Contacts of the helix formed by residues 323 - 342 (chain A) in PDB entry 2NUP
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 TYR 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A MET* 3.6 47.1 - - + +
301A VAL* 3.6 16.8 - - - +
302A VAL* 3.7 18.4 - - + -
303A GLY* 3.8 26.3 - - - -
321A ALA 3.2 1.2 + - - -
322A LYS* 1.3 122.1 + - + +
324A VAL* 1.3 59.2 + - - +
325A LYS 3.2 2.5 + - - -
326A LYS* 3.3 7.5 + - + +
327A GLY* 2.7 33.4 + - - -
359A GLU* 5.5 0.2 - - - -
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ARG* 3.9 16.8 - - + +
316A ILE* 5.0 14.4 - - + -
321A ALA* 3.6 30.5 + - + +
323A TYR* 1.3 76.7 - - + +
325A LYS* 1.3 63.5 + - + +
327A GLY 3.7 0.2 - - - -
328A THR* 2.7 48.8 + - - +
358A LEU* 4.2 15.9 - - + -
359A GLU* 3.5 26.5 + - - +
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ILE* 6.3 2.7 - - - -
321A ALA 5.0 1.0 + - - -
322A LYS 5.3 1.0 + - - -
323A TYR 3.2 1.0 + - - -
324A VAL* 1.3 86.6 - - + +
326A LYS* 1.3 53.2 + - - +
328A THR* 3.1 5.9 + - + +
329A LYS* 2.7 37.7 + - - +
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Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLY 5.0 0.6 + - - -
322A LYS 5.1 7.3 + - - +
323A TYR* 3.3 9.3 + - + +
325A LYS* 1.3 77.0 - - - +
327A GLY* 1.3 63.7 + - - +
329A LYS* 3.5 12.0 + - + +
330A HIS* 3.2 21.3 + - - +
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Residues in contact with GLY 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLY* 3.9 13.9 - - - -
300A MET 3.7 18.4 - - - -
323A TYR 2.7 21.5 + - - -
324A VAL 3.8 0.2 - - - -
326A LYS* 1.3 71.2 - - - +
328A THR* 1.3 64.3 + - - +
330A HIS* 3.3 8.7 + - - +
331A PHE* 3.3 22.4 + - - -
359A GLU* 4.1 9.0 - - - -
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Residues in contact with THR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 2.7 33.0 + - - +
325A LYS* 3.4 6.7 - - - +
327A GLY* 1.3 72.7 - - - +
329A LYS* 1.3 65.7 + - - +
330A HIS 3.2 0.3 + - - -
331A PHE 3.2 2.8 + - - -
332A GLU* 2.9 44.8 + - - +
358A LEU* 4.0 7.7 + - - +
359A GLU* 3.5 33.4 - - - +
361A LYS* 5.5 5.2 - - - -
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS 2.7 20.9 + - - +
326A LYS* 3.7 11.9 - - + +
328A THR* 1.3 76.3 - - - +
330A HIS* 1.3 55.4 + - - +
332A GLU* 3.2 10.8 + - + +
333A ALA* 2.9 30.5 + - + +
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Residues in contact with HIS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASP* 3.3 28.1 + - - -
265A GLY* 3.0 31.5 + - - -
269A SER* 4.4 0.7 - - - -
298A PRO* 3.6 14.8 + - + +
299A GLY* 3.3 32.5 - - - +
326A LYS 3.2 12.9 + - - +
327A GLY 3.5 7.6 - - - +
328A THR 3.2 0.2 - - - -
329A LYS* 1.3 76.7 - - - +
331A PHE* 1.3 75.8 + + - +
333A ALA* 3.3 7.6 + - - +
334A LEU* 3.2 38.8 + - + +
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Residues in contact with PHE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A SER* 4.4 6.7 - - - -
265A GLY* 3.8 30.5 - - - -
268A LEU* 3.7 31.2 - - + -
288A MET* 5.8 0.2 - - - -
294A ALA* 5.0 0.9 - - + -
299A GLY* 3.3 31.6 - - - -
301A VAL* 5.2 1.6 - - + -
327A GLY 3.3 19.4 + - - -
328A THR 3.2 2.2 + - - -
330A HIS* 1.3 78.7 - + - +
332A GLU* 1.3 59.4 + - - +
334A LEU* 4.2 7.2 - - + -
335A ALA* 2.8 29.1 + - - +
359A GLU* 3.2 25.4 - - + +
360A MET* 3.5 50.3 - - + -
362A CYS* 5.2 1.6 - - - -
363A CYS* 3.5 8.8 + - - -
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Residues in contact with GLU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A THR* 2.9 35.7 + - - +
329A LYS* 3.3 9.9 - - + +
330A HIS 3.1 0.2 - - - -
331A PHE* 1.3 77.2 - - - +
333A ALA* 1.3 64.8 + - - +
335A ALA* 3.4 7.9 + - - +
336A ASN* 3.2 29.5 + - - +
361A LYS* 5.5 3.6 - - - -
362A CYS* 3.8 32.3 - - + -
366A LEU* 5.4 2.2 - - + -
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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
----------------------------------------------------------
329A LYS* 2.9 13.2 + - + +
330A HIS* 3.6 9.9 - - - +
332A GLU* 1.3 77.6 - - - +
334A LEU* 1.3 57.5 + - - +
336A ASN* 3.2 7.0 + - - +
337A ARG* 2.9 35.7 + - + +
