Contacts of the helix formed by residues 326 - 343 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A PRO 3.0 25.0 + - - -
81A GLY* 3.7 4.8 - - - -
82A TYR 4.6 4.9 - - - -
93A THR* 5.7 1.8 + - - -
115A ASN* 5.6 0.2 - - - +
292A PHE* 3.5 28.6 - + + -
294A MET* 3.6 5.7 - - - -
325A GLY* 1.3 75.2 - - - +
327A PRO* 1.3 69.9 - - + +
328A VAL* 3.0 38.4 + - + +
329A GLY 3.2 0.7 + - - -
330A CYS* 2.9 32.1 + - - -
58B ASN* 6.2 0.7 - - - -
290B GLY 2.9 28.3 + - - -
291B PHE 3.3 17.4 + - - -
292B PHE 4.5 2.0 - - - -
293B PRO* 4.6 9.4 - - + -
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Residues in contact with PRO 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLN* 3.6 18.3 - - - +
79A PHE* 3.8 13.7 - - + +
81A GLY* 3.6 19.3 - - - +
82A TYR* 3.5 39.7 - - + +
90A SER* 4.0 23.6 - - - +
92A GLN* 3.7 12.8 - - + +
93A THR* 5.5 0.7 - - - +
326A HIS* 1.3 88.1 - - + +
328A VAL* 1.3 56.9 + - - +
330A CYS* 3.4 1.9 + - + -
331A ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 4.2 7.9 - - - +
75A GLN* 3.6 20.6 - - + -
76A TYR* 3.6 50.3 - - + +
79A PHE 4.1 0.4 - - - +
80A PRO* 4.0 10.5 - - + +
292A PHE* 3.6 13.2 - - + -
326A HIS* 3.0 26.6 + - + +
327A PRO* 1.3 72.5 - - - +
329A GLY* 1.3 65.3 + - - +
331A ALA* 3.3 1.4 + - - +
332A ILE* 2.9 38.8 + - + +
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Residues in contact with GLY 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A THR* 3.8 4.8 - - - +
292A PHE* 3.3 39.8 - - - -
294A MET* 3.7 13.8 - - - +
326A HIS 3.2 7.1 + - - -
328A VAL* 1.3 79.3 - - - +
330A CYS* 1.3 56.0 + - - +
332A ILE 3.4 0.3 + - - -
333A ALA* 2.8 30.5 + - - +
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Residues in contact with CYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLN* 3.7 26.7 - - + +
93A THR* 4.0 26.2 - - - -
96A LEU* 3.9 23.7 - - + +
113A TYR* 4.6 11.0 - - - -
294A MET* 4.0 11.7 - - - -
326A HIS 2.9 21.6 + - - +
327A PRO 4.4 0.2 - - - -
328A VAL 3.2 0.4 - - - -
329A GLY* 1.3 78.2 - - - +
331A ALA* 1.3 57.2 + - - +
333A ALA* 3.3 2.6 + - - +
334A LEU* 3.0 33.8 + - - +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 4.5 10.2 - - + +
75A GLN* 3.7 27.8 - - + +
92A GLN* 3.4 23.2 + - - +
327A PRO 3.0 16.5 + - - +
328A VAL 3.8 1.3 - - - +
330A CYS* 1.3 74.3 - - - +
332A ILE* 1.3 64.0 + - - +
334A LEU* 3.4 7.0 + - - +
335A LYS* 3.1 21.5 + - - +
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Residues in contact with ILE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.5 13.8 - - + +
71A ALA* 4.8 2.0 - - - +
72A ALA* 3.6 40.8 - - + +
288A THR* 3.3 31.6 - - - +
291A PHE* 3.8 19.3 - - + +
292A PHE* 3.6 26.0 - - + -
328A VAL* 2.9 30.3 + - + +
329A GLY 3.9 2.9 - - - +
331A ALA* 1.3 77.9 - - - +
333A ALA* 1.3 52.4 + - - +
335A LYS* 3.3 5.1 + - - +
336A ALA* 2.7 32.4 + - - +
76B TYR* 4.1 2.0 - - + +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 3.7 26.7 - - + -
287A LEU* 3.2 33.9 - - + +
288A THR* 4.2 3.8 - - + +
294A MET* 4.4 1.1 - - + -
329A GLY 2.8 21.9 + - - +
330A CYS 3.6 4.9 - - - +
331A ALA 3.3 0.2 - - - -
332A ILE* 1.3 70.6 - - - +
334A LEU* 1.3 57.7 + - - +
336A ALA* 3.2 0.7 + - - +
337A ILE* 2.8 39.7 + - - +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLN* 3.7 24.0 - - - +
95A MET* 3.8 35.2 - - + +
96A LEU* 3.7 30.1 - - + +
99A LYS* 3.9 21.8 - - + +
