Contacts of the helix formed by residues 298 - 318 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297E VAL* 1.3 81.4 - - - +
299E VAL* 1.3 73.0 + - + +
300E GLU* 2.9 28.0 - - + +
301E GLY* 3.5 9.4 - - - -
302E MET* 2.8 27.0 + - - +
415E CYS* 3.9 1.1 - - - -
416E SER 5.0 4.3 - - - -
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Residues in contact with VAL 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E THR* 1.3 77.5 - - + +
300E GLU* 1.3 63.4 + - - +
302E MET* 3.4 3.4 + - - +
303E ILE* 3.1 34.0 + - + +
415E CYS* 3.7 22.6 - - - -
416E SER 5.4 1.7 + - - +
417E ILE* 3.9 27.8 - - + -
461E CYS* 4.3 7.9 - - - -
463E ALA* 3.4 29.4 - - + -
464E LEU* 4.5 0.4 - - + -
499E GLU* 4.4 14.1 - - - +
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Residues in contact with GLU 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E THR* 2.9 16.0 - - + +
299E VAL* 1.3 77.7 - - - +
301E GLY* 1.3 66.2 + - - +
303E ILE* 3.1 14.9 + - + +
304E LYS* 3.0 50.1 + - + +
499E GLU* 6.1 5.6 - - + -
500E GLY 4.8 14.9 - - - +
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Residues in contact with GLY 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E VAL* 3.4 23.8 - - - -
298E THR* 3.2 11.2 + - - -
300E GLU* 1.3 81.3 - - - +
302E MET* 1.3 61.5 + - - +
304E LYS* 3.1 20.6 + - - +
305E LEU* 3.1 18.2 + - - +
345E GLY 4.8 0.2 - - - +
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Residues in contact with MET 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E VAL* 3.6 16.4 - - + +
298E THR 2.8 19.8 + - - +
299E VAL* 3.6 9.9 - - + +
301E GLY* 1.3 71.2 - - - +
303E ILE* 1.3 67.7 + - + +
305E LEU* 3.4 3.8 + - - +
306E ALA* 3.0 22.0 + - - +
411E ILE* 3.7 22.9 - - + +
412E ALA* 3.9 17.0 - - - -
415E CYS* 3.8 26.9 - - - -
463E ALA* 3.9 28.7 - - + -
464E LEU* 4.3 8.3 - - + -
467E MET* 3.9 32.3 - - + -
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Residues in contact with ILE 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E VAL* 3.1 26.4 + - + +
300E GLU* 3.1 10.7 + - + +
302E MET* 1.3 83.3 - - + +
304E LYS* 1.3 59.5 + - + +
306E ALA* 3.3 4.4 + - - -
307E LEU* 2.7 42.3 + - + +
467E MET* 6.0 1.3 - - + -
492E LEU* 4.2 15.4 - - + +
495E LEU* 3.8 33.2 - - + +
496E SER* 3.7 31.4 - - - +
499E GLU* 4.2 21.5 - - + -
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Residues in contact with LYS 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E GLU* 3.0 44.8 + - + +
301E GLY* 3.3 11.7 - - - +
303E ILE* 1.3 76.5 - - + +
305E LEU* 1.3 58.1 + - - +
307E LEU* 3.8 4.1 - - - +
308E SER* 2.9 33.8 + - - -
344E ASN 3.5 25.7 + - - -
345E GLY* 3.4 16.2 + - - +
346E THR* 4.9 5.7 - - + +
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Residues in contact with LEU 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E LEU* 3.9 19.1 - - + -
291E TYR* 4.1 18.6 - - + +
292E LEU* 4.4 4.7 - - + -
297E VAL* 5.0 7.4 - - + -
301E GLY 3.1 15.8 + - - +
302E MET* 3.7 5.6 - - - +
