Contacts of the helix formed by residues 338 - 353 (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 THR 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B GLU* 3.2 22.0 - - + +
313B LEU* 4.2 16.6 - - + -
316B ILE* 3.6 17.0 - - + -
333B LYS 3.9 0.9 - - - +
334B VAL* 3.1 22.3 + - - +
336B ASP 3.8 1.2 - - - -
337B SER* 1.3 83.8 - - - +
339B PRO* 1.3 64.1 - - - +
340B VAL 3.2 3.6 - - - -
341B LEU* 3.2 8.0 + - + -
342B ASP* 3.0 23.9 + - - -
452B LYS* 2.6 34.7 + - - +
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Residues in contact with PRO 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B GLU* 3.1 9.2 - - - +
337B SER* 3.4 10.3 - - - +
338B THR* 1.3 88.6 - - - +
340B VAL* 1.3 61.5 + - + +
342B ASP* 3.3 13.6 + - + +
343B SER 3.0 23.4 + - - -
410B LEU* 3.4 12.9 - - + +
414B GLY 3.7 24.0 - - - +
415B SER* 5.4 3.4 - - - -
416B GLU* 5.5 3.6 - - + +
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA* 4.0 36.8 - - + +
309B VAL* 4.1 9.0 - - + +
312B GLU* 2.9 24.4 + - + +
339B PRO* 1.3 80.5 - - + +
341B LEU* 1.3 59.8 + - - +
343B SER* 3.3 4.3 + - - -
344B VAL* 2.9 26.6 + - + +
406B TYR* 4.1 16.9 - - + +
410B LEU* 3.9 21.5 - - + -
414B GLY* 5.7 1.3 - - - +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 4.4 12.3 - - + -
309B VAL* 4.3 15.5 - - + +
312B GLU* 2.9 17.6 + - - +
313B LEU* 4.4 17.3 - - + -
334B VAL* 5.3 1.1 - - + +
338B THR* 3.2 11.0 + - + +
340B VAL* 1.3 75.4 - - - +
342B ASP* 1.3 58.4 + - - +
344B VAL* 3.3 18.7 + - + +
345B LEU* 2.9 28.3 + - - +
452B LYS* 3.6 46.9 - - + +
455B VAL* 3.9 27.6 - - + -
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Residues in contact with ASP 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A HIS* 6.2 3.4 - - - -
335B LEU 5.0 1.4 - - - +
336B ASP* 5.9 1.6 - - - -
338B THR 3.0 13.5 + - - +
339B PRO* 3.3 16.9 - - + +
341B LEU* 1.3 75.0 - - - +
343B SER* 1.3 57.7 + - - +
345B LEU* 3.3 7.1 + - - +
346B SER* 3.0 32.4 + - - +
416B GLU* 6.4 3.6 - - + -
448B VAL* 4.7 7.4 - - - +
452B LYS* 2.5 37.6 + - - +
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Residues in contact with SER 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B PRO 3.0 8.3 + - - -
340B VAL 3.3 5.6 + - - -
342B ASP* 1.3 72.7 - - - +
344B VAL* 1.3 60.3 + - - +
346B SER* 3.4 1.3 + - - -
347B GLU* 2.8 30.8 + - - +
406B TYR 2.7 22.9 + - - -
407B ASN* 3.6 3.3 - - - -
408B ARG 3.7 0.2 + - - -
409B PHE* 3.2 38.3 + - - -
410B LEU* 3.6 26.0 - - - -
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.6 27.8 - - + -
299B LEU* 3.8 20.0 - - + -
309B VAL* 3.8 20.0 - - + -
340B VAL 2.9 17.8 + - - +
341B LEU* 3.3 15.0 + - + +
343B SER* 1.3 77.2 - - - +
345B LEU* 1.3 57.3 + - - +
347B GLU* 3.3 4.8 + - - +
348B SER* 2.9 32.4 + - - -
404B PHE* 4.0 8.7 - - + -
406B TYR* 3.8 33.0 - - + +
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA* 5.1 3.8 - - + +
295B LEU* 3.8 25.1 - - + -
341B LEU* 2.9 17.4 + - + +
342B ASP* 3.7 6.5 - - - +
344B VAL* 1.3 75.0 - - - +
346B SER* 1.3 65.4 + - - +
348B SER* 3.2 4.6 + - - -
349B LEU* 3.0 52.4 + - + +
434B TRP* 5.4 0.2 - - + -
448B VAL* 4.0 42.2 - - + +
451B ILE* 4.1 31.6 - - + -
452B LYS* 4.7 7.0 - - + -
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ASP* 3.0 17.8 + - - +
343B SER* 3.8 0.8 - - - -
345B LEU* 1.3 77.8 - - - +
347B GLU* 1.3 57.1 + - - +
349B LEU* 3.6 6.4 + - - +