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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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265A GLY 4.0 1.1 - - - +
268A LEU* 3.9 20.9 - - + -
269A SER* 3.4 43.1 - - - +
272A VAL* 4.0 15.7 - - + +
330A HIS* 3.2 40.5 + - + +
331A PHE* 3.6 12.3 - - + +
333A ALA* 1.3 76.4 - - + +
335A ALA* 1.3 66.7 + - - +
337A ARG* 3.0 25.9 + - - +
338A ALA* 2.9 27.5 + - - +
345A ILE* 4.7 1.8 - - + -
363A CYS* 4.5 4.9 - - - -
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Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A PHE 2.8 19.9 + - - +
332A GLU 3.4 7.2 - - - +
334A LEU* 1.3 76.3 - - - +
336A ASN* 1.3 57.4 + - - +
338A ALA* 3.8 2.3 - - - +
339A ALA* 2.8 31.4 + - - +
345A ILE* 4.4 3.1 - - - -
362A CYS* 3.6 16.4 - - + +
363A CYS* 3.5 34.7 - - - +
366A LEU* 3.9 9.0 - - + -
367A THR* 4.1 3.5 - - - +
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Residues in contact with ASN 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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332A GLU* 3.2 13.6 + - - +
333A ALA* 3.2 9.8 + - - +
335A ALA* 1.3 76.4 - - - +
337A ARG* 1.3 55.7 + - - +
339A ALA* 3.9 4.8 - - - +
340A THR* 2.3 48.6 + - - +
366A LEU* 3.9 16.3 - - - +
424A VAL* 4.3 23.6 - - - +
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Residues in contact with ARG 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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194A ASP* 4.7 4.9 + - - -
195A LEU 4.4 4.2 + - - -
196A SER* 2.8 32.8 + - - +
197A ALA* 4.2 0.8 - - - +
269A SER* 3.9 10.7 + - - -
272A VAL* 4.0 6.4 - - + +
273A GLY* 3.8 19.6 - - - +
276A GLU* 3.5 24.5 + - - +
333A ALA* 2.9 22.5 + - + +
334A LEU* 3.0 34.4 + - - +
336A ASN* 1.3 75.7 - - - +
338A ALA* 1.3 62.6 + - - +
340A THR* 3.6 5.3 - - - -
341A THR* 2.9 29.6 + - - -
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Residues in contact with ALA 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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272A VAL* 4.2 18.3 - - + +
286A ILE* 5.2 0.9 - - + -
334A LEU 2.9 14.6 + - - +
335A ALA 3.8 0.9 - - - +
337A ARG* 1.3 75.8 - - - +
339A ALA* 1.3 60.6 + - - +
340A THR 3.1 0.2 + - - -
341A THR* 3.2 6.2 + - - -
342A GLY 2.8 25.3 + - - -
343A HIS* 3.0 28.5 + - + +
345A ILE* 3.6 27.6 - - + -
367A THR* 4.6 0.7 - - + -
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Residues in contact with ALA 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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335A ALA 2.8 22.6 + - - +
336A ASN* 3.9 8.7 - - - +
338A ALA* 1.3 74.0 - - - +
340A THR* 1.3 58.1 + - - +
342A GLY 3.5 0.2 + - - -
366A LEU* 4.6 3.1 - - + +
367A THR* 4.0 13.8 - - + +
424A VAL* 3.6 33.5 - - + +
447A LYS* 3.1 26.0 - - - +
449A CYS* 3.4 18.3 - - - -
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Residues in contact with THR 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASN* 4.3 4.2 - - - +
336A ASN* 2.3 39.6 + - - +
337A ARG* 3.6 7.2 - - - -
339A ALA* 1.3 70.8 - - - +
341A THR* 1.3 62.4 + - - +
342A GLY 3.1 1.3 - - - -
424A VAL* 6.1 2.5 - - - +
447A LYS* 2.8 24.2 + - - +
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Residues in contact with THR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL* 6.3 0.4 - - - -
276A GLU* 3.6 27.0 + - + +
280A PRO* 3.4 36.8 - - + -
281A ASN* 2.9 41.1 + - - +
337A ARG 2.9 16.7 + - - -
338A ALA* 3.7 4.9 - - - -
340A THR* 1.3 78.5 - - - +
342A GLY* 1.3 58.8 + - - +
343A HIS* 3.6 21.3 - - + -
447A LYS* 4.3 0.2 - - - -
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Residues in contact with GLY 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASN* 5.2 1.3 - - - -
282A THR 4.0 10.9 + - - +
283A GLY* 4.8 2.4 - - - -
284A ALA 4.9 0.2 + - - -
338A ALA 2.8 7.5 + - - -
339A ALA 3.8 1.8 - - - -
340A THR 3.1 3.4 - - - -
341A THR* 1.3 80.2 - - - +
343A HIS* 1.3 64.1 + - - -
344A VAL* 4.4 0.5 + - - +
403A GLY* 4.7 9.3 + - - -
447A LYS* 4.0 12.1 - - - -
449A CYS* 3.4 30.8 - - - +
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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