330A CYS 3.0 18.9 + - - +
331A ALA* 3.5 7.6 - - - +
333A ALA* 1.3 74.8 - - - +
335A LYS* 1.3 63.6 + - - +
337A ILE* 3.5 4.6 + - - +
338A ASP* 3.2 22.0 + - - +
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Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A HIS* 4.9 0.7 - - - -
67A GLY* 3.8 40.7 - - - +
68A LEU* 3.9 11.7 - - + -
71A ALA* 3.8 20.0 - - + -
331A ALA 3.1 6.1 + - - +
332A ILE 3.7 6.1 - - - +
334A LEU* 1.3 79.3 - - - +
336A ALA* 1.3 58.7 + - - +
338A ASP* 3.1 17.0 + - + +
339A VAL* 2.8 46.5 + - + +
343A GLU* 4.1 16.7 + - - -
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.5 8.8 - - + +
286A ASN 4.1 4.9 - - - +
287A LEU 3.5 20.0 - - - +
288A THR 3.9 2.0 - - - -
289A ALA* 3.8 28.9 - - + +
332A ILE 2.7 20.4 + - - +
333A ALA 3.5 0.4 - - - +
335A LYS* 1.3 73.6 - - - +
337A ILE* 1.3 64.6 + - + +
339A VAL* 3.3 5.1 + - - +
340A VAL* 2.9 30.7 + - + +
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 3.7 24.9 - - + -
99A LYS* 3.8 34.1 - - + -
100A LEU* 3.8 19.5 - - + -
103A VAL* 4.4 4.3 - - + -
262A PHE* 3.6 24.9 - - + -
287A LEU* 4.7 6.7 - - + +
333A ALA 2.8 24.0 + - - +
334A LEU* 3.9 4.3 - - - +
336A ALA* 1.3 72.8 - - + +
338A ASP* 1.3 58.0 + - - +
340A VAL* 4.7 3.4 - - - -
341A MET* 2.9 54.2 + - + +
342A ASN* 6.2 0.2 - - - +
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Residues in contact with ASP 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A LEU 3.2 12.7 + - - +
335A LYS* 3.1 23.7 + - + +
337A ILE* 1.3 76.8 - - - +
339A VAL* 1.3 58.1 + - - +
342A ASN* 2.7 70.9 + - - +
343A GLU* 3.4 12.6 + - - +
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA* 4.5 6.1 - - + -
65A HIS* 3.7 39.5 - - + +
68A LEU* 4.7 3.8 - - + -
335A LYS* 2.8 44.5 + - + +
336A ALA* 3.7 5.6 - - - +
338A ASP* 1.3 75.9 - - - +
340A VAL* 1.3 65.7 + - + +
343A GLU* 2.9 45.0 + - + +
344A GLY 3.7 0.2 + - - -
345A LEU* 3.7 28.1 - - + +
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 3.9 28.3 - - + -
262A PHE* 3.4 36.8 - - + +
286A ASN 5.3 1.8 - - - +
289A ALA* 5.8 0.2 - - + -
336A ALA* 2.9 23.9 + - + +
337A ILE* 3.9 4.5 - - - +
339A VAL* 1.3 80.5 - - + +
341A MET* 1.3 68.7 + - + +
344A GLY 4.1 0.7 + - - -
345A LEU* 3.4 18.3 + - + -
346A ALA* 3.0 46.3 + - + +
347A GLU 4.7 0.2 + - - -
427A PHE* 4.4 3.8 - - + -
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Residues in contact with MET 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A VAL* 3.8 29.8 - - + +
262A PHE* 4.8 5.2 - - + -
268A THR* 3.8 29.4 - - + +
337A ILE* 2.9 36.9 + - + +
340A VAL* 1.3 89.2 - - + +
342A ASN* 1.3 73.3 + - - +
343A GLU 3.7 0.4 - - - -
344A GLY* 4.6 2.9 + - - -
346A ALA* 5.0 6.9 - - + +
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Residues in contact with ASN 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LYS* 5.9 3.4 - - - +
337A ILE* 6.2 0.4 - - - +
338A ASP* 2.7 45.1 + - - +
341A MET* 1.3 84.3 - - - +
343A GLU* 1.3 67.3 + - + +
344A GLY 3.5 2.6 + - - -
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Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A HIS* 4.4 9.7 + - - -
335A LYS* 4.1 16.2 + - - -
338A ASP* 4.0 14.5 - - - +
339A VAL* 2.9 39.4 + - + +
342A ASN* 1.3 86.5 - - + +
344A GLY* 1.3 61.0 + - - +
345A LEU* 3.4 13.6 + - - +
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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