Contacts of the helix formed by residues 307 - 323 (chain B) in PDB entry 3PDC
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 CYS 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304B GLU* 3.0 21.8 - - - +
306B TYR* 1.3 82.3 - - - +
308B MET* 1.3 69.9 + - - +
309B GLU* 3.2 9.9 + - + +
310B VAL* 3.2 30.3 + - - +
311B LEU* 3.2 16.0 + - - +
467B ASN* 2.9 30.9 - - + +
470B ARG* 3.8 26.5 - - + +
471B ASN* 3.7 4.5 - - - +
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Residues in contact with MET 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B TYR 3.7 2.9 + - - +
307B CYS* 1.3 70.0 - - - +
309B GLU* 1.3 65.5 + - - +
311B LEU* 3.2 5.8 + - + +
312B CYS* 2.8 28.3 + - - +
334B TRP* 3.9 31.0 - - + -
337B MET* 4.1 13.2 - - + -
338B LEU* 4.0 33.0 - - - +
341B TYR* 3.9 18.6 - - + -
464B TRP* 4.9 8.7 - - + +
471B ASN* 2.7 36.4 + - + +
474B TRP* 3.3 28.0 - - + -
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B CYS* 3.2 10.1 + - - +
308B MET* 1.3 77.5 - - - +
310B VAL* 1.3 65.6 + - + +
312B CYS* 3.7 1.0 - - - +
313B LYS* 2.9 58.9 + - + +
470B ARG* 6.1 1.9 - - - +
471B ASN* 4.6 0.6 + - - -
474B TRP* 2.9 53.4 + - + +
477B LYS* 4.5 9.3 + - - -
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LYS* 3.4 28.7 - - - +
292B LYS* 3.8 21.1 - - - +
304B GLU 3.7 9.0 - - - +
305B GLU* 4.1 9.2 - - - +
307B CYS* 3.2 28.7 + - - +
309B GLU* 1.3 76.1 - - + +
311B LEU* 1.3 65.0 + - - +
313B LYS* 3.1 9.7 + - - +
314B GLU* 2.9 30.9 + - + +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B MET* 6.2 0.2 - - + -
292B LYS* 3.5 42.2 - - + +
305B GLU 4.3 1.3 - - - +
306B TYR* 3.1 38.6 - - + +
307B CYS 3.2 5.5 + - - +
308B MET* 3.2 10.6 + - + +
310B VAL* 1.3 78.6 - - - +
312B CYS* 1.3 61.1 + - - +
314B GLU* 3.5 9.0 + - - +
315B MET* 3.4 33.5 + - + +
338B LEU* 4.1 14.4 - - + -
464B TRP* 3.9 41.7 - - + -
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Residues in contact with CYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B MET* 2.8 22.4 + - - +
309B GLU 3.7 2.9 - - - +
311B LEU* 1.3 71.1 - - - +
313B LYS* 1.3 65.6 + - - +
315B MET* 3.0 19.4 + - - +
316B VAL* 3.3 6.2 + - - +
338B LEU* 3.9 20.9 - - - -
341B TYR* 3.9 14.1 - - - -
342B MET* 3.3 38.3 - - - +
346B TYR* 4.5 7.2 - - + -
474B TRP* 3.9 26.5 - - + -
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Residues in contact with LYS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLU* 2.9 55.1 + - + +
310B VAL* 3.6 6.3 - - - +
312B CYS* 1.3 76.2 - - - +
314B GLU* 1.3 60.8 + - + +
316B VAL* 3.3 8.9 + - - +
317B THR* 3.0 25.6 + - - -
346B TYR* 3.2 28.3 + - + +
474B TRP* 4.0 13.5 - - - +
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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
----------------------------------------------------------
242B VAL* 3.5 15.9 - - + +
243B LYS* 3.4 26.0 - - + +
246B VAL* 3.2 21.8 - - - +
248B LEU* 4.4 8.7 - - + +
292B LYS* 3.1 43.6 + - - +
310B VAL* 2.9 22.2 + - + +
311B LEU* 3.6 17.5 - - - +
312B CYS 3.2 0.2 - - - -
313B LYS* 1.3 75.6 - - + +
315B MET* 1.3 57.4 + - - +
317B THR* 3.3 11.0 + - - -
318B PHE* 2.7 31.4 + - - +
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 3.4 31.2 - - + -
262B CYS* 5.2 1.1 - - - -
289B MET* 4.1 28.3 - - + +
291B MET* 4.5 18.2 - - + +
292B LYS 5.3 3.8 - - - +
311B LEU* 3.4 25.7 + - + +
312B CYS 3.0 10.1 + - - +
314B GLU* 1.3 77.0 - - + +
316B VAL* 1.3 65.7 + - - +
318B PHE* 3.0 20.2 + - - +
319B LEU* 3.0 17.5 + - - +
329B PHE* 4.7 11.0 - - + -
338B LEU* 4.1 23.8 - - + -
