Contacts of the helix formed by residues 287 - 301 (chain B) in PDB entry 2IAG
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 ASN 287 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B TRP* 5.9 2.9 - - - -
283B ALA 5.3 4.4 + - - -
284B THR 5.3 0.8 + - - -
285B GLN 3.3 0.8 - - - -
286B GLY* 1.3 86.1 - - - +
288B MET* 1.3 68.6 + - - +
289B GLY 3.4 1.8 - - - -
290B PRO* 3.7 3.3 - - - +
291B ALA* 3.0 26.7 + - - +
483B PHE 4.2 6.5 + - - +
484B GLY* 3.9 9.8 - - - -
485B LEU* 3.0 36.8 + - + +
600B HEM 3.5 55.7 + - + +
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Residues in contact with MET 288 (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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140B MET* 4.5 14.1 - - + -
172B LEU* 3.5 26.2 - - + +
284B THR 3.9 4.0 + - - +
285B GLN* 3.4 33.1 + - - +
287B ASN* 1.3 76.9 - - - +
289B GLY* 1.3 58.1 + - - +
291B ALA* 3.2 3.1 + - - +
292B ALA* 3.0 26.0 + - - +
446B TYR* 4.3 8.7 - - + +
447B ALA* 4.0 7.0 - - + +
450B SER* 3.6 30.3 - - - -
451B ILE* 4.2 8.2 - - + +
600B HEM 3.3 54.2 - - + +
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Residues in contact with GLY 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 4.5 0.7 - - - -
168B SER* 3.5 11.4 - - - -
169B TYR* 3.8 28.9 - - - -
172B LEU* 3.9 14.8 - - - +
173B LEU 5.7 0.2 - - - +
285B GLN 4.5 4.2 + - - -
288B MET* 1.3 80.0 - - - +
290B PRO* 1.4 68.7 - - - +
292B ALA* 3.4 0.5 + - - +
293B PHE* 3.1 18.5 + - - +
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Residues in contact with PRO 290 (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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165B LEU* 3.9 12.3 - - + -
169B TYR* 3.7 35.0 - - + -
286B GLY 3.6 16.4 - - - +
287B ASN 3.7 8.3 - - - +
289B GLY* 1.4 88.5 - - - +
291B ALA* 1.3 61.6 + - - +
293B PHE* 3.3 2.6 + - + +
294B TRP* 3.1 30.7 + - + -
485B LEU* 3.9 18.2 - - + -
486B MET 3.9 12.3 - - - +
487B GLN* 4.0 15.9 - - + +
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Residues in contact with ALA 291 (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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287B ASN 3.0 21.6 + - - +
288B MET 3.4 5.2 - - - +
290B PRO* 1.3 77.1 - - - +
292B ALA* 1.3 63.5 + - - +
294B TRP* 3.4 4.1 + - - +
295B LEU* 3.2 21.8 + - - +
345B LEU* 5.1 3.2 - - + +
348B SER* 4.7 4.2 - - - -
349B LEU* 4.1 15.4 - - + +
352B THR* 5.3 0.6 + - - -
451B ILE* 3.9 19.7 - - + -
485B LEU* 3.9 21.3 - - + +
600B HEM 4.7 1.6 - - + -
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Residues in contact with ALA 292 (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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168B SER* 4.1 3.1 - - - -
172B LEU* 3.3 33.4 - - + -
288B MET 3.0 6.0 + - - +
289B GLY 3.7 2.5 - - - +
291B ALA* 1.3 73.4 - - - +
293B PHE* 1.3 59.6 + - - +
295B LEU* 3.7 7.4 - - - +
296B LEU* 2.9 34.6 + - + +
451B ILE* 4.5 14.0 - - + +
454B PHE* 4.0 18.2 - - + -
455B VAL* 5.6 2.0 - - + -
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 3.7 18.7 - - + +
165B LEU* 3.4 49.6 - - + -
168B SER* 3.7 13.4 - - - +
289B GLY 3.1 9.0 + - - +
290B PRO 3.4 7.4 - - - +
291B ALA 3.3 0.4 - - - -
292B ALA* 1.3 76.6 - - - +
294B TRP* 1.3 94.2 + + - +
296B LEU* 3.9 2.2 - - - +
297B LEU* 2.9 47.6 + - + +
474B PRO* 4.7 0.2 - - + -
488B PRO* 3.4 37.2 - - + -
491B ASP* 3.9 9.2 - - - -
492B VAL* 4.1 15.3 - - + -
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Residues in contact with TRP 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PRO* 3.1 24.1 + - - +
291B ALA 3.9 4.5 - - - +
292B ALA 3.4 0.2 - - - -
293B PHE* 1.3 93.9 - + - +
295B LEU* 1.3 56.6 + - - +
297B LEU* 3.2 12.8 + - + +
298B PHE* 2.8 58.3 + + + -
348B SER* 4.7 1.6 - - - -
352B THR* 3.4 42.6 - - + +
473B ILE* 3.9 24.2 - - + -
474B PRO* 3.8 15.5 - - + -
476B PHE* 3.5 32.1 - + - -
