Contacts of the helix formed by residues 343 - 362 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B GLY* 2.9 23.3 + - - -
323B ARG* 4.0 26.7 - - - +
325B ILE* 3.9 3.5 - - - +
341B THR 3.5 1.6 + - - -
342B VAL* 1.3 78.5 - - - +
344B SER* 1.3 60.3 + - - +
345B SER* 3.4 10.5 + - - -
346B GLY* 3.0 17.8 + - - -
347B LEU* 2.8 26.3 + - - +
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Residues in contact with SER 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ARG* 5.1 1.2 - - - +
325B ILE* 3.8 30.6 - - - +
343B SER* 1.3 73.6 - - - +
345B SER* 1.3 59.2 + - - +
347B LEU* 3.4 1.2 + - - +
348B TYR* 3.1 54.7 + - - -
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Residues in contact with SER 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B SER* 3.2 9.3 + - - -
344B SER* 1.3 75.8 - - - +
346B GLY* 1.3 68.2 + - - +
348B TYR* 3.2 14.6 + - - +
349B ARG* 3.1 27.6 + - - +
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Residues in contact with GLY 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE 5.6 0.2 - - - -
207B GLY* 3.3 24.0 - - - -
208B THR* 3.8 12.2 - - - +
343B SER* 3.0 11.2 + - - -
345B SER* 1.3 78.1 + - - +
347B LEU* 1.3 55.8 + - - +
349B ARG* 3.1 7.5 + - - +
350B ILE* 2.9 37.7 + - - +
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PRO* 4.0 20.0 - - + -
286B ARG* 6.2 4.5 - - + -
325B ILE* 3.5 37.2 - - + +
326B LEU* 4.5 28.5 - - + -
342B VAL* 3.7 8.1 - - + +
343B SER 2.8 16.0 + - - +
344B SER 3.7 5.2 - - - +
345B SER 3.2 0.2 - - - -
346B GLY* 1.3 71.5 - - - +
348B TYR* 1.3 71.6 + - + +
350B ILE* 4.3 11.0 - - + -
351B ARG* 2.8 49.6 + - + +
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Residues in contact with TYR 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ARG* 4.9 12.6 + - - -
325B ILE* 6.2 0.4 - - + -
344B SER* 3.1 40.9 + - - -
345B SER* 3.2 12.5 + - - +
347B LEU* 1.3 88.5 - - + +
349B ARG* 1.3 59.4 + - + +
351B ARG* 3.9 6.0 - - + +
352B GLY* 2.9 24.1 + - - -
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Residues in contact with ARG 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LYS 3.4 22.2 + - - -
200B GLN* 2.4 31.2 + - - +
201B ILE* 3.7 7.8 - - + +
206B PHE 5.9 0.6 + - - -
208B THR* 4.1 14.6 + - - +
345B SER* 3.1 15.7 + - - +
346B GLY* 3.7 8.1 - - - +
348B TYR* 1.3 77.0 - - + +
350B ILE* 1.3 59.8 + - - +
352B GLY* 3.3 2.4 + - - +
353B GLU* 2.9 39.3 + - + +
377B ALA 5.0 2.2 + - - -
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Residues in contact with ILE 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 3.8 20.1 - - + +
208B THR* 4.1 16.6 - - + -
209B LEU* 4.4 4.9 - - + -
214B TYR* 3.6 27.4 - - + +
217B MET* 5.5 3.4 - - + -
326B LEU* 4.8 9.4 - - + -
342B VAL* 4.2 21.5 - - + -
346B GLY 2.9 27.2 + - - +
347B LEU* 3.7 12.8 - - + +
349B ARG* 1.3 75.2 - - - +
351B ARG* 1.3 64.3 + - + +
353B GLU* 3.0 5.5 + - - +
354B PHE* 3.0 46.9 + - + -
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Residues in contact with ARG 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR 2.9 27.3 + - - -
280B ALA* 3.4 21.2 + - - -
281B TYR* 5.0 4.2 + - - +
283B PHE* 2.9 30.2 + - - +
284B GLU* 5.7 0.2 - - - +
285B PRO* 3.7 22.3 - - - +
347B LEU* 2.8 41.7 + - + +
348B TYR* 3.9 6.1 - - + +
350B ILE* 1.3 74.1 - - + +
352B GLY* 1.3 62.9 + - - +
354B PHE* 3.2 8.4 + - - +
355B MET* 3.0 45.5 + - + +
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Residues in contact with GLY 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B TYR 2.9 18.8 + - - -
349B ARG* 3.6 3.1 - - - -
350B ILE 3.2 0.4 - - - -
351B ARG* 1.3 75.3 - - - +
353B GLU* 1.3 59.1 + - - +
355B MET* 3.5 10.7 + - - +
356B ALA* 3.0 27.5 + - - +
359B ARG* 5.0 1.7 + - - -
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Residues in contact with GLU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B TRP* 3.7 21.5 + - + -
199B LYS* 3.7 39.4 - - + +
201B ILE* 3.9 13.5 - - + -
349B ARG* 2.9 24.2 + - + +
350B ILE 3.0 3.8 + - - +
352B GLY* 1.3 76.8 - - - +
354B PHE* 1.3 64.8 + - - +
356B ALA* 3.4 12.8 + - - +
