Contacts of the helix formed by residues 339 - 358 (chain L) in PDB entry 5LN3
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 ASN 339 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L LEU* 4.3 3.2 - - - +
177L GLY* 3.5 39.1 - - - +
178L THR* 3.7 21.2 - - + +
301L ILE* 3.9 12.9 - - - +
302L ASP 3.8 12.5 + - - -
303L LEU* 3.6 12.0 - - - +
304L PRO* 3.8 21.4 - - - +
312L ILE* 5.0 1.3 - - - -
337L GLY 5.0 0.5 - - - +
338L PHE* 1.3 77.2 - - - +
340L GLY* 1.4 61.0 + - - +
341L ALA 3.3 1.1 - - - -
342L ASP* 3.1 9.5 + - - +
343L LEU* 3.0 30.1 + - - +
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Residues in contact with GLY 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L ILE* 3.5 23.4 - - - +
138L LEU* 3.9 12.3 - - - +
312L ILE* 3.9 24.1 - - - +
316L HIS* 3.3 22.7 + - - -
339L ASN* 1.4 71.7 - - - +
341L ALA* 1.3 63.8 + - - +
343L LEU 3.5 0.6 + - - -
344L ARG* 3.3 6.8 + - - +
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Residues in contact with ALA 341 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L ILE* 3.8 19.4 - - + +
177L GLY 3.6 18.3 + - - +
178L THR* 3.9 17.7 + - - +
182L LEU* 4.7 2.7 - - + -
339L ASN 3.3 0.4 - - - -
340L GLY* 1.3 75.6 - - - +
342L ASP* 1.4 55.2 - - - +
344L ARG* 3.3 13.6 - - - +
345L ASN* 2.9 29.7 + - - +
343M LEU 5.1 0.2 - - - -
344M ARG* 4.2 21.3 - - + -
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Residues in contact with ASP 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177L GLY* 2.9 28.6 - - - +
337L GLY 4.2 2.4 - - - +
338L PHE* 3.5 25.0 - - + -
339L ASN* 3.2 26.2 + - - +
341L ALA* 1.4 74.1 - - - +
343L LEU* 1.4 61.1 + - - +
344L ARG 3.5 0.5 + - - -
345L ASN* 3.6 17.5 + - - +
346L VAL* 3.6 13.9 - - - +
374L VAL* 4.9 1.7 - - - +
378L LYS* 3.3 30.0 + - - +
343M LEU* 4.2 16.0 - - - +
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Residues in contact with LEU 343 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304L PRO* 6.3 0.2 - - + -
309L ARG* 3.7 48.7 - - + +
312L ILE* 3.6 40.8 - - + -
313L LEU* 4.3 17.3 - - + +
316L HIS* 4.0 11.4 - - + +
335L SER* 4.3 11.0 - - - +
338L PHE* 4.2 16.4 - - + +
339L ASN 3.0 17.7 + - - +
340L GLY 4.2 0.2 - - - +
341L ALA 3.5 0.4 - - - -
342L ASP* 1.4 70.9 - - - +
344L ARG* 1.3 63.4 + - - +
346L VAL* 3.1 24.1 + - + +
347L CYS* 3.1 14.5 - - - -
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Residues in contact with ARG 344 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134L GLU* 3.8 34.5 + - - +
135L ILE* 3.9 25.6 - - + +
182L LEU* 6.0 0.4 - - - +
316L HIS* 3.6 28.2 - - + +
340L GLY 3.3 11.3 + - - +
341L ALA* 3.3 13.7 - - - +
343L LEU* 1.3 76.2 - - - +
345L ASN* 1.4 66.8 + - - +
347L CYS* 3.2 7.1 + - - +
348L THR* 3.2 31.2 + - + +
218M GLN* 3.4 32.3 + - - +
321M GLN* 4.5 13.0 + - - +
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Residues in contact with ASN 345 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341L ALA 2.9 21.4 + - - +
342L ASP* 3.6 10.6 - - - +
344L ARG* 1.4 82.3 - - - +
346L VAL* 1.4 51.4 + - + +
348L THR* 2.7 22.5 + - - -
349L GLU* 2.8 24.2 + - - +
374L VAL* 5.0 10.5 - - + -
378L LYS* 4.9 1.2 + - - -
343M LEU 2.8 26.0 - - - +
344M ARG* 3.9 2.5 - - - +
345M SER* 3.7 30.1 - - - +
349M ASP* 3.8 20.5 - - - +
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Residues in contact with VAL 346 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313L LEU* 4.4 12.6 - - + -
331L ILE* 5.5 0.2 - - + -
335L SER* 5.9 0.7 - - - +
338L PHE* 5.5 7.2 - - + -
342L ASP 3.6 14.1 - - - +
343L LEU* 3.1 24.6 + - + +
345L ASN* 1.4 59.8 - - - +
347L CYS* 1.3 64.5 + - - +
349L GLU* 3.2 9.6 + - - +
350L ALA* 3.1 24.4 + - - +
367L PHE* 5.0 7.2 - - + -
370L ALA* 3.7 9.1 - - + +
371L VAL* 4.3 30.5 - - + +
374L VAL* 3.9 27.1 - - + +
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Residues in contact with CYS 347 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313L LEU* 3.9 23.1 - - - -
316L HIS* 3.7 40.8 - - + +
317L ALA* 5.2 3.6 - - + +
320L ILE* 4.3 16.6 - - + +
343L LEU 3.1 17.7 - - - -
344L ARG 3.2 7.4 + - - +
346L VAL* 1.3 73.2 - - - +
348L THR* 1.4 68.6 + - + +
350L ALA* 3.5 4.7 + - - +
351L GLY* 3.2 17.3 + - - -
367L PHE* 4.6 15.6 - - + -
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Residues in contact with THR 348 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320L ILE* 5.9 1.3 - - + -
