Contacts of the helix formed by residues 326 - 343 (chain B) in PDB entry 3NUI
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 HIS 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A GLY 4.9 5.7 + - - -
291A PHE 5.1 2.0 + - - -
293A PRO* 3.9 17.9 - - + +
79B PHE* 4.3 16.7 - + - -
80B PRO* 5.7 0.2 - - + -
82B TYR* 3.6 39.0 + + + +
113B TYR* 5.0 0.2 - - - +
115B ASN* 5.6 4.7 - - - +
292B PHE* 3.5 37.7 - + + -
293B PRO 5.6 0.4 - - - +
294B MET* 4.1 11.2 - - + +
324B SER 4.0 0.2 + - - -
325B GLY* 1.3 68.1 - - - -
327B PRO* 1.4 69.0 - - + +
328B VAL* 3.2 33.1 + - + -
329B GLY* 3.2 0.7 + - - +
330B CYS* 2.8 27.9 + - - -
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Residues in contact with PRO 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PRO* 3.5 35.7 - - + -
82B TYR* 3.4 35.4 - - + -
90B SER* 3.4 25.6 - - - +
92B GLN* 3.6 13.9 + - + +
93B THR* 4.0 6.1 - - - +
325B GLY 3.4 7.0 - - - +
326B HIS* 1.4 86.1 - - - +
328B VAL* 1.3 60.4 + - - +
330B CYS* 3.8 2.8 - - + +
331B ALA* 3.0 23.7 + - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 3.8 25.4 - - + +
76B TYR* 3.7 19.7 - - + -
79B PHE* 3.8 15.5 - - + -
80B PRO* 3.6 26.9 - - + -
292B PHE* 3.6 22.2 - - + -
326B HIS* 3.2 23.9 + - + +
327B PRO* 1.3 76.6 - - - +
329B GLY* 1.3 63.0 + - - +
331B ALA* 3.1 4.5 + - - +
332B ILE* 2.9 30.7 + - + +
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Residues in contact with GLY 329 (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 THR* 3.9 1.2 - - - +
292B PHE* 3.4 37.6 - - - -
294B MET* 3.5 15.0 - - - +
326B HIS 3.2 6.1 + - - -
328B VAL* 1.3 80.3 - - - +
330B CYS* 1.3 55.7 + - - +
332B ILE* 3.3 2.7 + - - +
333B ALA* 2.8 30.5 + - - +
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Residues in contact with CYS 330 (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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92B GLN* 3.7 20.6 - - - +
93B THR* 3.8 22.0 - - - +
96B LEU* 3.8 25.1 - - + +
113B TYR* 4.4 3.6 - - - -
294B MET* 4.1 5.6 - - - -
325B GLY* 3.8 23.6 - - - -
326B HIS 2.8 24.5 + - - +
327B PRO 3.8 4.7 - - - +
329B GLY* 1.3 71.4 - - - +
331B ALA* 1.3 63.1 + - - +
333B ALA* 3.3 2.9 + - - +
334B LEU* 3.1 27.6 + - - +
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Residues in contact with ALA 331 (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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71B ALA* 5.5 2.7 - - - +
75B GLN* 3.3 39.3 - - + +
92B GLN* 3.9 15.8 - - + +
327B PRO 3.0 14.0 + - - +
328B VAL 3.1 0.9 + - - +
330B CYS* 1.3 77.0 - - - +
332B ILE* 1.3 61.9 + - - +
334B LEU* 3.5 10.5 + - - +
335B LYS* 3.2 20.4 + - - +
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Residues in contact with ILE 332 (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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76A TYR* 3.7 18.2 - - + +
68B LEU* 4.0 8.9 - - + +
71B ALA* 4.8 3.8 - - + +
72B ALA* 3.5 37.7 - - + +
75B GLN* 4.6 3.8 - - + -
288B THR* 3.9 16.8 - - - +
291B PHE* 3.7 26.0 - - + +
292B PHE* 4.0 10.1 - - + -
328B VAL* 2.9 37.1 + - + +
329B GLY* 3.8 5.4 - - - +
331B ALA* 1.3 74.6 - - - +
333B ALA* 1.3 52.4 + - - +
335B LYS* 3.2 8.6 + - - +
336B ALA* 2.7 33.0 + - - +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.8 23.8 - - + -
287B LEU* 3.3 26.8 - - + +
288B THR* 3.9 9.4 - - + +
294B MET* 4.1 3.4 - - + -
329B GLY 2.8 17.5 + - - +
330B CYS 3.6 4.7 - - - +
332B ILE* 1.3 73.6 - - - +
334B LEU* 1.3 56.8 + - - +
337B ILE* 2.7 42.7 + - - +
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Residues in contact with LEU 334 (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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92B GLN* 3.9 26.9 - - + +
95B MET* 3.7 30.3 - - + +
96B LEU* 3.9 9.6 - - + +
99B LYS* 3.7 40.8 - - + -
330B CYS 3.1 14.9 + - - +
331B ALA* 3.6 12.1 - - - +
333B ALA* 1.3 74.2 - - - +
335B LYS* 1.3 61.8 + - - +
337B ILE* 3.5 4.1 + - - +
338B ASP* 3.1 23.9 + - - +
