Contacts of the helix formed by residues 301 - 318 (chain B) in PDB entry 2RIO
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 PRO 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B PHE 3.9 5.4 - - - +
300B TRP* 1.3 89.3 - - + +
302B LYS* 1.3 61.2 + - - +
303B SER* 4.0 14.4 - - - +
304B LYS* 3.0 21.0 + - + +
305B LYS* 3.0 23.4 + - - +
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Residues in contact with LYS 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP* 4.2 13.4 + - - -
268B LEU* 5.8 8.3 - - - +
300B TRP 3.8 1.0 + - - +
301B PRO* 1.3 73.0 - - - +
303B SER* 1.3 53.4 + - - +
305B LYS* 3.7 13.7 - - + +
306B LEU* 2.7 35.5 + - - +
396B PRO* 5.1 0.7 - - - -
397B ASP* 3.6 33.7 + - + +
400B TYR* 3.8 25.3 - - + -
401B ASP* 2.7 40.3 + - - +
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A GLU* 4.5 17.7 + - - +
301B PRO* 4.0 12.2 - - - +
302B LYS* 1.3 76.7 - - - +
304B LYS* 1.3 62.2 + - - +
306B LEU* 3.9 2.7 - - - +
307B GLU* 3.0 29.5 + - - +
396B PRO* 3.8 33.4 - - - -
397B ASP* 4.0 4.7 + - - -
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TRP* 3.5 43.8 - - + +
301B PRO* 3.0 25.6 + - + +
303B SER* 1.3 79.0 + - - +
305B LYS* 1.3 59.5 + - - +
307B GLU* 3.2 5.2 + - - +
308B PHE* 2.9 30.1 + - - +
430B GLU 4.7 0.6 + - - -
431B PHE* 3.6 43.2 + - + +
434B SER* 4.0 22.6 + - - -
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B SER* 5.2 1.0 + - - -
268B LEU* 3.5 19.6 - - - +
271B GLU* 2.5 38.0 + - - -
297B PRO 3.1 21.6 + - - -
298B LEU 4.7 2.4 + - - -
300B TRP* 3.6 39.9 + - + +
301B PRO 3.0 12.5 + - - +
302B LYS* 3.7 15.2 - - + +
304B LYS* 1.3 76.3 - - - +
306B LEU* 1.3 62.1 + - - +
308B PHE* 3.4 3.5 - - - +
309B LEU* 3.3 24.9 + - - +
400B TYR* 3.4 33.1 + - + +
411B LEU* 3.7 11.4 - - + +
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LYS 2.7 20.8 + - - +
303B SER 3.9 3.8 - - - +
305B LYS* 1.3 72.8 - - - +
307B GLU* 1.3 61.9 + - - +
309B LEU* 3.3 4.4 + - + +
310B LEU* 3.1 31.3 + - + +
374B LEU* 3.8 19.3 - - + -
378B TYR* 4.0 17.3 - - + -
395B VAL* 4.5 0.2 - - + -
396B PRO* 3.9 36.8 - - + +
399B PHE* 3.8 35.7 - - + -
400B TYR* 3.7 19.6 - - + -
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Residues in contact with GLU 307 (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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307A GLU* 3.5 22.4 - - + +
311A LYS* 2.9 44.0 + - - -
431A PHE* 4.6 3.6 - - - -
303B SER 3.0 19.9 + - - +
304B LYS* 3.2 5.3 + - - +
306B LEU* 1.3 73.8 - - - +
308B PHE* 1.3 65.0 + - - +
310B LEU* 3.4 15.5 + - + +
311B LYS* 2.9 43.2 + - - +
378B TYR* 4.2 2.6 + - - -
431B PHE* 3.9 19.3 - - + -
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Residues in contact with PHE 308 (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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300B TRP* 3.7 14.8 - + + -
304B LYS 2.9 13.2 + - - +
305B LYS 3.4 9.2 - - - +
307B GLU* 1.3 77.7 - - - +
309B LEU* 1.3 60.4 + - + +
311B LYS* 3.5 2.6 - - - +
312B VAL* 2.9 47.1 + - + +
411B LEU* 4.0 18.6 - - + -
414B VAL* 4.2 3.6 - - + -
415B TYR* 3.8 39.9 - + + -
418B VAL* 3.8 36.8 - - + -
428B LEU* 4.5 7.2 - - + -
431B PHE* 3.6 38.9 - + + -
432B LEU* 4.2 4.9 - - + -
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LYS 3.3 9.7 + - - +
306B LEU* 3.3 7.8 + - - +
308B PHE* 1.3 80.5 - - + +
310B LEU* 1.3 56.7 - - - +
312B VAL* 3.6 4.1 + - - +
313B SER* 3.0 28.2 + - - -
371B LEU* 3.9 19.0 - - + +
374B LEU* 3.8 19.9 - - + +
400B TYR* 4.0 26.5 - - + +
404B THR* 5.2 0.2 - - + -
410B LEU* 3.8 26.9 - - + +
411B LEU* 3.9 24.0 - - + +
414B VAL* 3.9 35.4 - - + -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LYS* 4.6 2.7 - - - +
306B LEU* 3.1 23.5 + - + +
307B GLU* 3.6 29.4 - - + +
308B PHE 3.2 0.2 - - - -
309B LEU* 1.3 77.3 - - - +
