Contacts of the helix formed by residues 343 - 363 (chain A) in PDB entry 4NKU
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 SER 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A PHE 5.0 0.2 + - - -
207A GLY* 2.9 20.0 + - - -
323A ARG* 3.7 25.4 - - - +
325A ILE* 3.8 4.0 - - - -
341A THR 3.4 1.8 + - - -
342A VAL* 1.3 77.2 - - - +
344A SER* 1.3 56.6 + - - +
345A SER* 3.2 10.1 + - - -
346A GLY* 3.1 16.8 + - - -
347A LEU* 2.8 31.5 + - - +
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Residues in contact with SER 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ILE* 3.4 26.6 - - - +
343A SER* 1.3 74.6 - - - +
345A SER* 1.3 62.0 + - - +
347A LEU* 3.5 2.5 + - - +
348A TYR* 3.2 21.8 + - - +
54B GLU* 4.1 7.2 + - - +
371B ASP* 4.9 9.5 + - - -
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER* 3.2 11.2 + - - -
344A SER* 1.3 76.7 - - - +
346A GLY* 1.3 68.3 + - - +
348A TYR* 3.2 3.3 + - - +
349A ARG* 3.0 33.1 + - - +
54B GLU* 4.1 15.9 - - - -
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Residues in contact with GLY 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE 5.8 0.4 - - - -
207A GLY 3.4 23.8 - - - -
208A THR* 3.7 10.2 - - - +
343A SER* 3.1 7.1 + - - -
345A SER* 1.3 83.3 + - - +
347A LEU* 1.3 56.6 + - - +
349A ARG* 3.3 7.4 + - - +
350A ILE* 3.0 38.9 + - - +
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Residues in contact with LEU 347 (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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285A PRO* 4.2 23.1 - - + -
286A ARG* 5.7 5.4 - - + +
325A ILE* 3.6 34.8 - - + +
326A LEU* 4.4 22.2 - - + -
342A VAL* 3.7 12.0 - - + +
343A SER 2.8 18.9 + - - +
344A SER* 3.9 3.6 - - - +
346A GLY* 1.3 70.5 - - - +
348A TYR* 1.3 61.2 + - - +
350A ILE* 4.3 11.0 - - + -
351A ARG* 2.9 48.8 + - + +
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Residues in contact with TYR 348 (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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344A SER 3.2 14.6 + - - +
345A SER 3.2 8.9 + - - +
347A LEU* 1.3 79.1 - - - +
349A ARG* 1.3 61.6 + - + +
351A ARG* 3.7 4.9 + - + +
352A GLY* 2.9 25.7 + - - -
54B GLU* 3.4 59.5 + - + +
55B ILE* 4.2 12.3 - - + +
98B LYS* 4.1 25.2 - - + +
194B HIS* 5.5 0.9 - - - -
198B ARG* 4.3 19.9 + - - -
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Residues in contact with ARG 349 (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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199A LYS 3.1 18.4 + - - -
200A GLN* 2.8 38.6 + - - +
201A ILE* 3.8 7.4 - - + +
206A PHE 5.6 2.6 + - - -
208A THR* 3.7 20.2 + - - +
345A SER* 3.0 20.0 + - - +
346A GLY* 3.3 7.3 + - - +
347A LEU 3.2 0.2 - - - -
348A TYR* 1.3 80.1 - - + +
350A ILE* 1.3 63.2 + - - +
352A GLY* 3.2 2.3 + - - -
353A GLU* 3.0 30.1 + - + +
377A ALA 5.8 0.2 + - - -
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Residues in contact with ILE 350 (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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201A ILE* 3.7 19.5 - - + -
208A THR* 3.9 19.1 - - + -
209A LEU* 4.3 10.1 - - + +
214A TYR* 3.6 26.0 - - + +
217A MET* 5.5 2.5 - - + -
326A LEU* 5.0 10.3 - - + -
342A VAL* 4.2 16.2 - - + -
346A GLY 3.0 25.3 + - - +
347A LEU* 3.4 12.1 + - + +
349A ARG* 1.3 75.1 - - - +
351A ARG* 1.3 64.6 + - + +
353A GLU* 3.1 4.9 + - - +
354A PHE* 3.0 48.0 + - + -
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Residues in contact with ARG 351 (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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279A TYR 3.6 16.3 + - - +
280A ALA* 3.0 28.2 + - - -
281A TYR* 4.1 7.1 + - - +
283A PHE 3.2 22.2 + - - -
284A GLU* 5.2 0.2 - - - +
285A PRO* 3.6 29.7 - - + +
286A ARG* 5.8 4.8 - - - +
347A LEU* 2.9 39.6 + - + +
348A TYR* 4.0 5.2 - - + +
350A ILE* 1.3 74.4 - - + +
352A GLY* 1.3 62.6 + - - +
354A PHE* 3.3 9.8 + - + +
355A MET* 3.0 43.0 + - + +
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Residues in contact with GLY 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TYR* 2.9 18.9 + - - -
349A ARG* 3.2 4.7 + - - -
351A ARG* 1.3 76.5 - - - +
353A GLU* 1.3 59.3 + - - +
355A MET* 3.4 12.1 + - - +
356A ALA* 3.0 26.7 + - - +
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Residues in contact with GLU 353 (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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195A TRP* 3.7 18.4 + - + -
199A LYS* 3.5 43.2 + - + +
201A ILE* 3.9 14.8 - - + -
349A ARG* 3.0 18.0 + - + +
350A ILE 3.1 6.7 + - - +
352A GLY* 1.3 76.2 - - - +
354A PHE* 1.3 60.2 + - - +
356A ALA* 3.8 11.5 - - - +
