Contacts of the helix formed by residues 298 - 318 (chain B) in PDB entry 1IAS
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 THR 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297B VAL* 1.3 81.3 - - - +
299B VAL* 1.3 73.4 + - + +
300B GLU* 2.9 28.0 - - + +
301B GLY* 3.5 9.0 - - - -
302B MET* 2.8 27.2 + - - +
415B CYS* 3.8 0.6 - - - -
416B SER 4.8 5.2 - - - -
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B THR* 1.3 78.0 - - + +
300B GLU* 1.3 63.6 + - - +
302B MET* 3.4 3.2 + - + +
303B ILE* 3.1 34.2 + - + +
415B CYS* 3.6 22.6 - - - -
416B SER 5.2 1.7 + - - +
417B ILE* 3.7 29.6 - - + -
461B CYS* 4.3 8.1 - - - -
463B ALA* 3.5 30.1 - - + -
464B LEU* 4.5 0.2 - - + -
499B GLU* 5.0 9.6 - - - +
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B THR* 2.9 15.4 - - + +
299B VAL* 1.3 77.5 - - - +
301B GLY* 1.3 66.0 + - - +
303B ILE* 3.1 6.0 + - - +
304B LYS* 3.0 44.4 + - + +
499B GLU* 6.3 0.4 - - + -
501B ILE* 3.5 45.9 - - + +
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Residues in contact with GLY 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B VAL* 3.4 24.2 - - - -
298B THR* 3.1 10.1 + - - -
300B GLU* 1.3 81.8 + - - +
302B MET* 1.3 61.1 + - - +
304B LYS* 3.2 12.5 + - - +
305B LEU* 3.1 25.7 + - - +
345B GLY 4.8 0.2 - - - +
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Residues in contact with MET 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B VAL* 3.6 15.3 - - + +
298B THR 2.8 18.4 + - - +
299B VAL* 3.5 11.9 - - + +
301B GLY* 1.3 73.2 - - - +
303B ILE* 1.3 69.1 + - + +
305B LEU* 3.4 2.6 + - - +
306B ALA* 3.0 22.9 + - - +
411B ILE* 3.7 22.1 - - + +
412B ALA* 3.7 29.8 - - - -
415B CYS* 3.7 19.5 - - - -
463B ALA* 3.9 23.3 - - + -
464B LEU* 4.2 9.4 - - + -
467B MET* 3.9 29.2 - - + -
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Residues in contact with ILE 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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299B VAL* 3.1 25.3 + - + +
300B GLU* 3.1 6.0 + - - +
302B MET* 1.3 82.5 - - + +
304B LYS* 1.3 57.2 + - - +
306B ALA* 3.3 3.9 + - - -
307B LEU* 2.7 42.4 + - + +
463B ALA* 4.5 1.1 - - + -
467B MET* 6.0 1.8 - - + -
492B LEU* 4.2 15.3 - - + +
495B LEU* 3.9 25.6 - - + +
496B SER* 4.0 20.4 - - - +
499B GLU* 3.8 22.2 - - + -
501B ILE* 3.7 27.6 - - + -
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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
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300B GLU* 3.0 41.7 + - + +
301B GLY* 3.3 10.6 - - - +
303B ILE* 1.3 77.0 - - - +
305B LEU* 1.3 61.4 + - - +
307B LEU* 3.9 5.2 - - - +
308B SER* 3.0 27.5 + - - -
344B ASN* 3.4 25.9 + - - +
345B GLY* 3.4 16.7 + - - +
346B THR* 4.8 6.8 - - + +
501B ILE* 4.0 21.7 - - + +
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Residues in contact with LEU 305 (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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288B LEU* 4.0 18.6 - - + -
291B TYR* 4.1 18.2 - - + +
292B LEU* 4.4 5.6 - - + -
297B VAL* 5.0 7.4 - - + -
301B GLY 3.1 16.0 + - - +
302B MET* 3.7 5.2 - - - +
304B LYS* 1.3 76.7 - - - +
306B ALA* 1.3 61.5 + - - +
308B SER* 2.8 20.3 + - - -