311B LYS* 1.3 57.6 + - + +
313B SER* 3.3 7.7 + - - -
314B ASP* 3.1 34.4 + - - +
374B LEU* 3.7 23.6 - - + -
375B ARG* 3.8 24.2 - - + +
378B TYR* 3.7 48.0 - - + -
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 2.9 34.9 + - - -
310A LEU* 4.6 0.8 - - - +
378A TYR* 2.7 34.2 + - + +
307B GLU* 2.9 33.3 + - + +
308B PHE* 3.5 4.0 - - - +
310B LEU* 1.3 72.8 - - + +
312B VAL* 1.3 66.5 + - - +
314B ASP* 3.3 7.6 + - + +
315B ARG* 2.9 24.6 + - - +
427B ILE* 3.9 18.0 - - + +
428B LEU* 3.8 18.3 - - + +
431B PHE* 3.9 20.9 - - + -
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 2.9 38.8 + - + +
309B LEU 3.9 4.0 - - - +
311B LYS* 1.3 73.3 - - - +
313B SER* 1.3 64.4 + - - +
315B ARG* 3.4 6.1 + - - +
316B LEU* 3.1 30.8 + - + +
331B PHE* 3.9 21.3 - - + -
371B LEU* 4.0 8.7 - - + -
414B VAL* 3.7 28.0 - - + -
418B VAL* 3.6 24.2 - - + -
428B LEU* 4.2 10.5 - - + -
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Residues in contact with SER 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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309B LEU 3.0 16.3 + - - -
310B LEU 3.3 9.4 + - - -
312B VAL* 1.3 78.1 - - - +
314B ASP* 1.3 62.6 + - - +
316B LEU* 3.1 13.3 + - - +
317B GLU* 3.2 15.6 + - - +
368B MET 5.2 0.5 + - - -
371B LEU* 3.6 22.3 + - - +
372B ARG* 3.0 32.4 + - - -
375B ARG* 3.5 16.8 - - - +
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Residues in contact with ASP 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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379A HIS* 4.0 21.1 + - + -
310B LEU* 3.1 21.4 + - - +
311B LYS* 3.8 8.3 - - + +
313B SER* 1.3 73.2 - - - +
315B ARG* 1.3 64.1 + - - +
316B LEU 3.4 0.2 + - - -
317B GLU* 3.5 11.5 - - - +
318B ILE* 3.3 18.7 - - - +
372B ARG* 2.9 30.3 + - - +
375B ARG* 2.9 26.3 + - - -
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Residues in contact with ARG 315 (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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382A MET* 3.6 29.1 - - - +
311B LYS 2.9 17.0 + - - +
312B VAL* 3.4 4.9 + - - +
314B ASP* 1.3 75.0 - - - +
316B LEU* 1.3 64.8 + - + +
317B GLU 3.5 0.7 + - - -
318B ILE* 3.5 23.5 - - - +
319B GLU* 3.0 28.5 + - - +
327B LEU* 4.2 8.6 - - + +
422B LEU* 3.7 26.5 - - + +
425B ASP* 2.6 40.5 + - - +
427B ILE* 6.4 1.8 - - - -
428B LEU* 4.1 21.5 - - + -
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Residues in contact with LEU 316 (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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312B VAL* 3.1 23.3 + - + +
313B SER* 3.1 6.5 + - - +
315B ARG* 1.3 78.4 - - + +
317B GLU* 1.3 58.5 + - - +
318B ILE 3.3 0.2 - - - -
319B GLU* 3.2 28.9 + - - +
327B LEU* 4.2 16.6 - - + -
328B LEU* 3.9 18.5 - - + +
331B PHE* 3.8 49.1 - - + -
368B MET* 3.3 36.3 - - + +
371B LEU* 4.2 15.0 - - + -
422B LEU* 4.7 5.2 - - + -
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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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313B SER 3.2 8.2 + - - +
314B ASP* 3.5 15.3 - - - +
316B LEU* 1.3 74.2 - - - +
318B ILE* 1.3 62.0 + - + +
319B GLU 3.3 6.2 + - - +
360B ARG* 2.9 19.5 + - - +
361B LYS* 3.1 26.9 + - - +
368B MET* 4.1 5.9 - - - +
372B ARG* 3.3 44.0 + - - +
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Residues in contact with ILE 318 (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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379A HIS 4.9 11.7 - - - +
382A MET* 3.8 54.1 - - + -
383A ASP* 5.7 5.6 - - - +
314B ASP 3.3 26.0 - - - +
315B ARG* 3.5 11.6 + - - +
317B GLU* 1.3 76.8 - - + +
319B GLU* 1.3 72.9 + - - +
320B ASN 3.5 1.9 + - - -
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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