344L ARG* 3.2 22.5 + - + +
345L ASN* 2.7 26.3 + - - -
347L CYS* 1.4 77.7 - - + +
349L GLU* 1.4 62.9 + - - +
351L GLY* 3.0 10.7 + - - -
352L MET* 3.1 24.8 + - - +
217M ILE* 3.5 33.8 - - + +
218M GLN* 4.7 20.0 - - - +
345M SER* 5.9 2.3 - - - -
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Residues in contact with GLU 349 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345L ASN 2.8 16.3 + - - +
346L VAL* 3.2 15.9 + - - +
348L THR* 1.4 75.5 + - - +
350L ALA* 1.4 60.0 - - - +
352L MET* 3.3 39.1 + - - +
353L PHE* 3.1 47.2 - - + -
370L ALA* 3.9 15.7 - - + +
373L LYS* 4.2 28.5 + - + +
374L VAL* 5.0 4.7 - - + +
349M ASP* 4.9 7.4 - - - +
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Residues in contact with ALA 350 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346L VAL 3.1 11.7 + - - +
347L CYS 3.7 9.4 - - - +
349L GLU* 1.4 74.1 - - - +
351L GLY* 1.4 63.1 + - - +
353L PHE* 3.1 25.9 + - - +
354L ALA* 3.3 12.1 + - - +
362L VAL* 5.0 5.5 - - + +
366L ASP* 3.9 24.9 - - + +
367L PHE* 3.8 31.4 - - + -
370L ALA* 4.3 0.6 - - - +
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Residues in contact with GLY 351 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320L ILE* 5.5 2.0 - - - -
347L CYS 3.2 7.6 + - - -
348L THR 3.0 8.5 + - - -
350L ALA* 1.4 77.3 - - - +
352L MET* 1.4 62.8 + - - +
354L ALA* 3.4 15.6 + - - +
355L ILE* 3.4 15.9 + - - +
362L VAL* 5.5 4.3 - - - -
215M LEU* 4.2 14.8 - - - +
217M ILE* 3.4 17.2 - - - +
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Residues in contact with MET 352 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348L THR* 3.1 26.8 + - - +
349L GLU* 3.3 33.4 + - - +
351L GLY* 1.4 75.1 - - - +
353L PHE* 1.3 67.0 + - + +
355L ILE* 3.3 9.2 + - - +
356L ARG* 3.1 25.3 + - + +
200M GLU* 5.7 0.4 - - - +
212M PHE* 5.4 8.5 - - + -
217M ILE* 3.4 9.8 - - + +
218M GLN 4.9 12.6 - - - +
219M PRO 5.5 0.9 - - - -
220M PRO* 5.3 9.4 - - + -
345M SER* 5.8 3.8 - - - +
350M ARG* 3.6 35.4 - - - +
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Residues in contact with PHE 353 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349L GLU* 3.1 51.8 - - + -
350L ALA* 3.1 13.3 + - - +
352L MET* 1.3 81.7 - - + +
354L ALA* 1.3 55.1 + - - +
356L ARG* 3.3 14.1 - - + +
357L ALA* 3.0 27.6 + - - +
366L ASP* 3.4 29.3 - - + +
369L LYS* 3.9 30.3 - - + -
370L ALA* 4.0 10.8 - - + -
373L LYS* 5.5 7.2 - - + -
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Residues in contact with ALA 354 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350L ALA 3.3 8.8 + - - +
351L GLY* 3.4 10.8 - - - +
352L MET 3.2 0.2 - - - -
353L PHE* 1.3 75.1 - - - +
355L ILE* 1.4 58.1 + - - +
357L ALA* 3.3 8.1 + - - +
358L ASP 2.8 23.7 + - - -
359L HIS 3.1 25.9 + - - +
361L PHE 4.5 8.1 - - - +
362L VAL* 4.4 19.5 - - + -
366L ASP* 5.0 4.6 + - - +
215M LEU* 4.3 10.1 - - + -
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Residues in contact with ILE 355 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351L GLY 3.4 11.8 + - - +
352L MET* 3.3 10.2 + - - +
354L ALA* 1.4 73.3 - - - +
356L ARG* 1.4 58.0 + - + +
358L ASP* 3.0 30.8 + - - +
359L HIS 4.8 2.2 - - - +
208M HIS* 6.3 0.4 - - + -
211M LYS* 3.9 31.5 - - + +
212M PHE* 4.3 38.4 - - + +
215M LEU* 4.1 29.6 - - + -
217M ILE* 4.4 9.9 - - + -
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Residues in contact with ARG 356 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352L MET* 3.1 21.0 + - + +
353L PHE* 3.3 18.2 - - + +
355L ILE* 1.4 77.7 - - + +
357L ALA* 1.4 55.5 + - - +
358L ASP* 3.2 13.5 - - - +
196M GLN* 4.4 17.6 - - - +
200M GLU* 4.6 25.8 - - - +
204M LEU* 5.3 8.9 - - - +
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Residues in contact with ALA 357 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353L PHE 3.0 17.7 + - - +
354L ALA* 3.4 10.5 - - - +
356L ARG* 1.4 72.8 - - - +
358L ASP* 1.4 64.4 + - - +
359L HIS* 3.2 29.4 + - + +
361L PHE 5.8 1.1 - - - +
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Residues in contact with ASP 358 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354L ALA 2.8 6.2 + - - -
355L ILE* 3.0 20.6 + - - +
356L ARG* 3.2 12.6 - - - +
357L ALA* 1.4 77.5 - - - +
359L HIS* 1.3 71.7 + - - +
211M LYS* 4.1 20.4 - - - +
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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