Contacts of the helix formed by residues 298 - 316 (chain B) in PDB entry 5I0H
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 LYS 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B LYS* 3.5 44.1 - - - +
216B ASN* 4.2 18.0 + - - +
258B ARG* 3.9 27.8 - - - +
296B GLU* 3.2 21.9 + - + +
297B ASP* 1.3 74.8 - - - +
299B THR* 1.4 53.2 + - - +
300B ILE 3.3 2.5 - - - -
301B SER* 3.0 18.0 + - - +
302B ASP* 2.8 49.4 + - - +
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ALA* 3.8 18.1 - - + +
297B ASP* 3.3 26.3 + - - -
298B LYS* 1.4 76.8 + - - +
300B ILE* 1.3 53.7 + - - +
302B ASP* 3.4 6.6 + - - +
303B GLN* 2.8 40.2 + - + +
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Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ASP* 4.4 4.1 + - - +
298B LYS 3.3 0.6 - - - -
299B THR* 1.3 76.3 - - - +
301B SER* 1.4 57.6 + - - +
303B GLN* 3.2 10.5 + - - +
304B GLU* 3.0 28.5 + - - +
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LYS* 3.0 30.4 + - - +
300B ILE* 1.4 76.2 - - - +
302B ASP* 1.3 58.3 + - - +
304B GLU* 3.4 7.3 + - - +
305B SER* 2.9 32.4 + - - -
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ARG* 2.9 42.2 + - - -
261B HIS* 4.8 2.3 - - - +
264B TYR* 3.4 30.7 - - - +
265B ALA* 3.4 17.1 + - - +
268B ALA* 3.9 4.7 - - + -
298B LYS* 2.8 32.1 + - - +
299B THR* 3.8 4.7 - - - +
301B SER* 1.3 71.0 + - - +
303B GLN* 1.3 65.0 + - - +
305B SER* 3.3 7.0 + - - -
306B PHE 3.0 17.5 + - - -
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Residues in contact with GLN 303 (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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268B ALA* 3.7 31.2 + - + +
269B GLY* 4.3 8.8 + - - +
299B THR* 2.8 26.2 + - + +
300B ILE* 3.6 8.8 - - - +
302B ASP* 1.3 74.2 - - - +
304B GLU* 1.4 61.1 + - - +
306B PHE* 3.2 5.8 + - - +
307B ARG* 3.2 20.1 + - - +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ILE 3.0 16.3 + - - +
301B SER* 3.7 8.5 - - - +
302B ASP 3.3 0.2 - - - -
303B GLN* 1.4 73.6 - - - +
305B SER* 1.4 63.9 + - - +
307B ARG* 3.3 9.3 + - - +
308B GLU* 3.1 23.8 + - - +
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA* 6.1 2.5 - - - -
261B HIS* 5.9 7.0 - - - +
265B ALA* 4.4 9.9 - - - -
301B SER 2.9 16.0 + - - -
302B ASP* 3.3 12.7 + - - -
304B GLU* 1.4 71.9 - - - +
306B PHE* 1.4 60.5 + - - +
308B GLU* 3.2 13.9 + - - +
309B VAL* 2.9 37.3 + - - +
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE* 4.7 12.6 - - + -
265B ALA* 3.3 38.7 - - + +
266B LEU* 3.7 23.8 - - + -
269B GLY* 3.6 31.2 - - - -
270B LEU* 4.0 23.6 - - + -
302B ASP 3.0 7.9 + - - +
303B GLN 3.2 9.2 + - - +
305B SER* 1.4 75.1 - - - +
307B ARG* 1.3 58.1 + - - +
309B VAL* 3.2 6.3 + - + +
310B ILE* 2.9 64.0 + - + +
323B VAL* 5.7 0.4 - - + -
327B SER* 4.6 6.1 - - - -
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Residues in contact with ARG 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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303B GLN 3.2 9.0 + - - +
304B GLU* 3.5 11.7 - - - +
305B SER 3.3 0.2 - - - -
306B PHE* 1.3 78.0 - - - +
308B GLU* 1.3 60.9 + - - +
310B ILE* 3.4 9.0 + - - +
311B THR* 3.1 29.5 + - - -
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLU* 4.6 2.8 - - - +
202B PRO* 3.7 28.5 - - + +
304B GLU 3.1 14.7 + - - +
