Contacts of the helix formed by residues 304 - 318 (chain M) 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 ARG 304 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236L ASP 4.7 6.0 + - - -
237L ALA 4.7 9.0 - - - -
240L GLY* 3.8 21.8 - - - -
241L ARG* 4.2 15.0 - - - +
242L ARG 4.8 0.2 - - - +
243L PHE* 3.3 41.1 - - - -
250L ASP* 3.4 21.3 - - - +
253L ILE* 5.9 1.1 - - - +
254L GLN* 4.7 6.3 - - - +
284L THR* 4.8 9.6 + - - -
296M PHE 5.1 5.5 + - - -
297M ASP* 5.4 5.3 - - - +
298M SER 5.4 1.2 + - - +
302M GLY* 3.1 10.4 + - - +
303M ASP* 1.3 78.4 + - - +
305M GLU* 1.3 57.5 + - - +
306M VAL 3.5 0.2 - - - -
307M GLN* 3.3 14.6 + - - +
308M ARG* 2.7 79.5 + - - +
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Residues in contact with GLU 305 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H VAL* 4.8 13.2 - - + -
256M LEU 4.3 0.3 - - - +
257M VAL* 4.8 2.3 - - + -
258M GLN 4.0 31.1 + - - +
259M MET 4.9 6.5 - - - +
260M PHE 3.5 7.3 - - - +
261M ILE* 4.9 7.6 - - + -
262M GLY* 3.4 24.3 + - - -
264M GLY 3.8 10.7 + - - -
304M ARG* 1.3 74.4 - - - +
306M VAL* 1.3 64.9 + - + +
307M GLN 2.9 2.3 + - - -
308M ARG* 2.9 9.6 + - - +
309M THR* 2.5 68.2 + - - +
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Residues in contact with VAL 306 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H VAL* 4.9 2.9 - - + -
297H ARG* 3.0 38.6 - - - +
257M VAL* 4.6 12.1 - - + -
290M ALA 3.3 26.0 - - - +
291M ILE* 3.6 17.6 - - + +
293M THR* 5.4 7.0 - - - +
303M ASP* 3.4 20.2 - - + +
304M ARG 3.5 0.2 - - - -
305M GLU* 1.3 78.9 - - + +
307M GLN* 1.3 59.9 + - - +
309M THR* 2.7 16.8 + - - -
310M MET* 3.3 14.2 + - - +
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Residues in contact with GLN 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236L ASP 6.2 0.4 - - - +
293M THR 5.0 4.3 - - - +
294M LYS 4.8 1.8 - - - -
295M ARG* 3.2 52.5 - - + +
296M PHE* 4.1 22.6 + - - +
302M GLY 5.0 0.6 - - - -
303M ASP* 1.9 50.3 + - - +
304M ARG* 3.3 21.6 + - - +
305M GLU 2.9 0.8 + - - -
306M VAL* 1.3 78.2 - - - +
308M ARG* 1.3 54.7 + - + +
310M MET* 2.8 14.9 + - - +
311M LEU* 2.6 36.0 + - + +
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Residues in contact with ARG 308 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L SER* 4.1 7.5 + - - +
204L VAL* 4.0 18.8 - - + +
237L ALA* 3.7 33.3 - - + +
249L ALA* 5.8 1.4 - - - +
250L ASP* 4.4 4.6 + - - +
253L ILE* 3.0 52.5 - - - +
261M ILE* 4.0 14.3 - - - +
265M ALA* 5.8 1.8 - - + -
304M ARG* 2.7 64.6 + - - +
305M GLU* 2.9 8.4 + - - +
307M GLN* 1.3 70.1 - - + +
309M THR* 1.3 55.1 + - + +
311M LEU* 2.7 14.6 + - + +
312M GLU* 2.3 40.1 + - - +
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Residues in contact with THR 309 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256M LEU* 4.1 9.2 - - - +
257M VAL* 5.6 1.0 - - - +
264M GLY* 3.5 27.6 - - - -
265M ALA* 4.0 4.5 - - - +
268M VAL* 4.6 4.7 - - - +
291M ILE* 4.6 14.4 - - - +
305M GLU* 2.5 51.9 + - - +
306M VAL* 2.7 22.2 + - - -
308M ARG* 1.3 73.3 - - + +
310M MET* 1.3 51.2 + - - +
312M GLU* 3.4 7.8 - - - +
313M LEU* 2.6 37.9 + - - +
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Residues in contact with MET 310 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291M ILE* 3.7 18.1 + - - +
293M THR 3.9 11.7 - - - +
295M ARG* 3.4 26.2 - - - +
306M VAL 3.3 11.2 + - - +
307M GLN* 2.8 17.1 + - - +
309M THR* 1.3 79.9 + - - +
311M LEU* 1.3 49.4 + - - -
313M LEU* 2.9 11.3 + - - +
314M LEU* 2.4 66.3 + - + +
