Contacts of the helix formed by residues 310 - 329 (chain B) in PDB entry 5A6C
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 ASP 310 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B HIS* 5.7 1.9 + - - -
305B ALA* 3.1 27.3 + - - +
306B GLN* 4.9 1.0 - - - +
308B LEU* 4.5 10.5 - - + +
309B ASN* 1.3 73.2 - - - +
311B ARG* 1.3 57.6 + - - +
312B ILE* 3.7 5.4 + - - +
313B GLY* 2.9 26.3 + - - -
314B GLU* 2.9 24.9 + - - +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ASN* 3.6 8.3 + - - +
310B ASP* 1.3 73.8 + - - +
312B ILE* 1.3 57.9 + - + +
314B GLU* 2.7 32.7 + - - +
315B GLY 2.9 24.1 + - - -
340B LYS* 5.8 4.9 - - - +
343B GLU* 6.2 1.4 - - - +
344B ILE* 3.3 35.3 - - + +
347B GLU* 2.7 54.1 + - - +
348B VAL* 5.2 8.1 - - + -
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASP* 3.3 4.4 + - - +
311B ARG* 1.3 77.1 - - + +
313B GLY* 1.3 58.5 + - - +
315B GLY* 3.3 2.5 + - - +
316B ARG* 3.0 65.5 + - - +
344B ILE* 5.1 2.2 - - - -
348B VAL* 3.8 36.8 - - + -
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Residues in contact with GLY 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B HIS* 3.5 20.7 + - - -
305B ALA* 4.1 7.2 - - - -
310B ASP* 2.9 27.3 + - - -
312B ILE* 1.3 80.3 - - - +
314B GLU* 1.3 55.2 + - - +
316B ARG* 3.3 7.2 + - - +
317B ALA* 2.9 24.4 + - - +
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 3.5 22.7 - - + +
305B ALA* 4.0 8.0 - - + +
306B GLN* 3.3 34.5 - - + +
310B ASP 2.9 14.0 + - - +
311B ARG* 2.7 46.7 + - - +
313B GLY* 1.3 75.1 - - - +
315B GLY* 1.3 58.1 + - - +
317B ALA* 3.4 3.4 + - - +
318B CYS* 2.9 30.7 + - - +
340B LYS* 4.4 15.0 - - - +
344B ILE* 3.7 13.8 - - + +
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Residues in contact with GLY 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG 2.9 12.1 + - - -
312B ILE* 3.3 4.0 + - - -
314B GLU* 1.3 77.0 - - - +
316B ARG* 1.3 56.4 + - - +
318B CYS* 3.2 6.0 + - - +
319B TRP* 3.0 25.5 + - - +
341B HIS* 3.7 19.9 + - - -
344B ILE* 3.7 24.1 - - - +
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 3.4 32.9 + - + +
301B HIS* 5.4 0.4 - - - +
312B ILE* 3.0 45.3 + - + +
313B GLY* 3.3 7.6 + - - +
315B GLY* 1.3 71.7 - - - +
317B ALA* 1.3 66.2 + - - +
319B TRP* 3.4 7.2 + - - +
320B SER* 3.0 20.1 + - - -
341B HIS* 5.6 0.7 - - - -
370B ALA* 6.4 0.4 - - - +
371B LYS* 3.3 54.2 - - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 4.0 8.6 - - - -
298B HIS* 4.2 8.1 - - - +
301B HIS* 3.5 21.5 - - + -
302B LEU* 4.1 23.1 - - + -
313B GLY 2.9 16.9 + - - +
314B GLU* 3.6 5.6 - - - +
316B ARG* 1.3 74.1 - - - +
318B CYS* 1.3 66.6 + - - +
320B SER* 3.2 3.4 + - - -
321B LEU* 2.9 30.7 + - - +
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Residues in contact with CYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 5.2 7.9 - - - +
314B GLU* 2.9 18.5 + - - +
315B GLY* 3.3 10.1 - - - +
317B ALA* 1.3 74.3 - - - +
319B TRP* 1.3 57.1 + - - +
321B LEU* 3.9 0.6 - - - +
322B GLY* 2.9 24.4 + - - -
337B PHE* 3.6 33.9 - - - +
340B LYS* 3.6 41.5 - - - -
341B HIS* 3.6 17.7 - - + -
344B ILE* 4.1 8.3 - - - -
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Residues in contact with TRP 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 4.6 5.2 - - - -
315B GLY 3.0 8.9 + - - +
316B ARG* 3.7 11.0 - - - +
318B CYS* 1.3 74.1 - - - +
320B SER* 1.3 89.3 + - - +
322B GLY* 3.0 3.6 + - - -
323B ASN* 3.0 57.1 + - - +
337B PHE 6.0 0.2 - - - -
338B ALA* 6.1 1.1 - - - +
341B HIS* 3.3 40.7 - + + +
358B LYS* 3.3 35.1 + - + +
359B THR 5.8 0.2 - - - -
360B GLN 3.6 25.4 - - - -
362B LEU* 4.3 14.4 - - + -
369B THR* 3.6 32.3 - - - -
370B ALA* 5.0 5.2 - - + -
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Residues in contact with SER 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 3.0 25.6 + - - -
283B ASN* 3.8 8.1 + - - -
286B THR* 5.3 2.3 + - - +
