Contacts of the helix formed by residues 281 - 300 (chain B) in PDB entry 1IYH
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 281 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B GLY 3.5 0.4 - - - -
280B ASN* 1.3 85.2 - - + +
282B GLU* 1.3 66.2 + - - +
283B MET* 3.6 5.7 + - - +
284B GLU* 3.0 39.5 + - - +
285B GLN* 2.9 28.6 + - - +
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B THR* 1.3 73.9 - - - +
283B MET* 1.3 63.0 + - + +
285B GLN* 3.3 14.7 + - - +
286B CYS* 3.2 15.1 + - - -
670D TYR* 3.6 26.8 - - + +
673D LYS* 3.1 32.6 + - - +
674D ASN* 4.6 9.2 + - - -
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Residues in contact with MET 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B THR* 3.3 4.8 + - - +
282B GLU* 1.3 78.3 - - + +
284B GLU* 1.3 62.9 + - + +
286B CYS* 3.0 7.9 + - - +
287B HIS* 2.9 40.4 + - + +
656D VAL* 4.4 13.7 - - + -
659D LEU* 3.6 44.0 - - + -
661D LEU* 3.6 32.1 - - + -
670D TYR* 3.5 28.3 - - + +
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Residues in contact with GLU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLY* 4.7 0.9 - - - -
280B ASN* 3.4 35.7 + - - +
281B THR* 3.0 29.1 + - - +
283B MET* 1.3 74.8 - - + +
285B GLN* 1.3 61.1 + - - +
287B HIS* 3.2 13.9 + - + +
288B VAL* 2.9 33.3 + - - +
342B ILE* 3.6 13.7 - - + +
343B GLY* 3.6 25.4 + - - -
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Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ALA* 3.7 29.9 - - - +
279B GLY 3.5 23.5 + - - +
280B ASN 5.5 0.2 - - - -
281B THR 2.9 28.4 + - - +
282B GLU* 3.4 24.1 + - - +
283B MET 3.2 0.2 - - - -
284B GLU* 1.3 77.4 - - - +
286B CYS* 1.3 61.9 + - - +
288B VAL* 3.3 3.0 + - - +
289B ASP* 3.1 29.0 + - - +
673D LYS* 3.8 19.0 + - + +
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Residues in contact with CYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLU 3.2 12.2 + - - +
283B MET* 3.0 11.6 + - - +
285B GLN* 1.3 79.3 - - - +
287B HIS* 1.3 56.8 + - - +
289B ASP* 3.3 7.8 + - - +
290B ALA* 2.9 29.6 + - - +
661D LEU* 4.2 26.2 - - + -
662D HIS 4.8 2.9 - - - -
666D ALA* 3.5 32.0 - - - +
667D ILE* 4.1 6.7 - - - -
670D TYR* 3.9 22.0 - - + -
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Residues in contact with HIS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B MET* 2.9 32.2 + - + +
284B GLU* 3.2 16.4 + - + +
286B CYS* 1.3 74.7 - - - +
288B VAL* 1.3 60.2 + - - +
290B ALA* 3.6 5.1 - - - +
291B ILE* 2.9 34.7 + - - +
334B TYR* 3.8 24.3 + + - +
342B ILE* 4.0 12.1 - - + -
659D LEU* 6.3 0.2 - - - +
660D THR 3.5 14.8 - - - -
661D LEU* 3.5 31.3 - - + +
662D HIS* 5.0 12.5 + - - -
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ALA 3.7 16.6 - - - +
279B GLY* 4.4 0.9 - - - -
284B GLU 2.9 19.1 + - - +
285B GLN 3.5 7.2 - - - +
286B CYS 3.2 0.2 - - - -
287B HIS* 1.3 76.4 - - - +
289B ASP* 1.3 63.5 + - - +
291B ILE* 3.3 1.7 + - - +
292B VAL* 3.1 28.4 + - - +
342B ILE* 4.1 21.5 - - + -
347B THR* 3.9 23.1 - - + +
348B TRP* 3.4 40.4 - - + +
349B ALA* 3.9 13.4 - - + +
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Residues in contact with ASP 289 (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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269B ARG* 2.9 37.3 + - - +
285B GLN* 3.1 15.3 + - - +
286B CYS* 3.6 9.4 - - - +
288B VAL* 1.3 80.3 - - - +
290B ALA* 1.3 58.0 + - - +
292B VAL* 3.4 5.2 + - - +
293B ASP* 2.9 34.7 + - - +
348B TRP* 3.8 10.4 + - - -
666D ALA* 3.7 16.2 - - + +
669D ARG* 3.0 29.7 + - - +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B CYS* 2.9 17.7 + - - +
287B HIS* 3.6 7.4 - - - +
289B ASP* 1.3 73.8 - - - +
291B ILE* 1.3 65.7 + - - +
293B ASP 3.4 0.3 + - - -
294B THR* 2.9 28.1 + - - -
662D HIS* 3.4 47.3 - - + +
663D GLN* 3.3 14.9 - - + +
666D ALA* 3.7 1.1 - - + +
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B HIS 2.9 23.8 + - - +
288B VAL 3.8 3.6 - - - +
290B ALA* 1.3 71.2 - - - +
292B VAL* 1.3 65.4 + - - +
294B THR* 3.1 5.9 + - - -
295B LEU* 3.0 37.8 + - + +
331B LEU* 4.7 7.6 - - + -
334B TYR* 3.6 26.5 - - + +
341B LEU* 3.8 26.0 - - + -
342B ILE* 3.8 18.6 - - + -
349B ALA* 4.2 7.4 - - + -
