B VAL* 2.9 37.8 + - + +
368B LEU* 3.6 32.1 - - + -
407B ILE* 4.0 20.2 - - + -
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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
----------------------------------------------------------
316B ASP* 2.9 34.1 + - - +
317B GLU* 3.6 8.5 + - + +
319B VAL* 1.3 79.7 - - + +
321B ARG* 1.3 63.6 + - + +
323B VAL* 3.4 6.2 + - - +
324B ALA* 3.1 23.3 + - - +
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Residues in contact with ARG 321 (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 MET* 3.6 25.3 - - - +
284B ASP* 2.5 33.9 + - - +
287B VAL* 3.9 20.3 - - + +
317B GLU* 2.8 50.5 + - + +
318B PHE 3.8 2.7 - - - +
320B GLU* 1.3 77.5 - - + +
322B SER* 1.3 58.5 + - - +
324B ALA* 3.4 7.5 + - - +
325B ARG* 3.0 28.8 + - - +
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Residues in contact with SER 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 4.1 13.8 + - - +
291B HIS* 4.9 3.8 + - - -
318B PHE* 2.7 48.9 + - - -
319B VAL 3.6 3.8 - - - -
321B ARG* 1.3 75.8 - - - +
323B VAL* 1.3 57.6 + - - +
325B ARG* 3.4 4.7 + - - +
326B ALA* 3.0 28.8 + - - +
385B VAL* 4.6 3.6 - - - +
405B MET* 4.5 14.3 - - - +
407B ILE* 4.2 18.8 - - - -
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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
----------------------------------------------------------
319B VAL* 2.9 23.9 + - + +
320B GLU* 3.8 6.3 - - - +
322B SER* 1.3 73.0 - - - +
324B ALA* 1.3 59.7 + - - +
326B ALA* 3.2 6.4 + - - +
327B LYS* 2.9 47.5 + - + +
368B LEU* 3.7 52.7 - - + +
369B CYS* 4.2 5.2 - - + -
385B VAL* 4.2 11.4 - - + -
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Residues in contact with ALA 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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320B GLU 3.1 17.6 + - - +
321B ARG* 3.7 8.1 - - - +
323B VAL* 1.3 76.7 - - - +
325B ARG* 1.3 62.3 + - - +
327B LYS* 3.5 8.3 + - - +
328B SER* 3.2 23.9 + - - -
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 4.7 9.4 - - + -
288B GLU* 2.9 41.8 + - - +
291B HIS* 3.5 46.0 + - + +
321B ARG 3.0 17.1 + - - +
322B SER* 3.8 7.2 - - - +
323B VAL 3.3 0.2 - - - -
324B ALA* 1.3 75.5 - - - +
326B ALA* 1.3 61.4 + - - +
328B SER* 3.0 29.7 + - - -
329B ARG* 3.3 12.4 + - - +
340B GLU* 2.9 32.9 + - - -
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Residues in contact with ALA 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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291B HIS* 3.9 11.2 - - + -
295B PHE* 4.3 8.1 - - + -
322B SER 3.0 16.5 + - - +
323B VAL 3.2 4.2 + - - +
325B ARG* 1.3 76.8 - - - +
327B LYS* 1.3 62.6 + - - +
329B ARG* 3.3 16.0 + - - +
369B CYS* 3.8 10.1 - - - -
383B PRO* 3.5 25.6 - - + +
385B VAL* 3.6 25.6 - - + -
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Residues in contact with LYS 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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323B VAL* 2.9 30.9 + - + +
324B ALA* 4.0 6.7 - - - +
326B ALA* 1.3 77.9 - - - +
328B SER* 1.3 58.2 + - - +
329B ARG 3.2 4.6 + - - +
368B LEU 4.4 9.5 + - - -
369B CYS* 3.8 26.9 - - + +
370B GLY 5.6 0.2 - - - +
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Residues in contact with SER 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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324B ALA 3.2 13.9 + - - -
325B ARG* 3.0 28.9 + - - -
326B ALA 3.2 0.2 - - - -
327B LYS* 1.3 74.7 - - - +
329B ARG* 1.3 62.3 + - - +
330B VAL* 3.3 12.1 + - - +
340B GLU* 3.6 5.9 - - - +
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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
------------------------------------------------------------
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