485B LEU* 4.4 2.2 - - + -
486B MET 2.8 22.9 + - - -
487B GLN* 3.9 1.1 - - - +
488B PRO* 3.7 31.2 - - + -
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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
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291B ALA 3.2 15.8 + - - +
292B ALA* 3.7 5.6 - - - +
294B TRP* 1.3 78.6 - - - +
296B LEU* 1.3 65.9 + - + +
298B PHE* 3.3 3.1 + - - +
299B LEU* 3.0 50.5 + - + +
341B LEU* 4.4 7.9 - - + -
344B VAL* 3.6 18.3 - - + +
345B LEU* 3.8 43.3 - - + -
348B SER* 3.3 16.7 + - - +
451B ILE* 4.3 13.9 - - + -
455B VAL* 3.7 23.3 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.1 15.9 - - + -
167B PHE* 4.6 2.5 - - + -
168B SER* 3.6 22.0 - - - +
292B ALA* 2.9 17.7 + - + +
293B PHE 3.9 2.7 - - - +
295B LEU* 1.3 79.1 - - + +
297B LEU* 1.3 57.8 + - - +
299B LEU* 3.3 8.7 + - + +
300B LEU* 2.9 38.8 + - + +
454B PHE* 3.7 23.8 - - + -
455B VAL* 4.0 34.5 - - + -
458B VAL* 5.1 4.7 - - + -
459B LEU* 4.8 11.4 - - + -
464B LEU* 4.1 19.3 - - + -
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Residues in contact with LEU 297 (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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164B LEU* 3.8 12.5 - - + +
293B PHE* 2.9 34.1 + - + +
294B TRP* 3.6 18.6 - - + +
296B LEU* 1.3 74.1 - - - +
298B PHE* 1.3 61.0 + - + +
300B LEU* 3.2 4.3 + - - +
301B LYS* 3.0 42.3 + - + +
466B LEU* 4.3 9.6 - - + -
471B VAL* 5.2 3.1 - - + -
473B ILE* 4.0 18.2 - - + -
474B PRO* 3.9 27.4 - - + -
492B VAL* 4.0 28.5 - - + -
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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
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294B TRP* 2.8 54.2 + + + +
295B LEU 3.6 3.4 - - - +
297B LEU* 1.3 73.8 - - + +
299B LEU* 1.3 61.4 + - - +
301B LYS* 4.7 1.1 - - - -
302B ASN* 2.8 35.5 + - - +
348B SER* 3.7 17.7 - - - -
351B LEU* 3.6 29.8 - - + -
352B THR* 4.2 15.5 - - + -
404B PHE* 3.5 44.7 - + + -
473B ILE* 4.3 29.2 - - + -
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Residues in contact with LEU 299 (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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295B LEU* 3.0 39.2 + - + +
296B LEU* 3.6 12.6 - - + +
298B PHE* 1.3 74.2 - - - +
300B LEU* 1.3 67.0 + - + +
302B ASN 3.3 12.5 + - - +
303B PRO* 4.7 0.2 - - - +
305B ALA* 4.1 16.8 - - + -
306B LEU* 3.3 46.3 - - + +
309B VAL* 3.9 27.6 - - + -
341B LEU* 5.4 0.2 - - + -
344B VAL* 3.8 24.9 - - + -
404B PHE* 4.5 3.6 - - + -
455B VAL* 4.9 0.4 - - + -
459B LEU* 4.4 13.7 - - + -
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Residues in contact with LEU 300 (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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164B LEU* 3.9 24.2 - - + -
296B LEU* 2.9 27.8 + - + +
297B LEU 3.2 4.5 + - - +
299B LEU* 1.3 80.7 - - + +
301B LYS* 1.3 60.8 + - - +
302B ASN 3.5 1.4 + - - -
303B PRO* 4.9 4.2 - - - +
306B LEU* 4.8 18.5 - - + +
310B ARG* 5.9 0.2 - - - +
459B LEU* 5.7 4.5 - - + -
464B LEU* 4.4 35.0 - - + +
465B GLU* 4.8 1.6 - - - -
466B LEU* 4.0 43.0 - - + +
494B VAL* 4.1 11.4 - - + -
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Residues in contact with LYS 301 (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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297B LEU* 3.0 28.6 + - + +
298B PHE 4.6 0.2 - - - -
299B LEU 3.3 0.2 - - - -
300B LEU* 1.3 77.0 - - - +
302B ASN* 1.3 70.4 + - - +
303B PRO* 3.9 7.6 - - - +
466B LEU* 4.1 11.4 - - + -
469B ALA 2.8 27.9 + - - -
470B ASP* 3.5 10.5 + - - +
471B VAL* 2.8 29.3 + - + +
472B GLU* 5.1 2.2 + - - +
473B ILE* 4.3 30.5 - - + +
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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
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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