357B ALA* 3.0 25.5 + - - +
377B ALA 2.9 23.7 - - - +
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Residues in contact with PHE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B TRP* 3.8 23.5 - + - -
214B TYR* 4.6 3.8 - + - -
217B MET* 3.7 25.4 - - + -
275B PHE* 3.5 35.9 - + - -
276B PHE* 3.6 26.8 - + - +
279B TYR* 3.6 26.9 - + + +
280B ALA* 3.7 17.5 - - - -
350B ILE* 3.0 45.8 + - + -
351B ARG* 3.6 9.4 - - - +
353B GLU* 1.3 75.6 - - - +
355B MET* 1.3 58.1 + - - +
357B ALA* 3.3 4.4 + - - +
358B SER* 2.9 32.4 + - - -
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Residues in contact with MET 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA* 3.5 28.7 - - + +
281B TYR* 3.7 31.2 + - + +
351B ARG* 3.0 42.3 + - + +
352B GLY* 3.8 7.2 - - - +
354B PHE* 1.3 77.2 - - - +
356B ALA* 1.3 56.4 + - - +
358B SER* 3.2 2.1 + - - -
359B ARG* 2.8 51.2 + - - +
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Residues in contact with ALA 356 (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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352B GLY 3.0 18.5 + - - +
353B GLU* 3.7 17.5 - - - +
355B MET* 1.3 76.9 - - - +
357B ALA* 1.3 63.2 + - - +
359B ARG* 3.5 23.5 + - - +
360B LEU* 3.1 23.2 + - - +
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Residues in contact with ALA 357 (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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195B TRP* 4.3 2.7 - - - +
276B PHE* 3.7 30.5 - - + -
353B GLU 3.0 17.5 + - - +
354B PHE 3.6 4.5 - - - +
356B ALA* 1.3 75.1 - - - +
358B SER* 1.3 65.6 + - - +
360B LEU* 3.2 5.8 + - - +
361B LEU* 3.2 28.5 + - - +
373B LEU* 3.7 26.0 - - + -
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Residues in contact with SER 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B HIS* 4.3 6.0 + - - -
276B PHE* 3.2 29.6 + - - +
277B ARG* 3.4 9.5 + - - -
280B ALA* 3.4 4.5 - - - +
281B TYR* 3.7 24.9 - - - -
354B PHE 2.9 17.9 + - - -
355B MET 3.6 4.7 - - - -
357B ALA* 1.3 77.8 - - - +
359B ARG* 1.3 61.9 + - - +
361B LEU* 3.3 5.8 + - - +
362B ASN* 3.0 27.0 + - - +
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Residues in contact with ARG 359 (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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281B TYR* 4.5 9.9 + - - +
352B GLY 5.0 1.4 + - - -
355B MET* 2.8 47.9 + - - +
356B ALA* 3.6 27.6 - - - +
358B SER* 1.3 73.3 - - - +
360B LEU* 1.3 63.0 + - - +
362B ASN* 3.4 4.4 + - - -
363B SER* 3.4 20.6 + - - -
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Residues in contact with LEU 360 (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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356B ALA 3.1 14.7 + - - +
357B ALA* 3.5 8.5 - - - +
358B SER 3.2 0.2 - - - -
359B ARG* 1.3 76.3 - - - +
361B LEU* 1.3 65.4 + - + +
363B SER* 3.2 25.9 - - - -
368B ILE* 3.3 27.0 - - + +
369B PRO* 3.5 26.0 - - + +
370B TYR* 4.1 5.2 - - - +
372B SER* 3.2 28.5 - - - +
373B LEU* 3.6 35.0 - - + +
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Residues in contact with LEU 361 (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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41B HIS* 5.6 3.4 + - + +
44B PHE* 3.8 35.0 - - + -
273B HIS* 3.4 49.7 - - + +
276B PHE* 3.9 20.4 - - + -
357B ALA 3.2 14.5 + - - +
358B SER 4.1 0.4 - - - +
360B LEU* 1.3 83.0 - - + +
362B ASN* 1.3 58.1 + - - +
363B SER 3.2 7.4 + - - +
368B ILE* 3.8 14.9 - - - +
370B TYR* 3.8 31.9 - - + -
373B LEU* 5.0 3.8 - - + -
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Residues in contact with ASN 362 (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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273B HIS* 3.2 26.7 - - - -
277B ARG* 3.5 25.5 + - - +
358B SER 3.0 16.4 + - - +
359B ARG* 3.8 5.8 - - - +
360B LEU 3.4 0.4 - - - -
361B LEU* 1.3 74.5 - - - +
363B SER* 1.3 65.9 + - - +
364B ARG* 3.6 5.7 + - - +
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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