298B HIS* 3.4 35.0 - - - -
316B ARG 3.0 15.6 + - - -
317B ALA 3.9 0.7 - - - -
319B TRP* 1.3 89.3 - - - +
321B LEU* 1.3 57.2 + - - +
323B ASN* 3.4 6.3 + - - +
324B ALA* 3.0 27.5 + - - +
362B LEU* 5.7 0.2 - - - +
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 3.4 46.9 - - + +
298B HIS* 3.5 39.3 - - + +
299B LEU* 4.0 11.4 - - + +
302B LEU* 4.4 8.5 - - + -
317B ALA 2.9 17.4 + - - +
320B SER* 1.3 74.8 - - - +
322B GLY* 1.3 61.1 + - - +
323B ASN 3.2 0.4 - - - -
324B ALA* 3.8 1.7 - - + +
325B TYR* 2.9 42.2 + - + -
337B PHE* 3.3 34.1 - - + -
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Residues in contact with GLY 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B CYS 2.9 16.2 + - - -
319B TRP* 3.0 4.0 + - - -
321B LEU* 1.3 76.5 - - - +
323B ASN* 1.3 52.8 + - - +
325B TYR* 3.9 2.0 - - - +
326B THR* 2.7 38.6 + - - -
334B ALA* 4.0 15.2 - - - +
337B PHE* 4.2 13.4 - - - +
338B ALA* 5.0 4.0 - - - -
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Residues in contact with ASN 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B THR* 6.0 6.3 - - + -
319B TRP* 3.0 68.7 + - - -
320B SER* 3.6 6.2 - - - +
322B GLY* 1.3 76.8 - - - +
324B ALA* 1.3 56.7 + - - +
326B THR* 3.4 6.4 + - - -
327B ALA* 3.0 28.6 + - - +
358B LYS 5.7 0.3 - - - +
359B THR 5.4 0.9 - - - +
361B VAL* 3.7 30.3 - - + +
362B LEU* 5.2 1.7 - - + +
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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
----------------------------------------------------------
286B THR* 4.6 16.1 - - - +
291B TYR* 4.2 17.5 - - + +
294B ALA* 4.8 1.3 - - + -
295B ILE* 3.6 27.8 - - + +
298B HIS* 5.7 1.6 - - + -
320B SER 3.0 17.4 + - - +
321B LEU* 3.3 5.1 + - + +
323B ASN* 1.3 76.4 - - - +
325B TYR* 1.3 63.2 + - - +
327B ALA* 3.1 8.6 + - - +
328B LEU* 3.0 22.2 + - - +
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Residues in contact with TYR 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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295B ILE* 3.6 40.7 - - + +
299B LEU* 4.3 11.0 - - + +
321B LEU* 2.9 36.7 + - + +
322B GLY 3.9 3.4 - - - +
324B ALA* 1.3 75.5 - - - +
326B THR* 1.3 60.2 + - - +
328B LEU* 2.9 21.5 + - + +
329B GLY 3.0 10.7 + - - -
330B ASN* 3.2 40.1 + - + +
333B GLN* 3.3 45.4 + - + -
334B ALA* 4.1 8.1 - - - +
337B PHE* 4.5 14.2 - + - -
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Residues in contact with THR 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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322B GLY 2.7 23.4 + - - -
323B ASN* 3.6 7.8 - - - -
325B TYR* 1.3 75.1 - - - +
327B ALA* 1.3 63.6 + - - +
328B LEU 3.2 0.7 + - - -
329B GLY* 3.4 11.2 + - - +
330B ASN 4.7 2.5 - - - +
334B ALA* 3.4 19.2 - - + +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 3.6 41.2 - - + +
323B ASN 3.0 14.2 + - - +
324B ALA 3.1 8.5 + - - +
326B THR* 1.3 76.9 - - - +
328B LEU* 1.3 61.1 + - - +
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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
----------------------------------------------------------
291B TYR* 3.5 28.0 - - + +
292B GLU* 3.5 36.6 - - + +
295B ILE* 3.5 24.7 - - + -
324B ALA 3.0 10.3 + - - +
325B TYR* 2.9 17.6 + - + +
327B ALA* 1.3 80.4 - - - +
329B GLY* 1.3 57.1 + - - +
330B ASN* 3.5 6.1 - - + +
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Residues in contact with GLY 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B TYR 3.0 2.4 + - - -
326B THR* 3.4 10.8 + - - -
327B ALA 3.5 0.8 + - - -
328B LEU* 1.3 79.0 - - - +
330B ASN* 1.3 58.4 + - - +
331B HIS* 3.3 9.7 + - - +
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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
------------------------------------------------------------
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