305B SER* 3.2 16.2 + - - +
307B ARG* 1.3 73.7 - - - +
309B VAL* 1.3 59.7 + - - +
311B THR* 3.5 7.3 + - - -
312B ALA* 3.0 28.8 + - - +
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PRO* 3.8 13.9 - - + +
203B ILE* 4.8 6.1 - - + -
206B ALA* 3.5 27.4 - - + -
207B PHE* 4.6 8.5 - - + -
262B ILE* 4.2 21.1 - - + -
265B ALA* 5.6 0.7 - - + -
305B SER* 2.9 24.3 + - - +
306B PHE* 3.6 8.3 - - + +
308B GLU* 1.3 73.6 - - - +
310B ILE* 1.3 56.4 + - + +
312B ALA* 3.2 6.7 + - - +
313B MET* 2.8 56.5 + - + +
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PHE* 2.9 57.0 + - + +
307B ARG* 3.7 8.1 - - - +
309B VAL* 1.3 77.7 - - + +
311B THR* 1.3 62.8 + - - +
313B MET* 3.4 10.7 + - - +
314B ASP* 3.1 23.4 + - + +
323B VAL* 3.6 32.8 - - + +
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Residues in contact with THR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ARG* 4.6 17.7 - - - +
199B GLU* 4.7 9.4 - - - +
307B ARG 3.1 17.7 + - - -
308B GLU* 3.7 7.4 - - - -
310B ILE* 1.3 74.2 - - - +
312B ALA* 1.4 66.8 + - - +
314B ASP* 3.3 9.2 + - - +
315B VAL* 3.1 27.1 + - + +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLU* 3.3 48.4 + - - +
202B PRO* 3.9 5.6 - - + -
203B ILE* 3.6 13.5 - - + +
308B GLU 3.0 15.9 + - - +
309B VAL* 3.2 4.9 + - - +
311B THR* 1.4 77.2 - - - +
313B MET* 1.4 56.4 + - - +
315B VAL* 3.2 4.7 + - - +
316B MET* 2.9 30.3 + - - +
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Residues in contact with MET 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 3.9 19.7 - - + -
207B PHE* 5.1 10.1 - - + -
309B VAL* 2.8 41.1 + - + +
310B ILE* 3.8 7.4 - - - +
311B THR 3.3 0.2 - - - -
312B ALA* 1.4 70.7 - - - +
314B ASP* 1.3 60.5 + - - +
316B MET 3.2 5.4 + - - -
317B GLN 3.3 0.2 + - - -
318B PHE* 3.0 78.2 + - + -
323B VAL* 3.9 36.1 - - + -
326B VAL* 4.6 18.8 - - + -
413B VAL* 5.4 0.9 - - + -
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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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310B ILE* 3.1 13.7 + - + +
311B THR* 3.4 12.5 - - - +
313B MET* 1.3 75.5 - - - +
315B VAL* 1.3 69.3 + - - +
317B GLN* 3.1 16.1 + - - +
318B PHE 4.4 8.9 - - - +
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Residues in contact with VAL 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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190B THR 4.9 3.4 - - - +
195B ARG* 3.4 45.3 - - + +
196B ALA* 4.0 23.3 - - + +
199B GLU* 3.7 26.2 - - + -
311B THR* 3.1 17.4 + - + +
312B ALA 3.5 7.2 - - - +
314B ASP* 1.3 79.4 - - - +
316B MET* 1.4 56.3 + - - +
317B GLN* 3.3 5.4 + - - +
420B ARG* 3.1 26.0 + - - +
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Residues in contact with MET 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ALA* 3.2 30.3 - - - +
199B GLU* 3.6 16.2 - - + +
200B SER* 3.5 23.1 - - - +
203B ILE* 3.8 7.6 - - + -
312B ALA 2.9 11.6 + - - +
313B MET 3.6 5.8 - - - +
314B ASP 3.2 0.8 - - - -
315B VAL* 1.4 72.7 - - - +
317B GLN* 1.3 69.4 + - - +
318B PHE* 3.4 26.0 + - + -
416B LYS* 4.4 6.8 - - - +
417B ILE* 3.9 32.5 - - + +
420B ARG* 3.6 32.3 - - + +
421B ILE* 4.6 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
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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