Contacts of the helix formed by residues 356 - 370 (chain B) in PDB entry 3IOT
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 356 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ALA 4.1 6.1 - - - +
52A ALA 3.5 3.9 + - - +
53A THR 4.1 0.9 - - - -
54A GLY* 3.4 38.8 - - - +
74A GLY 5.4 0.5 + - - -
268A ALA* 6.1 0.5 - - - +
269A ALA* 4.7 9.1 - - + +
350B ALA* 4.8 2.5 - - - -
355B GLN* 1.3 77.0 - - - +
357B VAL* 1.3 58.8 + - - +
358B ASP* 3.8 11.2 + - - +
359B ALA* 3.1 20.4 + - + +
360B ALA* 2.8 34.0 + - - +
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Residues in contact with VAL 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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189B LYS* 3.3 17.7 - - + +
192B LEU* 3.6 23.1 - - + -
193B THR* 3.1 50.7 - - + +
196B VAL* 4.5 18.8 - - + -
350B ALA* 4.8 3.0 - - - +
356B THR* 1.3 76.4 - - - +
358B ASP* 1.3 69.6 + - - +
359B ALA 3.0 0.2 + - - -
360B ALA* 3.3 6.8 + - - +
361B LEU* 3.3 20.3 + - + +
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Residues in contact with ASP 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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74A GLY* 3.8 20.6 - - - +
268A ALA* 3.8 25.4 - - + +
184B ASP* 4.4 4.2 - - - +
189B LYS* 3.6 40.7 + - - +
193B THR* 5.5 0.9 + - - -
356B THR* 3.5 8.1 + - - +
357B VAL* 1.3 83.4 - - - +
359B ALA* 1.3 60.0 + - - +
361B LEU* 4.2 0.5 + - - +
362B ALA* 3.4 22.2 + - - +
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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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52A ALA* 4.8 8.7 - - + +
73A SER* 3.4 22.9 - - - +
74A GLY 4.6 2.7 - - - +
75A LEU* 4.4 17.5 - - + -
355B GLN* 4.4 5.6 - - + +
356B THR* 3.1 24.1 + - + +
357B VAL 3.1 0.8 - - - -
358B ASP* 1.3 78.0 - - - +
360B ALA* 1.3 64.2 + - - +
361B LEU 3.3 0.4 - - - -
362B ALA 3.4 0.7 + - - -
363B ALA* 3.2 22.7 + - - +
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Residues in contact with ALA 360 (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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192B LEU* 5.3 1.1 - - + -
346B ALA* 3.3 40.1 - - - +
349B ASN* 4.6 0.2 - - + -
350B ALA* 4.4 7.9 - - + +
355B GLN* 3.1 31.3 + - + +
356B THR 2.8 19.9 + - - +
357B VAL 4.3 1.3 - - - +
359B ALA* 1.3 73.7 - - - +
361B LEU* 1.3 58.9 + - - +
363B ALA* 3.6 4.1 + - - +
364B ALA 3.2 18.4 + - - -
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Residues in contact with LEU 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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158B TRP* 6.2 0.7 - - + -
161B ILE* 5.0 9.6 - - + -
183B VAL* 3.3 34.7 - - + +
184B ASP* 3.9 7.1 - - - +
188B ALA* 3.8 11.0 - - + +
189B LYS* 3.8 38.6 - - + +
192B LEU* 3.8 27.8 - - + -
343B VAL* 5.9 6.3 - - + -
346B ALA* 4.7 10.5 - - + -
347B VAL* 6.1 1.1 - - + -
357B VAL* 3.3 17.5 + - + +
358B ASP 4.5 1.3 - - - +
359B ALA 3.3 0.2 - - - -
360B ALA* 1.3 76.3 - - - +
362B ALA* 1.3 58.8 + - - +
363B ALA 3.2 0.7 - - - -
364B ALA* 3.2 5.8 + - + +
365B GLN* 3.1 28.8 + - - +
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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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72A GLN 3.6 22.5 - - - +
73A SER* 3.8 12.3 - - - -
74A GLY* 4.0 4.0 - - - +
184B ASP* 3.5 22.8 + - - +
189B LYS* 5.9 0.2 - - - -
358B ASP 3.4 19.0 + - - +
359B ALA 3.4 5.1 + - - +
360B ALA 3.4 0.2 - - - -
361B LEU* 1.3 77.8 - - - +
363B ALA* 1.3 59.7 + - - +
365B GLN* 4.2 2.6 - - - +
366B THR* 3.2 26.9 + - - +
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Residues in contact with ALA 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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73A SER* 5.5 2.4 - - - +
