Contacts of the helix formed by residues 344 - 359 (chain B) in PDB entry 4NSW
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 344 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254B GLU* 5.4 7.3 - - - +
327B PHE* 3.5 17.2 - - - +
342B ALA* 3.4 0.5 - - - +
343B ASP* 1.3 80.5 - - - +
345B GLU* 1.3 64.4 + - - +
346B ARG* 3.4 11.0 + - - +
347B LEU* 2.7 39.8 + - - +
348B LEU* 2.9 27.2 + - - +
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Residues in contact with GLU 345 (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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326B ARG* 5.3 0.5 + - - -
327B PHE* 3.1 36.6 - - + -
344B SER* 1.3 74.0 - - - +
346B ARG* 1.3 69.4 + - + +
348B LEU* 3.3 8.7 - - + +
349B GLN* 3.2 32.7 + - + +
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Residues in contact with ARG 346 (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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256B GLU* 3.3 36.1 + - - +
344B SER* 3.4 8.7 + - - +
345B GLU* 1.3 83.3 - - + +
347B LEU* 1.3 63.0 + - + +
349B GLN* 3.3 7.4 + - - +
350B LEU* 3.2 33.9 + - + +
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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
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254B GLU* 3.9 27.1 - - + -
255B PRO* 3.6 20.6 - - + +
256B GLU* 4.4 5.4 - - + -
257B PRO* 3.7 22.2 - - + -
271B HIS 5.8 2.2 - - - +
272B LEU* 6.5 0.2 - - + -
342B ALA* 3.8 13.2 - - + -
343B ASP* 3.9 28.9 - - + +
344B SER* 2.7 23.7 + - - +
346B ARG* 1.3 73.2 - - + +
348B LEU* 1.3 65.3 + - - +
349B GLN 3.4 0.2 + - - -
350B LEU* 3.4 13.1 + - + +
351B TRP* 3.0 36.9 + - + +
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Residues in contact with LEU 348 (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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319B LEU* 4.0 18.6 - - + -
327B PHE* 3.5 44.9 - - + +
328B CYS 4.0 7.6 - - - +
329B PHE* 3.6 21.1 - - + -
342B ALA* 3.4 10.9 - - + +
344B SER 2.9 14.6 + - - +
345B GLU* 3.3 9.4 - - + +
347B LEU* 1.3 77.9 - - - +
349B GLN* 1.3 75.9 + - - +
351B TRP* 3.4 2.1 + - - +
352B VAL* 2.9 42.2 + - + +
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Residues in contact with GLN 349 (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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319B LEU* 5.0 7.5 - - - +
345B GLU* 3.2 19.3 + - + +
346B ARG* 3.3 5.8 + - - +
348B LEU* 1.3 102.0 - - - +
350B LEU* 1.3 62.2 + - - +
352B VAL* 3.4 15.3 + - - +
353B SER* 3.1 28.2 + - - -
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Residues in contact with LEU 350 (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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256B GLU* 3.8 42.4 - - + +
257B PRO* 4.2 17.5 - - + +
259B LEU* 4.0 17.9 - - + +
268B MET* 4.8 3.1 - - - -
346B ARG* 3.2 24.9 + - - +
347B LEU* 3.5 17.3 - - + +
349B GLN* 1.3 78.3 - - - +
351B TRP* 1.3 62.4 + - + +
353B SER* 3.7 5.7 + - - +
354B ALA* 3.2 22.9 + - - +
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Residues in contact with TRP 351 (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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257B PRO* 4.1 13.4 - - + +
268B MET* 3.1 35.0 - - + -
269B GLU* 4.3 3.8 - - - -
270B GLY* 3.8 36.6 - - - -
271B HIS 4.1 4.0 + - - -
272B LEU* 3.4 46.1 - - + +
288B PHE* 4.0 20.6 - - + -
290B ILE* 3.8 26.5 - - + -
295B LEU* 4.8 4.3 - - + -
329B PHE* 3.9 16.8 - + + -
340B LEU* 6.3 0.2 - - + -
342B ALA* 4.5 1.1 - - + -
347B LEU* 3.0 39.0 + - + +
348B LEU 3.7 3.1 - - - +
350B LEU* 1.3 75.4 - - + +
352B VAL* 1.3 61.1 + - - +
354B ALA* 3.2 2.1 + - - +
355B VAL* 2.9 39.0 + - + +