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Residues in contact with LYS 335 (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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67B GLY* 3.8 29.2 + - - -
68B LEU* 3.6 18.2 - - + -
71B ALA* 3.9 22.9 - - + -
331B ALA 3.2 9.4 + - - +
332B ILE 3.2 9.0 + - - +
334B LEU* 1.3 74.5 - - - +
336B ALA* 1.3 61.5 + - - +
338B ASP* 3.1 13.7 + - + +
339B VAL* 2.8 43.6 + - + +
343B GLU* 4.4 14.5 + - - -
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 3.4 16.0 - - + +
286B ASN 4.1 3.4 - - - +
287B LEU 3.4 22.7 - - - +
288B THR 3.6 20.4 - - - -
289B ALA* 3.8 9.4 - - + +
332B ILE 2.7 18.1 + - - +
335B LYS* 1.3 72.8 - - - +
337B ILE* 1.3 61.7 + - - +
339B VAL* 3.3 4.5 + - - +
340B VAL* 3.0 30.5 + - + +
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Residues in contact with ILE 337 (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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96B LEU* 3.8 15.9 - - + -
99B LYS* 4.2 26.7 - - + -
100B LEU* 3.8 29.2 - - + -
103B VAL* 4.7 1.6 - - + -
262B PHE* 3.9 25.6 - - + -
286B ASN 5.8 0.2 - - - +
287B LEU* 4.2 13.0 - - + +
333B ALA 2.7 25.0 + - - +
334B LEU* 4.0 4.3 - - - +
336B ALA* 1.3 71.7 - - - +
338B ASP* 1.3 58.1 + - - +
340B VAL* 3.4 3.5 + - - -
341B MET* 2.9 54.7 + - + +
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Residues in contact with ASP 338 (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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334B LEU 3.1 18.2 + - - +
335B LYS* 3.5 14.3 + - + +
337B ILE* 1.3 75.7 - - - +
339B VAL* 1.3 66.4 + - - +
342B ASN* 2.8 60.5 + - - +
343B GLU* 3.5 13.3 + - - +
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Residues in contact with VAL 339 (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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61B ALA* 4.6 5.2 - - + -
65B HIS* 3.6 40.4 - - + +
68B LEU* 4.4 5.4 - - + -
335B LYS* 2.8 41.9 + - + +
336B ALA* 3.7 7.2 - - - +
338B ASP* 1.3 75.8 - - + +
340B VAL* 1.3 62.9 + - + +
343B GLU* 3.0 49.3 + - - +
345B LEU* 3.8 26.8 - - + +
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Residues in contact with VAL 340 (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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60B VAL* 4.0 26.5 - - + -
61B ALA* 6.0 0.4 - - + -
262B PHE* 3.4 36.1 - - + +
286B ASN 5.2 4.9 - - - +
289B ALA* 5.6 1.3 - - + -
336B ALA* 3.0 24.6 + - + +
337B ILE* 4.0 4.3 - - - +
339B VAL* 1.3 81.0 - - + +
341B MET* 1.3 67.4 + - + +
344B GLY 4.3 0.2 + - - -
345B LEU* 3.5 18.5 + - + -
346B ALA* 2.9 42.8 + - + +
347B GLU 4.8 0.2 + - - -
427B PHE* 4.1 7.9 - - + -
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Residues in contact with MET 341 (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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103B VAL* 3.9 25.1 - - + -
262B PHE* 4.6 8.3 - - + -
268B THR* 3.8 34.3 - - + +
337B ILE* 2.9 39.0 + - + +
340B VAL* 1.3 87.6 - - + +
342B ASN* 1.3 73.5 + - - +
343B GLU 3.8 0.4 - - - -
344B GLY* 4.8 3.0 + - - -
346B ALA* 4.8 8.3 - - + +
347B GLU* 5.8 0.9 + - - +
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Residues in contact with ASN 342 (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 ASP* 2.8 40.2 + - - +
341B MET* 1.3 90.5 + - - +
343B GLU* 1.3 62.4 + - + +
344B GLY 3.5 4.4 + - - -
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Residues in contact with GLU 343 (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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65B HIS* 4.3 12.2 + - + -
335B LYS* 4.4 13.3 + - - -
338B ASP* 4.1 11.3 - - - +
339B VAL* 3.0 43.6 + - + +
342B ASN* 1.3 82.5 - - + +
344B GLY* 1.3 60.1 + - - +
345B LEU* 3.4 14.3 + - + +
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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
------------------------------------------------------------
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