304E LYS* 1.3 79.9 - - - +
306E ALA* 1.3 60.1 + - - +
308E SER* 2.9 14.6 + - - -
309E THR* 2.9 22.7 + - - -
341E VAL* 4.4 13.0 - - + -
345E GLY* 3.3 27.1 - - - +
347E CYS* 3.7 21.9 - - - -
411E ILE* 4.1 26.5 - - + -
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Residues in contact with ALA 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302E MET 3.0 16.9 + - - +
303E ILE* 4.0 2.0 - - - +
305E LEU* 1.3 76.1 - - - +
307E LEU* 1.3 64.5 + - - +
310E ALA* 2.9 19.9 + - - +
408E PHE* 3.4 33.2 - - + -
411E ILE* 4.3 5.1 - - + +
467E MET* 4.0 22.9 - - + -
492E LEU* 3.5 18.6 - - + -
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Residues in contact with LEU 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E ILE* 2.7 24.8 + - + +
304E LYS* 3.8 4.3 - - - +
306E ALA* 1.3 72.1 - - - +
308E SER* 1.3 57.3 + - - +
310E ALA* 3.1 2.9 + - - +
311E SER* 2.8 44.0 + - - +
489E LYS* 4.0 29.2 - - + +
492E LEU* 3.5 25.7 - - + +
493E SER* 4.3 16.6 - - - +
496E SER* 4.4 15.9 - - - +
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Residues in contact with SER 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ASN* 3.5 16.7 - - - +
304E LYS 2.9 13.6 + - - -
305E LEU* 2.9 12.1 + - - -
307E LEU* 1.3 76.4 - - - +
309E THR* 1.3 71.3 + - - +
311E SER* 3.0 9.1 + - - -
312E GLY 2.9 20.6 + - - -
346E THR* 3.2 31.4 - - - -
347E CYS* 2.8 23.7 + - - +
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Residues in contact with THR 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ASN* 5.6 0.7 - - - -
288E LEU* 4.9 3.6 - - - +
305E LEU 2.9 17.5 + - - -
306E ALA 3.7 3.8 - - - -
308E SER* 1.3 81.2 + - - +
310E ALA* 1.3 62.2 + - - +
312E GLY* 3.4 1.2 + - - -
313E LEU* 3.0 18.7 + - - +
334E LEU* 5.4 1.8 - - + -
339E ILE* 3.8 27.5 - - + +
347E CYS* 3.5 21.6 - - - +
348E CYS* 6.3 0.2 - - - +
349E ILE* 3.9 14.6 - - + +
404E MET* 3.1 30.2 - - + +
407E VAL* 5.2 3.6 - - + -
408E PHE* 4.4 7.2 - - + -
411E ILE* 5.2 1.4 - - - +
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Residues in contact with ALA 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E ALA 2.9 18.3 + - - +
307E LEU* 3.4 5.6 - - - +
309E THR* 1.3 76.7 - - - +
311E SER* 1.3 51.5 - - - +
313E LEU* 3.2 1.7 + - - +
314E ALA* 2.8 37.6 + - - +
404E MET* 3.3 17.0 - - + +
408E PHE* 4.3 1.3 - - + -
485E ALA* 4.4 5.4 - - - +
488E ILE* 4.2 14.6 - - + -
489E LYS* 4.2 26.2 - - - +
492E LEU* 4.6 0.4 - - + -
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Residues in contact with SER 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E HIS* 3.9 5.3 + - - -
258E ASN* 3.1 25.3 + - - -
307E LEU* 2.8 36.4 + - - +
308E SER* 3.0 5.1 + - - -
310E ALA* 1.3 72.5 - - - +
312E GLY* 1.3 56.9 + - - +
314E ALA* 3.3 6.5 - - - +
315E HIS* 3.0 27.7 + - - +
489E LYS* 3.4 28.4 + - - +
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Residues in contact with GLY 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E HIS* 4.2 7.4 - - - -