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Residues in contact with VAL 352 (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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317B VAL* 4.4 11.4 - - + +
318B LYS 6.0 1.1 - - - -
319B LEU* 5.0 11.7 - - + -
329B PHE* 3.7 39.3 - - + -
348B LEU* 2.9 32.1 + - + +
349B GLN* 3.4 25.5 + - + +
351B TRP* 1.3 73.6 - - - +
353B SER* 1.3 54.8 + - - +
355B VAL* 3.3 7.4 + - - +
356B GLN* 2.7 49.2 + - + +
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Residues in contact with SER 353 (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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259B LEU* 4.8 5.4 - - - +
349B GLN 3.1 18.7 + - - -
350B LEU* 3.7 6.4 + - - +
352B VAL* 1.3 75.5 - - - +
354B ALA* 1.3 57.7 + - - +
356B GLN* 3.7 20.2 - - - +
357B SER* 2.7 37.1 + - - -
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Residues in contact with ALA 354 (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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259B LEU* 3.7 23.5 - - + +
266B LEU* 5.9 0.5 - - - +
268B MET* 3.6 24.9 - - + -
290B ILE* 4.1 8.3 - - + -
350B LEU 3.2 20.4 + - - +
351B TRP 3.3 5.8 - - - +
353B SER* 1.3 75.3 - - - +
355B VAL* 1.3 55.2 + - - +
357B SER* 3.3 3.9 + - - -
358B SER* 2.5 36.7 + - - -
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Residues in contact with VAL 355 (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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290B ILE* 4.3 14.4 - - + -
295B LEU* 5.6 6.1 - - + -
312B LEU* 3.9 23.1 - - + -
315B CYS* 6.4 0.2 - - + -
317B VAL* 3.4 24.5 - - + -
329B PHE* 4.7 15.0 - - + -
331B VAL* 4.5 18.4 - - + -
351B TRP* 2.9 22.0 + - + +
352B VAL* 3.7 6.5 - - - +
354B ALA* 1.3 72.7 - - - +
356B GLN* 1.3 67.0 + - - +
358B SER* 3.0 14.6 + - - -
359B ILE* 3.0 21.7 + - + +
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Residues in contact with GLN 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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317B VAL* 4.3 13.6 - - + +
352B VAL* 2.7 32.1 + - + +
353B SER* 3.7 27.6 - - - +
355B VAL* 1.3 72.1 - - - +
357B SER* 1.3 61.7 + - - +
359B ILE* 3.4 25.2 + - + +
360B ALA* 3.8 4.3 + - - +
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Residues in contact with SER 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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259B LEU* 4.6 7.2 - - - +
266B LEU* 4.6 27.3 - - - +
353B SER* 2.7 23.2 + - - -
354B ALA* 3.6 6.5 - - - -
355B VAL 3.1 0.4 - - - -
356B GLN* 1.3 73.3 - - - +
358B SER* 1.3 57.3 + - - +
359B ILE 3.0 4.9 - - - -
360B ALA* 2.9 31.6 + - - +
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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
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266B LEU* 4.9 16.5 - - - +
290B ILE* 3.5 24.7 - - - +
293B ASN* 3.7 25.5 + - - +
312B LEU* 3.4 30.3 - - - +
313B ARG* 4.7 1.6 + - - +
354B ALA 2.5 25.8 + - - -
355B VAL* 3.0 3.9 + - - -
357B SER* 1.3 75.0 - - - +
359B ILE* 1.3 60.2 + - - +
360B ALA 3.4 3.9 - - - +
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Residues in contact with ILE 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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312B LEU* 3.5 20.9 - - + +
313B ARG* 4.0 21.3 - - - +
315B CYS* 3.6 28.0 - - + +
316B THR* 4.3 4.9 - - + -
317B VAL* 3.6 29.6 - - + -
355B VAL* 3.0 18.8 - - + +
356B GLN* 3.4 14.8 - - + +
357B SER 3.0 1.0 - - - -
358B SER* 1.3 77.1 - - - +
360B ALA* 1.3 62.7 + - - +
361B SER* 3.5 3.5 + - - -
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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