309B THR* 3.0 16.1 + - - -
341B VAL* 4.4 12.8 - - + -
345B GLY* 3.2 28.5 - - - +
347B CYS* 3.7 20.6 - - - -
411B ILE* 4.0 27.4 - - + -
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Residues in contact with ALA 306 (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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302B MET 3.0 16.9 + - - +
303B ILE* 4.0 2.2 - - - +
305B LEU* 1.3 76.4 - - - +
307B LEU* 1.3 62.7 + - - +
309B THR 3.4 0.2 + - - -
310B ALA* 3.0 19.8 + - - +
408B PHE* 3.3 32.4 - - + -
411B ILE* 4.2 5.7 - - + +
467B MET* 3.9 23.8 - - + -
492B LEU* 3.4 17.7 - - + -
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Residues in contact with LEU 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 ILE* 2.7 23.9 + - + +
304B LYS* 3.9 4.7 - - - +
306B ALA* 1.3 72.4 - - - +
308B SER* 1.3 52.8 + - - +
310B ALA* 3.1 2.6 + - - +
311B SER* 2.8 51.0 + - - +
489B LYS* 4.0 27.6 - - + +
492B LEU* 3.5 26.2 - - + +
493B SER* 4.4 16.2 - - - +
496B SER* 4.6 14.6 - - - +
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Residues in contact with SER 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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258B ASN* 3.2 25.3 - - - +
304B LYS 3.0 12.8 + - - -
305B LEU* 2.8 14.0 + - - -
307B LEU* 1.3 76.4 - - - +
309B THR* 1.3 69.9 + - - +
311B SER* 3.0 3.5 + - - -
312B GLY 2.9 19.8 + - - -
346B THR* 3.2 33.0 - - - -
347B CYS* 2.9 21.1 + - - +
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Residues in contact with THR 309 (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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258B ASN* 5.4 0.7 - - - -
288B LEU* 4.8 3.3 - - - +
305B LEU 3.0 17.3 + - - -
306B ALA 3.8 3.1 - - - -
308B SER* 1.3 82.5 + - - +
310B ALA* 1.3 63.3 + - - +
312B GLY* 3.3 1.0 + - - -
313B LEU* 3.0 18.7 + - - +
334B LEU* 5.5 1.8 - - + -
339B ILE* 3.9 27.8 - - + +
347B CYS* 3.5 21.6 - - - +
349B ILE* 4.0 15.5 - - + +
404B MET* 3.1 30.9 - - + +
407B VAL* 5.2 3.6 - - + -
408B PHE* 4.4 7.2 - - + -
411B ILE* 5.2 1.3 - - - +
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Residues in contact with ALA 310 (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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306B ALA 3.0 18.1 + - - +
307B LEU* 3.5 5.8 - - - +
309B THR* 1.3 76.2 - - - +
311B SER* 1.3 53.8 + - - +
313B LEU* 3.2 1.6 + - - +
314B ALA* 2.8 38.2 + - - +
404B MET* 3.3 16.8 - - + +
408B PHE* 4.3 1.3 - - + -
485B ALA* 4.4 3.4 - - - +
488B ILE* 4.1 27.1 - - + -
489B LYS* 4.1 15.9 - - - +
492B LEU* 4.5 0.4 - - + -
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Residues in contact with SER 311 (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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256B HIS* 3.7 7.5 + - - -
258B ASN* 2.9 27.1 + - - -
307B LEU* 2.8 37.7 + - - +
308B SER* 3.3 2.9 - - - -
310B ALA* 1.3 72.4 - - - +
312B GLY* 1.3 54.6 + - - +
314B ALA* 3.4 5.9 + - - +
315B HIS* 3.0 27.2 + - - +
489B LYS* 3.5 29.1 + - - +
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Residues in contact with GLY 312 (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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256B HIS* 4.0 7.0 - - - -
