Contacts of the helix formed by residues 335 - 352 (chain B) in PDB entry 3IO6
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 GLN 335 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B PHE* 3.8 26.1 - - + -
178B ILE* 3.5 32.6 - - + +
333B ILE* 3.2 7.3 - - + +
334B PRO* 1.3 100.4 - - - +
336B MET* 1.3 63.9 + - - +
337B SER 3.2 0.2 - - - -
338B ALA* 3.1 20.8 + - - +
339B PHE 3.4 4.5 + - - -
372B ALA* 4.1 25.2 + - + +
373B THR* 6.2 2.7 - - + +
376B LYS* 4.9 15.8 - - - +
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Residues in contact with MET 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ALA* 4.0 6.3 - - + -
169B PHE* 4.0 15.2 - - - -
258B PHE* 4.0 8.7 - - + -
330B MET* 4.1 5.6 - - + -
331B PRO* 3.4 55.4 - - + +
333B ILE* 3.1 18.0 + - + +
334B PRO 3.0 0.6 - - - -
335B GLN* 1.3 76.5 - - - +
337B SER* 1.3 66.0 + - - +
339B PHE* 3.1 46.3 + - + +
340B TRP* 3.2 37.7 + - + +
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Residues in contact with SER 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PRO* 3.3 17.1 + - - +
336B MET* 1.3 78.4 - - - +
338B ALA* 1.3 62.6 + - - +
340B TRP* 3.7 11.5 + - - +
341B TYR* 3.5 16.8 + - - +
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PRO 4.7 0.2 + - - -
335B GLN 3.1 11.3 + - - +
336B MET 3.1 0.6 - - - -
337B SER* 1.3 76.4 - - - +
339B PHE* 1.3 66.5 + - - +
341B TYR* 2.8 10.0 + - - +
342B ALA* 2.8 25.6 + - - +
368B ALA* 3.4 31.0 - - + +
371B MET* 4.1 11.7 - - + -
372B ALA* 3.5 21.9 - - + +
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Residues in contact with PHE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TRP* 3.5 33.9 - + - -
168B ALA* 3.6 27.6 - - + -
169B PHE* 4.5 9.2 - + + -
181B VAL* 5.2 2.7 - - + -
183B VAL* 3.5 29.4 - - + -
258B PHE* 4.0 4.9 - + - -
335B GLN 3.4 4.2 + - - +
336B MET* 3.1 44.5 + - + +
338B ALA* 1.3 76.4 - - - +
340B TRP* 1.3 92.0 + + - +
342B ALA* 3.4 5.0 + - + +
343B VAL* 2.9 40.7 + - + +
368B ALA* 4.5 7.2 - - + +
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Residues in contact with TRP 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PRO* 4.0 21.5 - - + +
155B TYR* 4.1 26.2 - + + -
158B TRP* 5.4 1.1 - + + -
258B PHE* 3.3 34.3 - + - -
330B MET* 3.6 35.6 - - + -
336B MET* 3.2 30.0 + - + +
337B SER* 3.7 10.8 - - - +
338B ALA 3.2 0.6 - - - -
339B PHE* 1.3 101.6 - + - +
341B TYR* 1.3 53.3 + - - +
343B VAL* 3.8 1.3 - - + +
344B ARG* 2.7 45.1 + - + +
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Residues in contact with TYR 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LEU* 4.4 7.9 + - + +
387A PHE* 2.2 74.4 + + + +
388A GLN* 5.2 1.6 - - - +
337B SER 3.5 8.6 + - - +
338B ALA* 2.8 13.4 + - - +
340B TRP* 1.3 76.2 - - - +
342B ALA* 1.3 59.7 + - - +
344B ARG* 3.8 21.4 - - + +
345B THR* 2.9 29.7 + - - -
367B ASN* 6.3 0.4 - - + -
371B MET* 3.8 26.0 - - + -
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Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ALA 2.8 14.9 + - - +
339B PHE* 3.7 4.0 - - - +
341B TYR* 1.3 80.6 - - - +
343B VAL* 1.3 58.3 + - + +
345B THR* 3.5 4.0 + - - -
346B ALA* 3.2 24.3 + - - +
364B ALA* 3.4 38.2 - - + +
367B ASN* 4.2 11.6 + - + +
368B ALA* 3.8 17.7 - - + +
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PRO* 3.8 21.3 - - + -
158B TRP* 4.1 21.5 - - + -
161B ILE* 4.6 1.1 - - + -
183B VAL* 4.0 19.7 - - + -
339B PHE* 2.9 50.5 + - + +
340B TRP 4.0 1.3 - - - +
342B ALA* 1.3 76.0 - - + +
344B ARG* 1.3 65.4 + - - +
346B ALA* 3.6 8.2 - - + +
347B VAL* 3.0 36.6 + - + +
361B LEU* 5.8 3.1 - - + -
