Contacts of the helix formed by residues 355 - 372 (chain B) in PDB entry 5ICN
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 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ARG* 3.9 8.5 + - - +
352B ASN 5.3 3.8 - - - +
353B GLN* 3.6 7.4 + - - +
354B ASN* 1.3 78.5 - - - +
356B ASN* 1.3 65.7 + - - +
357B GLU* 3.8 22.5 + - - +
358B TYR* 2.9 29.1 + - - +
359B LEU* 3.2 9.2 + - - +
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Residues in contact with ASN 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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236B SER* 5.3 3.3 + - - -
354B ASN 3.6 3.8 + - - +
355B THR* 1.3 71.9 - - - +
357B GLU* 1.3 72.1 + - - +
359B LEU* 3.5 11.5 + - - +
360B GLU* 3.1 29.7 + - + +
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Residues in contact with GLU 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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355B THR* 3.1 20.7 + - - +
356B ASN* 1.3 88.3 + - + +
358B TYR* 1.3 62.8 + - - +
360B GLU* 3.6 3.2 + - - +
361B LYS* 3.1 31.8 + - + +
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Residues in contact with TYR 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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201B TYR* 5.9 0.2 - - - +
227B PRO* 3.0 30.1 + - - +
228B LEU* 3.9 2.8 + - - -
229B ARG* 3.2 45.5 - - - +
354B ASN* 3.4 31.0 - - - -
355B THR* 2.9 20.5 + - - +
357B GLU* 1.3 80.7 - - - +
359B LEU* 1.3 69.5 + - + +
361B LYS* 3.8 9.1 + - + +
362B ILE* 3.3 44.4 + - + +
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Residues in contact with LEU 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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226B TYR* 2.5 34.7 + - + +
228B LEU* 3.7 29.8 - - + -
232B ILE* 4.8 2.7 - - + -
236B SER* 4.1 24.7 - - - +
240B ILE* 4.1 20.0 - - + -
354B ASN* 3.6 34.1 - - + +
355B THR 3.2 10.4 + - - +
356B ASN* 4.0 13.5 - - - +
358B TYR* 1.3 79.5 - - + +
360B GLU* 1.3 59.5 + - + +
362B ILE 3.5 0.9 + - - -
363B LYS* 2.9 18.5 + - - +
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Residues in contact with GLU 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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356B ASN* 3.1 19.1 + - + +
357B GLU* 4.1 4.5 - - - +
359B LEU* 1.3 74.9 - - + +
361B LYS* 1.3 63.8 + - - +
363B LYS* 2.8 35.6 + - - +
364B GLN* 3.1 55.8 + - - +
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Residues in contact with LYS 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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357B GLU* 3.1 24.0 + - + +
358B TYR* 3.9 9.6 - - + +
360B GLU* 1.3 78.6 - - - +
362B ILE* 1.3 64.3 + - + +
364B GLN* 3.3 5.1 + - - +
365B ARG* 3.2 51.0 + - - +
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Residues in contact with ILE 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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211B LEU* 3.9 20.2 - - + -
225B ASN 4.8 0.2 - - - +
226B TYR* 3.7 24.0 - - + -
227B PRO* 3.5 30.1 - - + +
358B TYR* 3.3 52.4 + - + +
359B LEU 3.5 6.6 + - - +
360B GLU 3.3 0.2 - - - -
361B LYS* 1.3 75.9 - - + +
363B LYS* 1.3 69.2 - - - +
365B ARG* 3.0 19.2 + - - +
366B LEU* 3.0 25.1 + - + +
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Residues in contact with LYS 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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226B TYR* 3.6 15.0 + - - +
239B ALA 4.2 14.5 + - - -
240B ILE* 4.5 13.9 - - - -
243B PRO* 4.2 20.6 - - + +
244B VAL* 4.6 9.9 - - + -
359B LEU* 2.9 17.9 + - - +
360B GLU* 2.8 36.0 + - - +
362B ILE* 1.3 75.7 - - - +
364B GLN* 1.3 71.4 + - - +
366B LEU* 2.9 8.0 + - - +
367B PHE* 2.9 50.5 + - + -
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Residues in contact with GLN 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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360B GLU* 3.1 38.9 + - - +