355B GLN* 4.5 16.6 - - - +
359B ALA 3.2 15.2 + - - +
360B ALA 3.7 7.0 - - - +
361B LEU 3.2 0.2 - - - -
362B ALA* 1.3 74.9 - - - +
364B ALA* 1.3 55.6 + - - +
366B THR* 2.7 20.6 + - - -
367B ASN* 2.7 36.1 + - - +
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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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183B VAL* 4.3 10.8 - - + -
342B ALA* 3.8 29.9 - - + +
343B VAL* 4.6 3.8 - - + +
346B ALA* 3.9 8.5 - - + -
360B ALA 3.2 12.0 + - - +
361B LEU* 3.2 12.0 + - + +
363B ALA* 1.3 76.4 - - - +
365B GLN* 1.3 57.2 + - - +
367B ASN* 2.8 8.2 + - - +
368B ALA* 2.7 36.1 + - - +
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Residues in contact with GLN 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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181B VAL* 3.5 50.0 + - + +
182B GLY* 4.7 0.2 - - - -
183B VAL* 3.6 16.7 - - + +
184B ASP* 3.5 34.5 + - + +
361B LEU 3.1 12.5 + - - +
362B ALA 4.5 2.9 - - - +
363B ALA 3.5 0.2 - - - -
364B ALA* 1.3 75.9 - - - +
366B THR* 1.3 65.0 + - + +
368B ALA* 3.9 13.0 - - - +
369B ALA* 4.1 6.2 + - - +
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Residues in contact with THR 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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72A GLN* 4.2 33.2 - - + +
376A LYS* 3.2 29.8 + - - +
362B ALA 3.2 17.1 + - - +
363B ALA* 2.7 23.7 + - - -
365B GLN* 1.3 81.3 - - + +
367B ASN* 1.3 63.5 + - - +
369B ALA* 3.2 15.9 + - - +
370B ALA 3.3 1.4 + - - -
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Residues in contact with ASN 367 (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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376A LYS* 5.1 2.1 + - - -
379A LYS* 6.2 0.3 - - - +
383A SER* 4.6 14.3 + - - -
387A PHE* 4.8 16.6 - - - -
341B TYR* 6.1 4.4 - - + -
342B ALA* 4.1 14.7 + - + +
345B THR* 5.8 6.7 - - - +
363B ALA* 2.7 34.7 + - - +
364B ALA* 2.8 10.1 + - - +
366B THR* 1.3 76.6 + - - +
368B ALA* 1.3 61.1 + - - +
370B ALA* 3.1 24.6 + - - +
371B MET* 3.2 18.7 - - - +
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Residues in contact with ALA 368 (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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169B PHE* 5.9 5.6 - - + -
181B VAL* 4.9 18.2 - - + -
183B VAL* 6.1 0.4 - - + -
338B ALA* 3.7 9.3 - - + +
339B PHE* 4.8 13.0 - - + +
342B ALA* 4.1 11.8 - - + +
364B ALA 2.7 18.9 + - - +
365B GLN* 3.9 10.1 - - - +
366B THR 3.2 0.2 - - - -
367B ASN* 1.3 72.0 - - - +
369B ALA* 1.3 62.9 + - - +
371B MET* 3.0 24.9 + - - +
372B ALA 4.2 0.2 + - - -
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Residues in contact with ALA 369 (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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376A LYS* 5.0 7.0 - - + +
377A LEU* 5.6 1.2 - - - +
179B LYS* 6.3 1.3 - - - +
181B VAL* 6.1 0.4 - - - +
365B GLN 4.1 4.8 + - - +
366B THR* 3.2 12.7 + - - +
368B ALA* 1.3 71.9 - - - +
370B ALA* 1.3 53.7 + - - +
371B MET 2.8 15.3 + - - -
372B ALA* 2.8 26.5 + - - +
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Residues in contact with ALA 370 (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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376A LYS* 3.6 27.5 - - + +
377A LEU* 5.5 2.7 - - - -
380A ALA* 3.1 39.3 - - + +
384A LEU* 6.1 0.2 - - - +
366B THR 3.3 2.2 + - - -
367B ASN* 3.1 24.3 + - - +
369B ALA* 1.3 76.4 - - - +
371B MET* 1.3 64.6 + - - +
372B ALA 3.3 2.0 - - - -
373B THR* 3.5 11.9 - - - -
374B LEU* 5.2 0.7 - - - +
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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