258E ASN* 3.6 28.4 - - - +
259E ILE* 4.4 2.4 - - - +
308E SER 2.9 10.7 + - - -
309E THR 3.8 2.2 - - - -
311E SER* 1.3 74.8 - - - +
313E LEU* 1.3 64.1 + - - +
315E HIS* 3.0 4.5 + - - +
316E LEU* 2.9 24.8 + - - +
349E ILE* 4.3 7.9 - - - -
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Residues in contact with LEU 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E THR 3.0 7.0 + - - +
310E ALA 3.9 1.6 - - - +
312E GLY* 1.3 74.9 - - - +
314E ALA* 1.3 61.9 + - - +
316E LEU* 4.4 16.4 - - + -
317E HIS* 3.1 55.9 + - + +
331E HIS* 4.7 2.5 - - + -
334E LEU* 3.8 27.6 - - + -
349E ILE* 4.2 5.9 - - + +
400E ASP* 4.0 11.2 - - + +
401E ILE* 3.8 21.8 - - + -
404E MET* 3.5 44.2 - - + -
485E ALA* 4.0 3.4 - - + -
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Residues in contact with ALA 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E ALA 2.8 18.7 + - - +
311E SER* 3.3 9.9 - - - +
313E LEU* 1.3 78.2 - - - +
315E HIS* 1.3 58.2 + - - +
317E HIS* 3.3 3.4 + - - +
318E MET* 2.9 35.7 + - + +
485E ALA* 3.6 27.3 - - + +
486E LEU* 4.2 12.8 - - + +
489E LYS* 4.6 9.4 - - + +
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Residues in contact with HIS 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E LEU* 3.6 31.5 - - + +
255E ARG 4.6 7.2 + - - -
256E HIS* 3.0 45.3 + + + +
259E ILE* 4.4 1.9 - - + +
311E SER 3.0 14.0 + - - +
312E GLY 3.0 7.6 + - - +
314E ALA* 1.3 78.4 - - - +
316E LEU* 1.3 57.8 + - - +
318E MET* 3.4 18.8 + - - +
320E ILE* 4.9 12.4 - - + +
326E LYS* 2.9 35.1 + - + -
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Residues in contact with LEU 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E LEU* 4.0 25.4 - - + -
259E ILE* 3.6 18.2 - - + -
312E GLY 2.9 11.0 + - - +
313E LEU* 3.7 18.4 - - + +
315E HIS* 1.3 78.8 - - - +
317E HIS* 1.3 55.2 + - + +
326E LYS* 2.9 13.9 + - - +
329E ILE* 2.7 63.4 + - + +
331E HIS* 4.4 15.5 - - + +
349E ILE* 4.3 27.8 - - + -
352E LEU* 4.6 13.2 - - + -
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Residues in contact with HIS 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E LEU* 3.1 38.0 + - + +
314E ALA* 3.9 4.3 - - - +
316E LEU* 1.3 75.0 - - + +
318E MET* 1.3 63.4 + - - +
319E GLU* 3.5 1.0 + - - +
328E ALA* 3.2 17.6 - - - +
329E ILE 3.0 30.1 - - - +
330E ALA* 4.2 0.7 - - - -
397E LYS* 3.4 68.6 + - + +
400E ASP* 2.7 32.0 + - + -
401E ILE* 4.4 4.5 - - + +
485E ALA* 4.2 11.7 + - + +
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Residues in contact with MET 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E ALA* 2.9 24.0 + - + +
315E HIS* 3.7 14.8 - - + +
316E LEU 3.2 0.6 - - - -
317E HIS* 1.3 76.5 - - - +
319E GLU* 1.3 71.4 + - - +
320E ILE* 4.1 18.6 - - + -
326E LYS* 2.6 34.7 + - - +
327E PRO 3.6 1.0 - - - +
328E ALA* 4.2 0.4 - - - -
397E LYS* 5.5 0.4 - - - +
486E LEU* 3.8 32.3 - - + -
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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