361B LYS* 3.6 4.7 - - - +
363B LYS* 1.3 84.1 + - - +
365B ARG* 1.3 66.4 + - + +
367B PHE* 3.0 13.4 + - - +
368B GLU* 3.0 30.5 + - + +
371B ARG* 5.1 10.9 - - - +
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Residues in contact with ARG 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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211B LEU* 3.8 42.8 - - + +
212B ARG* 4.9 13.7 - - - +
361B LYS* 3.2 53.4 + - - +
362B ILE 3.0 7.4 + - - +
364B GLN* 1.3 78.2 - - - +
366B LEU* 1.3 56.1 + - - +
368B GLU* 3.4 21.4 - - - +
369B ASN* 3.1 29.6 + - - -
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Residues in contact with LEU 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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211B LEU* 5.0 12.6 - - + +
224B VAL* 4.0 26.2 - - + -
225B ASN 3.3 31.4 - - - +
226B TYR* 3.4 33.7 - - + -
244B VAL* 4.5 12.8 - - + -
362B ILE* 3.0 17.7 + - + +
363B LYS* 2.9 7.2 + - - +
365B ARG* 1.3 75.1 - - + +
367B PHE* 1.3 56.5 + - - +
368B GLU 3.2 0.2 - - - -
369B ASN* 3.1 19.5 + - + +
370B LEU* 2.8 42.1 + - + +
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Residues in contact with PHE 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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243B PRO* 4.0 32.1 - - + -
244B VAL* 4.5 9.9 - - + -
247B LYS* 3.9 31.7 - - + -
363B LYS* 2.9 48.4 + - + +
364B GLN* 3.0 18.1 + - - +
366B LEU* 1.3 76.4 - - - +
368B GLU* 1.3 56.1 + - - +
370B LEU* 3.6 8.9 + - + +
371B ARG* 3.0 60.2 + - - +
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Residues in contact with GLU 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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364B GLN* 3.0 16.4 + - + +
365B ARG* 3.4 33.1 + - - +
367B PHE* 1.3 74.0 - - + +
369B ASN* 1.3 70.2 + - - +
371B ARG* 3.0 26.0 + - - +
372B MET* 3.4 14.4 + - - +
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Residues in contact with ASN 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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211B LEU* 4.6 11.7 + - - +
214B ILE* 4.0 25.1 - - + +
221B TYR* 3.7 34.5 - - + -
224B VAL* 6.3 2.5 - - + -
365B ARG 3.1 15.2 + - - +
366B LEU* 3.1 25.1 + - + +
368B GLU* 1.3 81.0 - - - +
370B LEU* 1.3 65.2 + - + +
372B MET* 3.1 20.2 + - - +
373B LEU* 4.0 6.5 - - - +
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Residues in contact with LEU 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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194B MET* 4.2 17.3 - - + -
221B TYR 5.4 1.3 - - - +
224B VAL* 3.8 28.5 - - + -
244B VAL* 4.1 10.5 - - + +
247B LYS* 3.5 36.3 - - + -
248B VAL* 3.9 27.1 - - + +
251B MET* 3.2 25.7 - - + +
366B LEU* 2.8 28.6 + - + +
367B PHE* 4.0 6.7 - - + +
369B ASN* 1.3 73.7 - - + +
371B ARG* 1.3 63.4 + - - +
372B MET 3.2 1.0 + - - -
373B LEU* 3.2 15.5 + - + +
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Residues in contact with ARG 371 (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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247B LYS* 3.4 30.5 - - - +
251B MET* 4.7 6.3 - - - -
364B GLN* 5.1 8.3 - - - +
367B PHE* 3.0 53.1 + - - +
368B GLU* 3.0 17.8 + - - +
370B LEU* 1.3 76.0 - - - +
372B MET* 1.3 61.7 + - + +
373B LEU 3.1 11.4 - - - +
375B HIS* 3.7 14.7 + - - +
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Residues in contact with MET 372 (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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221B TYR* 3.6 51.9 - - + +
368B GLU 3.7 9.2 - - - +
369B ASN* 3.3 16.4 - - - +
370B LEU 3.1 0.8 - - - -
371B ARG* 1.3 77.7 - - - +
373B LEU* 1.3 61.9 + - - +
374B PRO* 3.9 1.7 - - - +
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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