Contacts of the helix formed by residues 337 - 348 (chain K) in PDB entry 5ANC
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 PRO 337 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308K VAL* 3.6 33.6 - - + +
311K LYS* 3.8 30.5 - - + +
312K ASP 5.8 1.1 - - - +
316K ILE* 4.5 6.4 - - + +
334K HIS* 5.2 0.9 - - + -
335K SER* 3.8 6.1 - - - +
336K ASP* 1.3 90.9 - - - +
338K LYS* 1.3 75.0 + - + +
339K VAL* 4.1 11.0 - - + +
340K GLN* 3.9 4.7 + - - +
341K ILE* 3.5 18.7 - - - +
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Residues in contact with LYS 338 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239K ASP* 5.6 3.3 - - + +
308K VAL* 4.3 8.4 - - + +
337K PRO* 1.3 85.9 - - + +
339K VAL* 1.3 72.6 + - + +
340K GLN 3.2 2.2 - - - -
341K ILE* 3.2 13.2 + - + +
342K ASN* 2.9 28.6 + - - +
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Residues in contact with VAL 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330K ARG* 3.4 39.0 + - - +
334K HIS* 3.7 27.4 - - + +
336K ASP* 3.9 10.1 - - - -
337K PRO* 3.4 10.5 - - + -
338K LYS* 1.3 87.2 - - + +
340K GLN* 1.3 55.5 + - - +
342K ASN* 3.2 8.8 + - + +
343K ALA* 2.9 28.5 + - - +
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Residues in contact with GLN 340 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316K ILE* 4.1 16.2 - - + +
317K ASP* 3.4 18.6 + - - +
320K VAL* 5.3 7.4 - - + +
327K ILE 3.7 17.7 + - - +
328K GLY* 4.9 0.9 - - - -
330K ARG* 3.0 32.2 + - - +
331K GLU* 3.4 24.4 - - - +
336K ASP* 3.7 24.4 - - + +
337K PRO 3.9 6.2 + - - +
338K LYS 3.2 0.4 - - - -
339K VAL* 1.3 78.2 - - - +
341K ILE* 1.3 64.7 + - + +
343K ALA* 3.2 8.7 + - - +
344K ILE* 2.9 35.8 + - + +
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Residues in contact with ILE 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239K ASP* 3.3 32.1 - - + +
241K TRP* 4.4 9.6 - - + -
304K LEU* 3.5 42.6 - - + -
308K VAL* 4.2 10.3 - - + -
316K ILE* 5.5 1.3 - - + -
337K PRO 3.5 19.3 - - - +
338K LYS* 3.2 10.9 + - - +
340K GLN* 1.3 83.2 - - + +
342K ASN* 1.3 51.0 + - - +
344K ILE* 3.0 15.5 - - + +
345K CYS* 2.8 45.5 + - - -
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Residues in contact with ASN 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49K ARG* 3.3 36.2 + - - +
239K ASP* 4.0 16.1 + - + +
338K LYS 2.9 12.6 + - - +
339K VAL* 3.3 15.0 - - + +
341K ILE* 1.3 77.5 - - - +
343K ALA* 1.3 62.9 + - - +
345K CYS* 3.3 7.2 + - - -
346K SER* 3.1 32.7 + - - -
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Residues in contact with ALA 343 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329K ALA 5.8 0.7 - - - +
330K ARG* 4.3 25.6 - - + +
339K VAL 2.9 13.2 + - - +
340K GLN* 3.4 17.9 - - - +
342K ASN* 1.3 77.7 - - - +
344K ILE* 1.3 61.6 + - + +
346K SER* 3.3 14.4 + - - -
347K GLN* 2.7 32.9 + - - +
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Residues in contact with ILE 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241K TRP* 6.0 0.4 - - + -
304K LEU* 4.4 4.7 - - + -
320K VAL* 4.0 20.9 - - + -
326K LYS 4.6 5.2 - - - +
327K ILE 3.9 27.4 - - - +
328K GLY* 4.8 1.1 - - - -
340K GLN* 2.9 25.0 + - + +
341K ILE* 3.0 39.3 - - + +
343K ALA* 1.3 77.0 - - + +
345K CYS* 1.3 54.0 + - - +
346K SER 3.1 0.2 - - - -
347K GLN* 3.0 14.9 + - - +
348K TRP* 2.7 79.8 + - + +
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Residues in contact with CYS 345 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K ARG* 4.6 9.9 + - - -
239K ASP* 3.3 21.8 - - - +
240K GLY 3.4 17.8 - - - +
241K TRP* 3.7 31.0 - - - -
341K ILE* 2.8 23.1 + - - +
342K ASN 3.4 6.5 - - - +
344K ILE* 1.3 82.0 - - - +
346K SER* 1.3 55.7 + - - +
348K TRP* 4.2 14.1 - - - -
349K LEU* 3.2 27.6 - - + +
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Residues in contact with SER 346 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K SER* 5.8 1.8 - - - -
49K ARG* 4.6 19.1 + - - +
50K LEU* 5.5 6.8 - - - +
342K ASN* 3.1 18.7 + - - -
343K ALA* 3.7 10.4 - - - -
344K ILE 3.1 0.6 - - - -
345K CYS* 1.3 76.5 + - - +
347K GLN* 1.3 61.7 + - - +
348K TRP 3.5 0.2 - - - -
349K LEU* 4.0 4.2 - - - +
350K PRO* 3.2 23.6 - - - +
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Residues in contact with GLN 347 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326K LYS* 3.6 34.6 + - - +
328K GLY* 3.6 28.6 + - - -
329K ALA* 4.8 4.0 - - - +
343K ALA* 2.7 35.4 + - - +
344K ILE* 3.0 13.0 + - - +
346K SER* 1.3 78.1 - - - +
348K TRP* 1.3 62.4 + - - +
349K LEU 3.5 0.5 + - - -
350K PRO* 3.7 9.9 - - - +
353K HIS* 6.0 0.7 - - - -
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Residues in contact with TRP 348 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241K TRP* 3.9 30.3 - + - -
242K GLY 4.8 5.6 - - - +
243K PHE* 6.1 0.9 - + - -
247K HIS* 4.6 21.6 + + - +
250K ARG* 5.6 2.8 + - - -
301K ILE* 4.6 3.1 - - + -
304K LEU* 5.4 2.2 - - + -
320K VAL* 4.2 16.4 - - + -
323K LEU* 3.6 31.4 - - + -
325K LEU* 3.4 41.8 - - + +
326K LYS* 3.9 25.2 + - - +
344K ILE* 2.7 63.5 + - + +
345K CYS* 4.2 11.0 - - - -
347K GLN* 1.3 75.0 + - + +
349K LEU* 1.3 65.1 + - + +
350K PRO 3.6 1.4 - - - -
351K ILE* 5.4 0.7 - - - +
353K HIS* 4.5 14.7 - - - -
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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
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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