350B ARG* 3.0 23.7 + - - +
409B PHE* 3.6 28.3 - - - +
431B ASN* 3.0 24.6 + - - +
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B SER 2.8 18.4 + - - +
344B VAL* 3.7 5.2 - - - +
345B LEU 3.1 0.2 - - - -
346B SER* 1.3 75.6 - - - +
348B SER* 1.3 62.6 + - - +
350B ARG* 2.8 36.8 + - - +
351B LEU* 3.4 21.0 + - - +
403B VAL 3.1 1.7 - - - +
404B PHE* 3.5 23.8 - - + -
405B LYS 2.9 36.5 + - - +
406B TYR 4.7 0.4 - - - +
408B ARG* 2.8 32.0 + - - -
409B PHE* 3.4 8.8 - - + -
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Residues in contact with SER 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA 4.7 4.3 - - - -
294B TRP* 4.7 1.6 - - - -
295B LEU* 3.3 40.5 - - - +
298B PHE* 3.7 21.5 - - - -
344B VAL 2.9 17.2 + - - -
345B LEU* 3.2 7.2 + - - -
347B GLU* 1.3 75.2 - - - +
349B LEU* 1.3 55.9 + - - +
351B LEU* 3.3 2.1 + - - +
352B THR* 2.7 39.5 + - - +
404B PHE* 3.8 4.4 - - - -
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA* 4.1 17.3 - - + -
345B LEU* 3.0 39.9 + - + +
346B SER* 3.8 7.0 - - - +
348B SER* 1.3 76.0 - - - +
350B ARG* 1.3 62.4 + - - +
352B THR* 4.1 1.3 - - - -
353B ALA* 2.8 31.9 + - + +
392B GLN* 3.8 2.6 + - - -
431B ASN* 4.5 0.9 - - - -
433B PRO* 3.8 29.1 - - + +
434B TRP* 3.7 32.5 - - + +
451B ILE* 5.8 0.9 - - + -
485B LEU* 4.0 30.3 - - + -
600B HEM 4.7 4.5 - - + -
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Residues in contact with ARG 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B SER 3.0 16.2 + - - +
347B GLU* 2.8 44.3 + - - +
348B SER 3.3 0.2 - - - -
349B LEU* 1.3 75.5 - - - +
351B LEU* 1.3 73.0 + - - +
388B PHE* 4.6 2.9 - - - -
392B GLN* 2.9 69.8 + - + +
393B ARG* 4.5 4.5 + - - +
398B TYR* 3.6 30.6 - - + -
401B PRO* 2.8 33.5 + - - +
403B VAL 3.0 16.6 + - - -
408B ARG* 3.1 14.5 - - - +
409B PHE* 4.0 2.7 - - + -
431B ASN* 3.4 21.7 + - - +
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Residues in contact with LEU 351 (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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298B PHE* 3.6 31.0 - - + -
347B GLU 3.4 12.3 + - - +
348B SER 3.3 5.3 + - - +
349B LEU 3.2 0.2 - - - -
350B ARG* 1.3 92.7 - - - +
352B THR* 1.3 65.5 + - + +
388B PHE* 3.4 13.7 - - - -
393B ARG* 3.0 39.2 + - - +
401B PRO 3.4 25.6 - - - +
402B GLU 3.9 15.5 - - - +
404B PHE* 3.8 28.3 - - + +
476B PHE* 3.5 4.9 - - - -
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Residues in contact with THR 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA* 5.3 1.0 - - - -
294B TRP* 3.4 52.5 - - + +
298B PHE* 4.2 5.4 - - + -
348B SER* 2.7 24.7 + - - +
349B LEU* 4.1 0.3 - - - -
351B LEU* 1.3 88.4 - - + +
353B ALA* 1.3 61.4 + - - +
388B PHE* 4.8 1.3 - - - -
476B PHE* 4.1 13.7 - - + -
485B LEU* 3.3 15.9 - - - +
486B MET* 2.8 35.8 + - - +
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Residues in contact with ALA 353 (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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349B LEU* 2.8 24.1 + - + +
352B THR* 1.3 72.4 + - - +
354B ALA* 1.3 56.8 + - - +
355B PRO* 3.5 8.5 - - + +
388B PHE* 3.5 7.3 + - - +
392B GLN* 2.9 25.2 + - - +
433B PRO* 3.5 33.7 - - + +
484B GLY 3.8 4.0 - - - +
485B LEU* 4.1 20.2 - - + -
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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