Contacts of the helix formed by residues 340 - 356 (chain L) in PDB entry 5GJQ
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 GLY 340 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177L GLY 3.2 12.9 + - - -
178L THR* 5.8 0.7 - - - -
304L PRO* 4.1 10.8 - - - +
312L ILE* 4.5 3.4 - - - +
316L HIS* 4.9 0.3 + - - -
339L ASN* 1.3 78.4 - - - +
341L ALA* 1.3 58.2 + - - +
343L LEU* 3.8 11.9 - - - +
344L ARG* 3.4 19.1 + - - +
401L ADP 4.0 32.8 + - - -
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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
----------------------------------------------------------
177L GLY* 4.2 7.5 + - - +
339L ASN* 4.2 2.7 - - + +
340L GLY* 1.3 72.8 - - - +
342L ASP* 1.3 55.3 + - - +
343L LEU 2.9 5.4 - - - -
344L ARG* 3.5 13.7 - - + -
345L ASN* 2.5 36.9 + - - +
401L ADP 4.1 19.9 + - + +
344M ARG* 4.6 9.0 - - - +
345M SER* 3.0 19.7 - - - +
346M GLY* 4.5 9.0 - - - +
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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
----------------------------------------------------------
338L PHE* 3.9 4.2 - - + -
339L ASN* 3.1 35.6 + - - +
341L ALA* 1.3 76.1 - - - +
343L LEU* 1.3 50.4 + - - +
345L ASN* 4.3 1.8 - - - -
346L VAL* 2.6 32.9 + - - +
374L VAL* 2.9 17.5 - - + +
378L LYS* 2.5 45.1 + - - +
381L GLU* 4.5 4.3 - - - +
344M ARG* 3.4 15.4 - - - +
345M SER* 3.3 15.5 + - - -
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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* 4.1 6.1 - - + -
309L ARG* 3.9 51.1 - - + +
312L ILE* 4.3 13.7 - - + -
313L LEU* 5.1 21.4 - - + +
331L ILE* 6.3 0.4 - - + -
335L SER* 4.2 13.9 - - - +
338L PHE* 4.0 11.4 - - + -
339L ASN 2.8 28.2 + - - +
340L GLY* 3.8 11.2 - - - +
341L ALA 2.9 0.6 - - - -
342L ASP* 1.3 76.5 - - - +
344L ARG* 1.3 58.7 - - - +
346L VAL* 2.7 34.0 + - + +
347L CYS* 3.0 11.4 + - - -
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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
----------------------------------------------------------
316L HIS* 3.9 41.3 + - + +
340L GLY 3.4 7.3 + - - +
341L ALA* 3.0 21.5 + - - +
343L LEU* 1.3 77.2 - - - +
345L ASN* 1.3 66.8 + - - +
347L CYS* 2.8 8.9 + - - +
348L THR* 2.8 30.6 + - - +
401L ADP 2.4 43.5 + - - +
218M GLN* 2.9 38.1 + - - +
221M LYS* 3.2 36.2 - - - +
346M GLY* 6.1 1.6 - - - -
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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 2.5 22.4 + - - +
342L ASP 3.9 5.4 - - - +
344L ARG* 1.3 74.1 - - - +
346L VAL* 1.3 53.2 + - - +
348L THR* 2.8 8.4 + - - -
349L GLU* 2.3 47.3 + - - +
374L VAL* 4.0 21.5 + - - +
377L SER* 5.8 1.4 + - - -
345M SER* 4.1 18.1 - - - +
349M ASP* 2.3 49.7 + - - +
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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* 5.3 3.6 - - + -
331L ILE* 4.2 12.1 - - + -
335L SER* 5.3 0.7 - - - +
338L PHE* 4.3 14.4 - - + -
342L ASP 2.6 26.9 - - - +
343L LEU* 2.7 25.2 + - + +
345L ASN* 1.3 71.1 - - - +
347L CYS* 1.3 59.9 + - - +
349L GLU* 3.6 1.0 - - - +
350L ALA* 3.0 23.7 + - - +
367L PHE* 4.2 10.3 - - + -
370L ALA* 3.6 1.0 - - - +
371L VAL* 3.6 33.9 - - + +
374L VAL* 3.4 25.1 - - + +
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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* 4.1 13.9 - - - -
316L HIS* 4.1 11.7 - - + +
317L ALA* 3.0 47.3 - - + -
320L ILE* 4.6 5.4 - - + -
343L LEU 3.0 13.9 + - - -
344L ARG* 2.8 9.0 + - - +
346L VAL* 1.3 76.9 - - - +
348L THR* 1.3 59.2 + - - +
349L GLU 3.1 0.5 + - - -
350L ALA* 3.2 2.4 + - - +
351L GLY* 2.8 27.5 + - - -
367L PHE* 4.4 12.5 - - + -
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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
----------------------------------------------------------