342B MET* 3.4 19.7 - - + -
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B CYS 3.6 13.5 - - - +
313B LYS* 3.6 6.5 - - - +
314B GLU 3.3 0.2 - - - -
315B MET* 1.3 74.5 - - - +
317B THR* 1.3 56.4 + - - +
319B LEU* 2.8 30.8 + - - +
320B ASP* 2.9 19.1 + - - +
342B MET* 4.4 6.5 - - + -
346B TYR* 3.8 44.9 - - + -
349B ARG* 3.5 35.4 - - + +
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B VAL* 3.6 28.3 + - + +
313B LYS* 3.0 15.4 + - - +
314B GLU* 3.4 10.2 - - - -
315B MET 3.2 0.2 - - - -
316B VAL* 1.3 78.8 - - - +
318B PHE* 1.3 60.0 + - - +
320B ASP* 3.0 18.4 + - + +
321B LYS* 3.0 50.1 + - + +
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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
----------------------------------------------------------
240B VAL* 3.9 24.5 - - + -
242B VAL* 3.8 8.5 - - + -
248B LEU* 4.5 12.6 - - + -
250B PHE* 3.7 30.1 - + - -
260B CYS* 4.8 8.7 - - - -
287B LEU* 4.1 13.7 - - + -
289B MET* 3.6 39.0 - - + -
314B GLU 2.7 17.7 + - - +
315B MET* 3.0 21.8 - - - +
317B THR* 1.3 74.5 - - - +
319B LEU* 1.3 70.4 + - + +
321B LYS* 3.7 2.8 + - - +
322B LEU* 3.3 51.2 + - + +
324B LEU* 5.5 0.7 - - + -
329B PHE* 6.0 1.1 - + - -
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Residues in contact with LEU 319 (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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260B CYS* 6.1 1.1 - - + -
315B MET 3.0 16.5 + - - +
316B VAL* 2.8 12.4 + - - +
318B PHE* 1.3 81.7 - - + +
320B ASP* 1.3 61.2 + - - +
322B LEU* 3.4 2.3 + - - +
323B GLY 2.8 24.4 + - - -
324B LEU* 2.9 46.3 + - + +
325B SER 5.1 0.2 - - - +
326B GLN 4.6 0.2 - - - +
327B ALA* 3.7 25.6 - - + -
329B PHE* 4.1 18.6 - - + -
342B MET* 4.9 1.6 - - + -
349B ARG* 3.9 46.0 - - + +
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Residues in contact with ASP 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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316B VAL* 2.9 18.9 + - - +
317B THR* 3.2 21.7 + - + +
319B LEU* 1.3 74.9 - - - +
321B LYS* 1.3 59.6 + - + +
323B GLY* 2.8 25.7 + - - -
349B ARG* 2.5 34.9 + - - +
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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
----------------------------------------------------------
240B VAL* 3.5 33.2 - - + -
241B THR* 3.2 19.3 + - - +
242B VAL* 4.1 6.3 + - - +
317B THR* 3.0 36.8 + - + +
318B PHE 3.9 0.4 - - - +
320B ASP* 1.3 80.7 - - + +
322B LEU* 1.3 59.4 + - - +
323B GLY* 4.7 0.2 - - - -
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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
----------------------------------------------------------
240B VAL* 4.2 12.3 - - + -
250B PHE* 4.5 13.7 - - + -
252B GLU* 4.8 2.2 - - - +
285B ARG* 4.4 19.7 + - - +
287B LEU* 4.1 11.7 - - + -
318B PHE* 3.3 58.7 + - + +
319B LEU 4.1 0.4 - - - +
320B ASP 3.2 1.0 - - - -
321B LYS* 1.3 79.5 - - - +
323B GLY* 1.3 64.0 + - - +
324B LEU* 3.9 22.7 - - + +
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Residues in contact with GLY 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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319B LEU 2.8 3.2 + - - -
320B ASP* 2.8 17.3 + - - -
321B LYS 3.3 0.8 + - - -
322B LEU* 1.3 81.6 - - - +
324B LEU* 1.3 62.7 + - - +
325B SER 4.1 1.1 + - - -
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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
------------------------------------------------------------
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