357A ALA* 3.0 30.1 + - - +
377A ALA 3.1 22.0 - - - +
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Residues in contact with PHE 354 (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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195A TRP* 3.8 24.2 - + - -
214A TYR* 4.5 5.2 - + - -
217A MET* 3.8 23.1 - - + -
275A PHE* 3.6 33.7 - + - -
276A PHE* 3.6 22.4 - + - +
279A TYR* 3.6 32.3 - + + +
280A ALA* 3.6 16.8 - - - -
350A ILE* 3.0 44.2 + - + -
351A ARG* 3.6 9.0 - - + +
353A GLU* 1.3 77.6 - - - +
355A MET* 1.3 57.0 + - - +
357A ALA* 3.4 3.5 + - - +
358A SER* 2.9 32.4 + - - -
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Residues in contact with MET 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ALA* 3.6 27.8 - - + +
281A TYR* 3.9 24.8 + - + +
351A ARG* 3.0 38.2 + - + +
352A GLY* 3.7 10.5 - - - +
354A PHE* 1.3 77.4 - - - +
356A ALA* 1.3 56.0 + - - +
358A SER* 3.3 3.0 + - - -
359A ARG* 2.8 36.7 + - + +
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Residues in contact with ALA 356 (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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352A GLY 3.0 16.5 + - - +
353A GLU* 3.8 12.8 - - - +
354A PHE 3.3 0.2 - - - -
355A MET* 1.3 75.2 - - - +
357A ALA* 1.3 66.6 + - - +
359A ARG* 3.3 9.8 + - - +
360A LEU* 3.0 23.9 + - - +
401A MG 4.1 13.2 - - - -
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Residues in contact with ALA 357 (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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195A TRP* 4.1 4.0 - - - +
276A PHE* 3.7 31.9 - - + -
353A GLU 3.0 17.2 + - - +
354A PHE 3.7 1.3 - - - +
356A ALA* 1.3 76.6 - - - +
358A SER* 1.3 63.8 + - - +
360A LEU* 3.4 3.6 + - - +
361A LEU* 3.1 29.2 + - - +
373A LEU* 3.7 28.7 - - + -
401A MG 4.0 3.7 - - - -
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Residues in contact with SER 358 (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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273A HIS* 4.9 0.4 - - - -
276A PHE* 3.2 29.1 + - - -
277A ARG* 3.4 9.2 + - - -
280A ALA* 3.4 3.5 - - - +
281A TYR* 3.5 28.3 - - - -
354A PHE 2.9 18.8 + - - -
355A MET 3.6 1.3 - - - -
357A ALA* 1.3 77.8 - - - +
359A ARG* 1.3 56.5 + - - +
361A LEU* 3.1 5.3 + - - -
362A ASN* 2.8 40.1 + - - +
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Residues in contact with ARG 359 (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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281A TYR* 4.1 8.5 + - - +
355A MET* 2.8 24.7 + - + +
356A ALA* 3.7 9.2 - - - +
358A SER* 1.3 72.4 - - - +
360A LEU* 1.3 65.0 - - - +
362A ASN* 3.3 17.1 + - - +
363A SER* 3.4 11.3 + - - -
146B THR 5.8 1.6 + - - -
157B PHE 4.5 20.0 - - - +
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Residues in contact with LEU 360 (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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356A ALA 3.0 14.1 + - - +
357A ALA 3.5 7.2 - - - +
358A SER 3.3 0.2 - - - -
359A ARG* 1.3 78.6 - - - +
361A LEU* 1.3 69.4 + - + +
363A SER* 3.3 17.8 - - - -
368A ILE* 3.5 27.4 - - + +
369A PRO* 3.6 25.1 - - + +
370A TYR* 4.3 5.2 - - - +
372A SER* 3.3 28.3 - - - +
373A LEU* 3.9 35.7 - - + +
401A MG 4.5 2.7 - - - -
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Residues in contact with LEU 361 (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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41A HIS* 5.7 2.5 - - + -
44A PHE* 3.7 49.8 - - + -
273A HIS* 3.4 49.6 - - + +
276A PHE* 4.0 17.0 - - + -
357A ALA 3.1 16.8 + - - +
360A LEU* 1.3 82.6 - - + +
362A ASN* 1.3 60.2 + - - +
363A SER 3.1 9.9 + - - +
368A ILE* 4.3 8.1 - - - +
370A TYR* 3.9 22.9 - - + -
373A LEU* 4.9 3.4 - - + -
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Residues in contact with ASN 362 (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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273A HIS* 2.6 34.7 + - - -
277A ARG* 3.0 30.4 + - - +
281A TYR* 3.7 22.4 + - - -
358A SER 2.8 22.4 + - - +
359A ARG* 3.3 9.3 + - + +
361A LEU* 1.3 76.2 - - - +
363A SER* 1.3 63.7 + - - +
364A ARG* 3.3 11.1 + - - +
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Residues in contact with SER 363 (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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359A ARG 3.4 7.8 + - - -
360A LEU* 3.3 18.4 - - - -
361A LEU 3.1 2.7 - - - +
362A ASN* 1.3 77.5 - - - +
364A ARG* 1.3 61.5 + - - +
365A SER* 3.4 24.3 + - - +
368A ILE* 3.3 28.6 - - - +
369A PRO* 6.4 0.2 - - - -
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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