648D PHE* 3.6 35.2 - - + -
662D HIS* 4.7 3.1 - - + +
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU* 3.7 26.0 - - + -
269B ARG* 5.6 1.1 - - - +
288B VAL 3.1 19.2 + - - +
289B ASP 3.6 4.9 - - - +
291B ILE* 1.3 76.0 - - - +
293B ASP* 1.3 58.6 + - - +
295B LEU* 3.3 4.3 + - - +
296B ASP* 2.8 27.2 + - - +
348B TRP* 3.7 39.7 - - + -
349B ALA* 3.9 24.0 - - + -
352B TYR* 3.7 22.5 - - + -
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Residues in contact with ASP 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU* 3.8 19.9 - - - +
269B ARG* 5.0 7.9 + - - -
289B ASP* 2.9 20.2 + - - +
290B ALA 3.9 0.4 - - - +
292B VAL* 1.3 78.7 - - - +
294B THR* 1.3 56.6 + - - +
296B ASP* 3.8 3.8 - - - +
297B ASP* 2.8 38.0 + - - +
1902B MG 4.3 12.7 - - - -
663D GLN* 3.6 26.8 - - + +
665D LEU* 4.2 24.8 - - - +
666D ALA* 4.7 5.5 + - - +
669D ARG* 5.5 3.6 + - - -
693D ASP* 5.2 5.4 - - - +
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Residues in contact with THR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA 2.9 16.6 + - - -
291B ILE* 3.1 11.9 + - - -
293B ASP* 1.3 76.3 - - - +
295B LEU* 1.3 62.3 + - - +
297B ASP* 3.5 4.5 + - - +
298B PHE* 3.4 19.9 + - - +
327B LEU* 4.0 18.0 - - + +
331B LEU* 5.4 2.9 - - + -
648D PHE* 3.9 30.6 - - + +
662D HIS* 3.6 16.9 + - - -
663D GLN* 3.1 18.2 + - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ILE* 3.0 33.9 + - + +
292B VAL 3.7 4.7 - - - +
294B THR* 1.3 76.3 - - + +
296B ASP* 1.3 63.5 + - - +
298B PHE* 3.2 7.5 + - - +
299B MET* 3.0 27.3 + - - +
327B LEU* 4.8 9.2 - - + -
328B MET* 5.8 0.2 - - + -
331B LEU* 3.9 22.2 - - + -
341B LEU* 5.3 0.2 - - + -
349B ALA 4.5 0.7 - - - +
352B TYR* 3.9 21.5 - - + +
353B TRP* 3.8 56.3 - - + +
356B CYS* 4.1 9.9 - - + -
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Residues in contact with ASP 296 (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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214B ARG* 3.1 30.1 + - - -
265B LEU* 3.8 22.9 - - + +
292B VAL 2.8 18.3 + - - +
293B ASP* 3.8 5.8 - - - +
295B LEU* 1.3 77.6 - - - +
297B ASP* 1.3 56.6 + - - +
299B MET* 3.3 6.2 + - - +
300B SER* 2.9 39.9 + - - -
352B TYR* 2.7 28.6 + - + -
1400B GSH 4.8 4.2 + - - -
1902B MG 3.9 13.3 - - - -
697D ASP* 5.3 1.2 - - - +
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ASP* 2.8 25.5 + - - +
294B THR* 3.7 6.5 - - - +
296B ASP* 1.3 73.6 - - - +
298B PHE* 1.3 61.7 + - - +
300B SER* 3.5 11.4 + - - -
301B CYS* 3.3 19.3 + - - -
1902B MG 4.0 16.5 - - - -
663D GLN* 3.1 18.6 + - - +
696D ASP* 5.3 2.1 - - - +
700D SER* 5.5 2.4 + - - -
1800D GSH 2.9 31.2 + - - +
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Residues in contact with PHE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B THR 3.4 4.7 + - - +
295B LEU 3.2 9.6 + - - +
297B ASP* 1.3 77.2 - - - +
299B MET* 1.3 69.8 + - - +
301B CYS* 3.0 28.4 + - - +
302B PHE* 3.4 38.4 - + - -
319B LEU* 3.9 13.2 - - + -
323B ASN* 4.0 23.6 - - + -
324B ALA* 3.8 35.9 - - + -
327B LEU* 3.6 32.3 - - + -
328B MET* 5.2 0.4 - - + -
360B LEU* 4.2 21.1 - - + -
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Residues in contact with MET 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ARG* 5.2 3.1 - - - +
295B LEU 3.0 21.0 + - - +
296B ASP* 3.3 10.7 + - - +
298B PHE* 1.3 79.2 - - - +
300B SER* 1.3 60.0 + - - +
301B CYS 3.3 0.9 + - - -
302B PHE* 3.4 10.0 + - + -
304B TRP* 2.9 48.9 + - + +
352B TYR* 5.4 0.9 - - - +
356B CYS* 3.6 41.3 - - - +
359B THR* 4.3 13.9 - - + -
360B LEU* 3.6 40.2 - - + -
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Residues in contact with SER 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ARG* 2.8 29.6 + - - +
296B ASP* 2.9 23.0 + - - -
297B ASP* 3.8 8.1 - - - -
298B PHE 3.1 0.4 - - - -
299B MET* 1.3 76.2 - - - +
301B CYS* 1.3 60.6 + - - +
302B PHE 3.2 7.5 + - - +
304B TRP* 4.7 3.9 - - - +
697D ASP* 5.7 0.5 + - - -
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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
------------------------------------------------------------
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