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Residues in contact with ARG 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLN 4.0 8.8 + - - +
153B GLU* 2.8 32.0 + - - -
154B PRO* 3.5 26.6 - - + +
340B TRP* 2.7 27.5 + - + +
341B TYR* 3.8 25.9 - - + +
342B ALA 3.3 0.2 - - - -
343B VAL* 1.3 73.9 - - - +
345B THR* 1.3 58.6 + - - +
347B VAL* 4.3 1.7 - - - +
348B ILE* 3.1 35.2 + - - +
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Residues in contact with THR 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PHE* 3.4 42.1 - - + -
341B TYR* 2.9 18.8 + - - -
342B ALA 3.9 4.9 + - - -
343B VAL 3.3 0.2 - - - -
344B ARG* 1.3 74.8 - - - +
346B ALA* 1.3 57.9 + - - +
348B ILE* 4.6 3.6 - - + -
349B ASN* 2.7 64.2 + - - +
367B ASN* 5.6 1.3 - - - -
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU* 5.1 2.0 - - - -
342B ALA 3.2 12.4 + - - +
343B VAL* 3.3 14.1 + - - +
345B THR* 1.3 78.6 - - - +
347B VAL* 1.3 58.5 + - + +
349B ASN* 4.8 0.9 - - - +
350B ALA* 2.9 32.7 + - - +
355B GLN* 5.7 0.2 - - - -
360B ALA* 3.7 35.7 - - - +
361B LEU* 4.3 15.0 - - + -
364B ALA* 4.2 7.2 - - + -
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.7 23.6 - - + +
152B GLN 5.9 0.7 - - - +
154B PRO* 5.0 4.9 - - + -
157B THR* 3.8 21.1 - - + +
161B ILE* 3.8 28.7 - - + -
192B LEU* 4.2 13.5 - - + +
195B LEU* 4.3 13.6 - - + +
196B VAL* 5.7 0.2 - - - +
343B VAL* 3.0 25.1 + - + +
344B ARG* 4.3 3.1 - - - +
346B ALA* 1.3 76.2 - - + +
348B ILE* 1.3 57.7 + - + +
350B ALA* 3.9 0.9 - - - +
351B ALA* 3.0 30.7 + - + +
361B LEU* 6.0 1.1 - - + -
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Residues in contact with ILE 348 (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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151B LEU 3.8 9.2 - - - +
152B GLN* 3.4 53.2 - - - +
206B ALA 5.3 2.2 - - - +
344B ARG* 3.1 23.3 + - - +
345B THR* 3.3 5.7 + - + +
347B VAL* 1.3 77.4 - - + +
349B ASN* 1.3 70.0 + - - +
351B ALA* 3.5 6.0 + - + +
352B SER* 3.1 27.5 + - - +
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Residues in contact with ASN 349 (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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345B THR* 2.7 43.8 + - - +
346B ALA* 4.0 2.9 - - - +
348B ILE* 1.3 80.2 - - - +
350B ALA* 1.3 60.3 + - - +
352B SER* 3.4 7.1 + - - -
353B GLY 3.4 0.2 + - - -
354B ARG* 3.3 41.1 + - - +
355B GLN* 3.2 58.7 + - + +
360B ALA* 4.7 0.9 - - + -
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Residues in contact with ALA 350 (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* 3.6 27.8 - - + -
196B VAL* 3.3 30.3 - - + +
346B ALA 2.9 19.1 + - - +
347B VAL 3.9 4.0 - - - +
348B ILE 3.3 0.2 - - - -
349B ASN* 1.3 76.1 - - - +
351B ALA* 1.3 62.2 + - - +
352B SER 3.6 0.2 + - - -
353B GLY* 3.6 8.5 + - - -
355B GLN 3.8 13.7 - - - +
356B THR 4.9 3.4 - - - +
357B VAL* 5.0 2.9 - - - -
360B ALA* 4.4 7.1 - - + +
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 5.7 4.7 - - + +
195B LEU* 6.0 0.9 - - + -
196B VAL* 4.1 5.0 - - + +
199B ILE* 3.6 48.1 - - + +
206B ALA* 3.8 19.8 - - + +
347B VAL* 3.0 20.9 + - + +
348B ILE* 4.0 8.5 - - + +
349B ASN 3.4 0.2 - - - -
350B ALA* 1.3 76.6 - - - +
352B SER* 1.3 60.3 + - - +
353B GLY 3.5 0.3 + - - -
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA* 5.0 4.9 - - - -
348B ILE* 3.1 21.9 + - - +
349B ASN* 3.4 10.6 + - - -
351B ALA* 1.3 77.7 - - - +
353B GLY* 1.3 57.1 + - - +
354B ARG* 3.1 21.8 + - - +
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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
------------------------------------------------------------
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