344L ARG* 2.8 29.1 + - - +
345L ASN* 2.8 16.5 + - - +
347L CYS* 1.3 73.9 - - - +
349L GLU* 1.3 65.6 + - - +
351L GLY* 3.1 10.0 + - - -
352L MET* 3.2 14.1 + - - +
217M ILE* 5.3 12.6 + - + +
218M GLN* 3.9 27.5 + - + +
219M PRO 4.8 0.7 - - - -
220M PRO* 4.4 28.0 - - + -
349M ASP* 4.8 2.7 - - - +
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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* 2.3 38.0 + - - +
346L VAL 3.6 4.5 - - - +
348L THR* 1.3 63.3 - - - +
350L ALA* 1.3 56.5 + - - +
352L MET* 2.6 36.8 + - - +
353L PHE* 3.4 8.0 + - + -
356L ARG* 6.0 0.3 - - - -
370L ALA* 3.6 22.0 - - + -
373L LYS* 3.9 28.8 + - + +
374L VAL* 3.6 16.6 - - + -
220M PRO* 5.7 0.2 - - - +
349M ASP* 4.2 7.1 - - - +
350M ARG* 3.0 39.4 + - - -
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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 3.0 14.2 + - - +
347L CYS 3.6 3.6 - - - +
349L GLU* 1.3 77.8 - - - +
351L GLY* 1.3 50.9 + - - +
353L PHE* 2.8 9.2 + - - +
354L ALA* 2.4 36.7 + - - +
362L VAL* 4.8 2.9 - - + -
366L ASP* 2.3 36.0 - - + +
367L PHE* 4.0 20.2 - - + -
370L ALA* 3.3 7.4 - - + +
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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* 6.4 0.4 - - - -
347L CYS 2.8 18.4 + - - -
348L THR* 3.4 7.6 - - - -
349L GLU 3.0 0.6 + - - -
350L ALA* 1.3 71.9 - - - +
352L MET* 1.3 54.7 + - - +
354L ALA* 3.0 11.1 - - - +
355L ILE* 2.6 39.7 + - - +
362L VAL* 5.3 1.1 - - - -
215M LEU* 4.2 15.3 - - - +
217M ILE* 4.9 7.6 - - - -
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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 3.2 12.7 + - - +
349L GLU* 2.6 19.0 + - - +
351L GLY* 1.3 70.5 - - - -
353L PHE* 1.3 53.0 + - + +
355L ILE* 3.6 14.0 - - + +
356L ARG* 2.4 64.5 + - - +
200M GLU* 3.6 34.5 - - + +
204M LEU* 5.8 3.1 - - + -
212M PHE* 4.0 27.6 - - + -
217M ILE* 5.4 2.7 - - - -
220M PRO* 4.3 20.0 - - + -
350M ARG* 4.1 23.3 - - - +
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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
----------------------------------------------------------
349L GLU* 3.4 17.8 + - - -
350L ALA* 2.8 15.6 + - - +
352L MET* 1.3 74.1 - - + +
354L ALA* 1.3 67.1 + - - +
356L ARG* 3.0 42.0 + - + +
359L HIS* 5.7 0.9 - - - +
366L ASP* 3.5 32.1 - - + +
369L LYS* 4.1 36.1 - - + -
370L ALA* 4.3 4.5 - - - -
373L LYS* 3.1 45.3 - - + -
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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 2.4 16.3 + - - +
351L GLY* 3.0 15.7 + - - +
353L PHE* 1.3 76.3 - - - +
355L ILE* 1.3 59.8 - - - +
356L ARG 3.3 5.4 - - - +
359L HIS* 3.3 27.4 + - - +
362L VAL* 3.4 25.1 - - + -
366L ASP* 4.0 10.2 - - - -
215M LEU* 3.3 22.9 - - + -
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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 2.6 19.0 + - - +
352L MET* 4.1 15.3 - - + +
354L ALA* 1.3 72.5 - - - +
356L ARG* 1.3 64.9 + - - +
357L ALA 3.8 1.7 + - - -
358L ASP* 3.9 11.4 + - - +
359L HIS 4.8 1.7 + - - +
360L ASP* 6.2 0.4 - - - +
200M GLU* 6.0 1.6 - - - +
204M LEU* 5.3 11.0 - - + -
211M LYS* 3.5 53.6 - - + +
212M PHE* 4.0 33.7 - - + +
215M LEU* 3.9 15.9 - - + +
217M ILE* 4.6 4.3 - - + -
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Residues in contact with ARG 356 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349L GLU* 6.0 0.2 - - - -
352L MET* 2.4 50.3 + - - +
353L PHE* 3.0 53.0 - - + +
354L ALA 2.9 3.9 - - - +
355L ILE* 1.3 74.3 - - + +
357L ALA* 1.3 61.8 + - + +
358L ASP 2.4 19.8 + - - -
359L HIS* 5.1 1.6 - - - +
373L LYS* 4.8 6.5 - - - +
196M GLN* 5.1 8.8 + - - +
197M GLU* 3.6 27.1 + - - +
200M GLU* 3.7 27.6 + - - +
350M ARG* 3.9 9.1 - - - +
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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