Contacts of the helix formed by residues 352 - 366 (chain B) in PDB entry 3IAD
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 352 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B VAL 5.3 0.2 - - - +
351B PHE* 1.3 77.5 - - - +
353B ASP* 1.3 65.8 + - - +
354B LEU* 3.6 8.6 + - - +
355B GLU* 2.9 39.7 + - - +
356B ILE* 3.0 23.7 + - - +
472B ARG* 4.5 7.2 - - - +
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Residues in contact with ASP 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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295B ARG 5.6 1.9 - - - +
297B LEU* 4.3 10.3 - - + +
300B THR* 3.7 22.4 - - + +
301B PHE* 3.8 21.8 - - + -
352B THR* 1.3 74.5 - - - +
354B LEU* 1.3 57.1 + - - +
356B ILE* 3.4 14.7 + - - +
357B LEU* 2.8 29.3 + - - +
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Residues in contact with LEU 354 (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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301B PHE* 3.8 27.4 - - + -
352B THR* 3.2 8.8 + - - +
353B ASP* 1.3 76.3 - - - +
355B GLU* 1.3 55.2 + - - +
357B LEU* 3.0 5.8 + - + +
358B ALA* 2.8 35.0 + - - +
418B LEU* 4.1 15.0 - - + -
422B GLN* 3.8 33.2 - - + +
425B SER* 3.4 33.9 - - - +
426B LEU* 3.7 10.5 - - + +
429B MET* 4.0 8.5 - - + -
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Residues in contact with GLU 355 (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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351B PHE* 3.4 16.7 - - + -
352B THR* 2.9 42.3 + - - +
354B LEU* 1.3 76.2 - - + +
356B ILE* 1.3 56.4 + - - +
358B ALA* 3.3 2.3 + - - +
359B ALA* 2.9 29.5 + - - +
429B MET* 3.5 32.0 - - + +
469B TYR* 5.8 2.6 - - - -
472B ARG* 2.8 46.4 + - - +
476B LEU* 4.2 16.2 - - + +
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Residues in contact with ILE 356 (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 ARG* 3.9 44.0 - - - +
297B LEU* 4.8 8.1 - - + -
342B LEU* 4.0 20.9 - - + -
351B PHE* 4.0 23.8 - - + +
352B THR 3.0 21.0 + - - +
353B ASP* 3.6 17.9 - - - +
355B GLU* 1.3 73.9 - - - +
357B LEU* 1.3 66.2 + - - +
359B ALA* 3.4 2.3 + - - +
360B ILE* 3.2 30.6 + - + +
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Residues in contact with LEU 357 (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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292B PHE* 3.6 35.7 - - + -
297B LEU* 4.4 13.0 - - + +
301B PHE* 3.8 39.3 - - + -
303B ILE* 5.0 3.8 - - + -
353B ASP 2.8 15.5 + - - +
354B LEU* 3.0 10.7 + - + +
356B ILE* 1.3 76.0 - - - +
358B ALA* 1.3 62.4 + - - +
360B ILE* 4.1 1.4 - - - +
361B PHE* 3.1 27.6 + - + +
415B PHE* 3.8 35.9 - - + -
418B LEU* 4.4 3.6 - - + -
426B LEU* 4.0 9.2 - - + -
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Residues in contact with ALA 358 (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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354B LEU 2.8 12.9 + - - +
355B GLU* 3.4 10.1 - - - +
357B LEU* 1.3 73.4 - - - +
359B ALA* 1.3 58.5 + - - +
361B PHE 3.3 0.3 + - - -
362B ALA* 2.9 32.4 + - - +
426B LEU* 3.2 25.3 - - + +
429B MET* 3.9 29.6 - - + -
430B VAL* 3.7 9.6 - - + +
433B ILE* 4.4 4.9 - - + -
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Residues in contact with ALA 359 (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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338B THR* 4.0 17.1 - - + +
342B LEU* 4.4 9.6 - - + -
355B GLU 2.9 16.2 + - - +
356B ILE 3.4 4.0 + - - +
358B ALA* 1.3 76.7 - - - +
360B ILE* 1.3 60.5 - - - +
362B ALA* 4.0 1.7 - - - +
363B SER* 2.9 29.1 + - - -
433B ILE* 4.0 15.2 - - + +
476B LEU* 4.2 21.3 - - + -
479B MET* 5.3 0.7 - - - -
480B VAL* 4.1 5.9 - - + +
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Residues in contact with ILE 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B MET* 3.6 24.7 - - - -