258B ASN* 3.6 29.5 - - - +
259B ILE* 4.3 3.0 - - - +
308B SER 2.9 10.7 + - - -
309B THR 3.8 2.2 - - - -
310B ALA 3.2 0.2 - - - -
311B SER* 1.3 73.8 - - - +
313B LEU* 1.3 63.8 - - - +
314B ALA 3.0 1.3 - - - -
315B HIS* 2.9 5.0 + - - +
316B LEU* 2.9 24.3 + - - +
349B ILE* 4.3 6.1 - - - -
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Residues in contact with LEU 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 THR 3.0 6.4 + - - +
310B ALA 3.9 1.3 - - - +
312B GLY* 1.3 74.0 - - - +
314B ALA* 1.3 61.8 + - - +
316B LEU* 3.4 17.2 + - + +
317B HIS* 3.1 57.7 + - + +
331B HIS* 4.8 1.6 - - + -
334B LEU* 3.7 28.7 - - + -
349B ILE* 4.2 5.3 - - + +
400B ASP* 3.9 10.5 - - - +
401B ILE* 3.8 21.1 - - + -
404B MET* 3.4 43.1 - - + -
485B ALA* 3.9 4.5 - - + -
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Residues in contact with ALA 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 ALA 2.8 17.6 + - - +
311B SER* 3.4 10.1 - - - +
312B GLY 3.0 0.2 - - - -
313B LEU* 1.3 77.6 - - - +
315B HIS* 1.3 56.8 + - - +
317B HIS* 3.3 2.3 + - - +
318B MET* 2.9 35.2 + - + +
485B ALA* 3.5 29.1 - - + +
486B LEU* 4.0 13.4 - - + +
489B LYS* 4.5 10.3 - - + +
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Residues in contact with HIS 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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253B MET 5.9 0.2 - - - -
254B LEU* 3.6 32.1 - - + +
255B ARG 3.9 15.2 + - - -
256B HIS* 3.1 36.6 + + + +
259B ILE* 4.3 0.8 - - + +
311B SER 3.0 12.8 + - - +
312B GLY 2.9 8.6 + - - +
314B ALA* 1.3 78.7 - - - +
316B LEU* 1.3 60.6 + - - +
318B MET* 3.5 19.0 + - - +
320B ILE* 5.0 12.2 - - + +
326B LYS* 3.1 29.6 + - + -
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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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254B LEU* 3.7 30.1 - - + -
259B ILE* 3.7 17.9 - - + -
312B GLY 2.9 9.6 + - - +
313B LEU* 3.7 17.7 - - + +
315B HIS* 1.3 78.7 + - - +
317B HIS* 1.3 54.5 + - + +
326B LYS* 3.0 13.9 + - - +
329B ILE* 2.7 61.4 + - + +
331B HIS* 4.4 15.7 - - + +
349B ILE* 4.4 26.7 - - + -
352B LEU* 4.6 12.8 - - + -
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Residues in contact with HIS 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 LEU* 3.1 40.8 + - + +
314B ALA* 3.9 4.3 - - - +
316B LEU* 1.3 75.8 - - + +
318B MET* 1.3 63.6 + - - +
319B GLU* 3.5 0.9 + - - +
328B ALA* 3.2 17.2 - - - +
329B ILE 3.0 29.2 - - - +
330B ALA* 4.2 0.7 - - - -
397B LYS* 3.4 69.6 + - + +
400B ASP* 2.8 30.6 + - + -
401B ILE* 4.3 5.0 - - + +
485B ALA* 4.1 13.3 + - + +
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Residues in contact with MET 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ALA* 2.9 22.8 + - + +
315B HIS* 3.7 14.8 - - + +
316B LEU 3.2 0.4 - - - -
317B HIS* 1.3 78.5 - - - +
319B GLU* 1.3 72.1 + - - +
320B ILE* 4.1 19.3 - - + -
326B LYS* 2.9 33.8 + - - +
327B PRO 3.6 0.5 - - - +
328B ALA* 4.3 0.4 - - - -
397B LYS* 5.5 0.2 - - - +
486B LEU* 3.6 34.8 - - + -
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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