Contacts of the helix formed by residues 379 - 392 (chain B) in PDB entry 1IW1
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 ARG 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353B TYR* 3.8 19.3 - - + -
357B GLU* 2.7 13.6 + - - +
376B ALA 3.8 9.9 + - - -
377B LEU 3.0 17.9 + - - +
378B ASN* 1.3 91.0 + - - +
380B ALA* 1.3 58.0 + - - +
381B GLU 3.3 2.0 - - - -
382B VAL* 3.2 21.3 + - - +
383B LEU* 2.8 30.5 + - + +
433B TYR* 4.0 4.0 - - + -
436B ASP* 4.2 1.6 - - - +
459B GLY 3.4 6.3 + - - -
460B PHE* 2.8 66.7 + - + +
462B HIS 2.9 26.1 + - - -
463B PHE* 3.4 33.7 - - - +
464B GLU 5.0 2.0 - - - +
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Residues in contact with ALA 380 (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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350B TRP* 3.3 19.2 + - + +
353B TYR* 4.5 5.8 - - - +
354B THR* 3.9 32.8 - - - +
357B GLU* 3.0 21.3 + - + +
378B ASN* 3.8 0.6 - - - +
379B ARG* 1.3 77.4 - - - +
381B GLU* 1.3 70.9 + - + +
383B LEU* 3.3 3.3 + - - -
384B ALA* 3.1 17.3 + - - +
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Residues in contact with GLU 381 (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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350B TRP* 5.7 1.9 + - - -
378B ASN* 5.5 1.0 - - - +
379B ARG 3.3 0.6 - - - -
380B ALA* 1.3 86.2 - - + +
382B VAL* 1.3 63.8 + - + +
384B ALA* 3.4 11.9 + - - +
385B ARG* 3.2 43.3 + - - +
681C GLU* 2.6 44.8 - - + +
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Residues in contact with VAL 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ASN 4.3 6.7 - - - +
379B ARG* 3.2 31.8 + - - +
381B GLU* 1.3 75.6 - - + +
383B LEU* 1.3 65.3 + - - +
385B ARG* 3.1 29.5 + - + +
386B ASP* 3.0 21.2 + - - +
459B GLY* 3.3 40.4 - - - +
460B PHE* 3.4 7.6 - - - +
462B HIS 5.7 0.4 - - - +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLN* 3.7 42.0 - - + +
349B ALA* 3.8 9.0 - - + +
350B TRP* 3.7 35.4 - - + +
353B TYR* 3.9 11.0 - - + -
379B ARG 2.8 16.0 + - - +
380B ALA* 3.3 4.9 + - - +
382B VAL* 1.3 77.0 - - - +
384B ALA* 1.3 57.7 + - - +
386B ASP* 3.2 9.2 + - + +
387B LEU* 2.9 34.3 + - - +
460B PHE* 3.4 43.3 - - + -
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B TRP* 3.8 21.5 - - + +
380B ALA 3.1 7.9 + - - +
381B GLU* 3.7 16.6 - - - +
382B VAL 3.2 0.4 - - - -
383B LEU* 1.3 77.1 - - - +
385B ARG* 1.3 58.2 + - + +
387B LEU* 3.3 2.3 + - - +
388B ASP* 3.0 35.5 + - - +
396B TRP* 3.7 14.7 - - + -
397B ARG* 3.7 21.1 - - - +
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Residues in contact with ARG 385 (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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381B GLU* 3.2 28.8 + - - +
382B VAL* 3.1 37.7 + - + +
384B ALA* 1.3 76.2 - - + +
386B ASP* 1.3 65.6 + - - +
388B ASP* 3.3 14.4 + - - +
389B LYS* 3.2 33.8 + - - +
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Residues in contact with ASP 386 (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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346B GLN* 4.8 3.2 - - + +
382B VAL* 3.0 14.8 + - - +
383B LEU* 3.4 13.1 - - + +
385B ARG* 1.3 77.5 - - - +
387B LEU* 1.3 57.3 + - + +
389B LYS* 3.0 6.1 + - - +
390B LEU* 2.8 37.4 + - + +
456B GLU 3.4 12.3 - - - +
457B ALA* 3.4 24.9 - - - +
458B LEU* 3.7 0.5 - - - -
459B GLY* 2.9 22.5 + - - -
460B PHE* 2.8 35.8 + - - +
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Residues in contact with LEU 387 (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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343B THR* 4.0 9.0 - - + +
346B GLN* 3.9 38.1 - - + +
347B GLU* 3.7 27.6 - - + -
350B TRP* 3.9 12.3 - - + -
383B LEU 2.9 20.6 + - - +
384B ALA 3.7 1.6 - - - +
385B ARG 3.2 0.2 - - - -
386B ASP* 1.3 73.6 - - + +
388B ASP* 1.3 65.5 + - - +
390B LEU* 4.3 5.8 - - + +
391B ASN* 2.9 37.0 + - - +
396B TRP* 3.5 45.1 - - + -
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Residues in contact with ASP 388 (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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384B ALA 3.0 20.4 + - - +
385B ARG* 3.3 15.7 + - - +
387B LEU* 1.3 75.3 - - - +
389B LYS* 1.3 59.8 + - + +
392B GLY* 2.9 24.3 + - - -
393B SER* 3.2 22.3 + - - +
394B SER* 3.3 2.5 - - - -
396B TRP* 2.9 14.2 + - - -
397B ARG* 2.8 32.1 + - - -
658C GLN* 3.0 28.9 + - - +
717C ARG* 5.9 2.2 - - - +
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Residues in contact with LYS 389 (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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385B ARG* 3.2 20.8 + - - +
386B ASP* 3.0 7.1 + - - +
388B ASP* 1.3 77.9 - - + +
390B LEU* 1.3 66.1 + - - +
391B ASN 3.4 0.3 + - - -
392B GLY* 3.6 8.8 + - - -
456B GLU* 3.1 56.9 + - + +
457B ALA* 4.3 10.8 - - + -
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Residues in contact with LEU 390 (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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339B VAL* 4.1 21.0 - - + +
342B PHE* 4.0 23.3 - - + -
343B THR* 3.7 33.5 + - + +
346B GLN* 4.6 5.8 - - + -
386B ASP* 2.8 28.4 + - + +
387B LEU* 4.1 16.4 - - + +
389B LYS* 1.3 72.8 - - - +
391B ASN* 1.3 61.0 + - - +
453B VAL* 4.2 13.5 - - + -
457B ALA* 3.7 28.0 - - + +
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 3.7 20.5 - - - +
347B GLU* 3.2 23.4 + - - +
387B LEU* 2.9 27.4 + - - +
390B LEU* 1.3 78.0 - - - +
392B GLY* 1.3 61.1 - - - +
393B SER* 3.4 5.5 + - - +
396B TRP* 3.4 32.0 - - + +
399B ARG* 3.8 16.2 + - - +
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Residues in contact with GLY 392 (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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388B ASP 2.9 13.2 + - - -
389B LYS* 3.6 8.1 + - - -
391B ASN* 1.3 76.9 - - - +
393B SER* 1.3 63.1 + - - +
717C ARG* 4.5 10.4 + - - -
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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