291B ILE* 3.7 27.4 - - + -
292B PHE* 3.8 15.9 - - + -
295B ARG* 3.7 25.1 - - - +
297B LEU* 4.3 8.1 - - + -
335B VAL* 3.7 11.8 - - + +
338B THR* 5.0 4.9 - - + -
339B HIS* 5.0 5.8 - - + +
342B LEU* 3.9 14.1 - - + -
356B ILE* 3.2 22.1 + - + +
357B LEU* 4.1 2.7 - - - +
359B ALA* 1.3 74.1 - - - +
361B PHE* 1.3 65.9 + - - +
363B SER* 3.4 7.7 + - - -
364B ALA* 3.0 20.3 + - - +
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Residues in contact with PHE 361 (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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288B MET* 5.0 7.9 - - + -
292B PHE* 5.7 2.4 - + + -
311B TYR* 3.2 45.3 - + - -
357B LEU* 3.1 21.5 + - + +
358B ALA* 3.8 2.5 - - - +
360B ILE* 1.3 75.3 - - - +
362B ALA* 1.3 67.3 + - - +
364B ALA* 3.0 18.2 + - + +
365B ILE* 3.0 36.8 + - + +
403B GLY 4.1 3.6 - - - -
404B PHE* 4.3 14.8 - + - -
407B LEU* 4.1 6.7 - - + -
414B ILE* 4.0 9.6 - - + -
415B PHE* 3.6 41.1 - + + -
426B LEU* 5.6 0.7 - - + -
430B VAL* 4.0 19.5 - - + -
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Residues in contact with ALA 362 (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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358B ALA 2.9 20.8 + - - +
359B ALA 4.0 2.7 - - - +
361B PHE* 1.3 72.2 - - - +
363B SER* 1.3 58.4 + - - +
365B ILE* 3.1 7.7 + - - +
366B HIS* 2.9 34.2 + - - +
430B VAL* 4.2 10.1 - - + +
433B ILE* 3.5 37.9 - - + -
434B VAL* 3.9 14.7 - - + +
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Residues in contact with SER 363 (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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331B ALA* 3.9 4.9 - - - +
334B VAL* 3.9 5.4 - - - -
335B VAL* 3.5 27.2 - - - +
338B THR* 2.8 24.1 + - - -
359B ALA 2.9 15.9 + - - -
360B ILE 3.5 6.1 - - - -
361B PHE 3.3 0.2 - - - -
362B ALA* 1.3 78.8 - - - +
364B ALA* 1.3 59.5 - - - +
366B HIS* 2.8 31.7 + - - -
480B VAL* 3.5 15.3 - - - +
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Residues in contact with ALA 364 (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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284B LEU* 4.4 7.5 - - + +
288B MET* 3.8 22.4 - - + -
315B LEU* 4.0 18.4 - - + +
319B TYR* 2.6 32.7 + - - -
331B ALA* 3.9 4.8 - - - +
335B VAL* 3.2 16.5 - - + +
360B ILE 3.0 12.7 + - - +
361B PHE* 3.0 11.5 + - + +
363B SER* 1.3 79.2 - - - +
365B ILE* 1.3 53.0 + - + +
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Residues in contact with ILE 365 (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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311B TYR* 3.5 24.9 - - - +
315B LEU* 3.8 19.5 - - + -
319B TYR* 3.6 2.9 - - - -
361B PHE* 3.0 39.0 + - + +
362B ALA* 3.6 12.3 - - - +
364B ALA* 1.3 74.2 - - - +
366B HIS* 1.3 59.1 - - - +
367B ASP 3.0 9.4 + - - -
368B VAL* 3.1 17.7 + - - +
399B HIS* 3.6 12.6 - - - +
400B LEU* 4.4 12.1 - - + -
403B GLY* 4.1 23.3 - - - -
404B PHE* 4.7 4.0 - - + -
430B VAL* 3.9 18.2 - - + -
434B VAL* 4.2 4.7 - - + -
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Residues in contact with HIS 366 (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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319B TYR* 4.7 1.0 + - - -
330B HIS* 3.5 6.5 - + - -
331B ALA* 4.4 6.3 - - - -
334B VAL* 3.4 31.2 - - + +
362B ALA 2.9 17.2 + - - +
363B SER* 2.8 23.8 + - - -
364B ALA 3.4 2.6 - - - -
365B ILE* 1.3 75.7 - - - +
367B ASP* 1.3 75.3 + - + +
399B HIS* 2.9 22.7 - - - +
433B ILE* 6.6 0.2 - - + -
434B VAL* 4.4 19.4 - - + +
437B THR* 4.5 21.4 + - + -
480B VAL* 5.2 2.7 - - + -
484B ASP* 3.3 13.3 + - + -
620B ZN 2.2 37.1 - - - -
621B MG 4.5 2.2 - - - -
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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
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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