339M ASP* 2.5 53.4 - - + +
341M ALA* 4.9 1.8 - - + -
342M LEU* 4.6 12.1 - - + -
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Residues in contact with LEU 311 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L SER* 3.8 12.1 - - - +
234L GLU* 3.0 51.3 - - + +
236L ASP* 3.8 10.3 - - + +
237L ALA* 3.7 28.3 - - + +
280L ASN* 6.3 1.3 - - - +
295M ARG* 3.6 23.8 - - - +
307M GLN* 2.6 17.6 + - + +
308M ARG* 2.7 12.2 + - + +
310M MET* 1.3 73.3 - - - +
312M GLU* 1.3 54.3 + - - +
314M LEU* 2.8 18.5 + - + -
315M ASN* 2.6 33.1 + - - +
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Residues in contact with GLU 312 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199L VAL* 4.3 2.1 - - - +
201L SER* 2.8 37.4 + - - -
202L SER* 3.4 17.1 + - - -
265M ALA* 3.1 45.1 - - + +
268M VAL* 4.6 2.5 - - + -
269M ARG* 3.2 25.3 - - - -
308M ARG 2.3 28.1 + - - +
309M THR* 3.4 5.2 - - - +
311M LEU* 1.3 67.2 - - - +
313M LEU* 1.3 57.8 + - - +
315M ASN* 3.1 6.9 + - - +
316M GLN* 2.5 54.4 + - + +
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Residues in contact with LEU 313 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256M LEU* 5.5 0.7 - - + -
268M VAL* 3.9 24.0 - - + +
272M PHE* 4.1 22.0 - - + -
285M ILE* 4.6 16.4 - - + -
288M LEU* 4.4 12.1 - - + -
291M ILE* 4.1 26.2 - - + -
309M THR 2.6 22.8 + - - +
310M MET* 3.1 6.7 - - - +
312M GLU* 1.3 73.5 - - - +
314M LEU* 1.3 57.5 + - + +
316M GLN* 2.6 28.6 + - - +
317M LEU* 3.0 26.9 + - + +
342M LEU* 4.7 12.8 - - + -
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Residues in contact with LEU 314 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234L GLU* 3.9 4.5 - - - +
280L ASN* 5.6 1.1 - - - +
295M ARG* 5.4 0.4 - - - +
310M MET* 2.4 56.0 + - + +
311M LEU* 2.8 28.1 + - + +
313M LEU* 1.3 68.2 - - - +
315M ASN* 1.3 54.8 + - - +
316M GLN 2.7 10.4 + - - -
317M LEU* 3.2 9.8 + - + +
318M ASP 3.3 11.3 + - - +
341M ALA* 3.2 33.9 - - + +
342M LEU* 2.5 42.6 - - + -
347M ARG* 3.7 28.7 + - - +
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Residues in contact with ASN 315 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199L VAL* 2.9 46.0 - - + +
233L ASP* 3.4 11.2 - - - +
234L GLU* 3.3 23.9 + - - +
311M LEU 2.6 12.4 + - - +
312M GLU* 3.4 12.6 + - - +
314M LEU* 1.3 70.4 - - - +
316M GLN* 1.3 75.7 + - - +
318M ASP 3.0 15.5 - - - +
319M GLY* 5.1 1.1 - - - -
320M PHE* 4.2 17.0 + - - +
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Residues in contact with GLN 316 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268M VAL* 3.6 8.0 - - + +
269M ARG* 3.2 35.8 + - - +
272M PHE* 2.6 37.8 - - + +
312M GLU* 2.5 45.8 + - - +
313M LEU* 2.6 24.6 + - - +
314M LEU 2.7 0.2 + - - -
315M ASN* 1.3 97.4 + - - +
317M LEU* 1.3 67.6 + - - +
318M ASP 3.2 6.7 + - - +
320M PHE 5.6 0.2 - - - +
321M GLN 5.1 1.7 - - - +
323M ASN* 4.1 9.4 + - - -
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Residues in contact with LEU 317 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272M PHE* 3.1 27.4 - - + -
313M LEU* 3.0 25.4 + - + +
314M LEU* 3.8 6.5 - - - +
316M GLN* 1.3 80.3 - - - +
318M ASP* 1.3 64.2 + - + +
323M ASN* 3.5 18.5 + - - +
328M VAL* 3.5 37.9 - - + -
342M LEU* 5.4 5.6 - - + -
347M ARG* 3.9 46.7 - - + +
348M LEU* 4.8 7.6 - - + -
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Residues in contact with ASP 318 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401L ADP 4.6 15.1 + - - +
221M LYS* 3.2 22.8 + - - +
314M LEU 3.3 5.7 + - - -
315M ASN 3.0 20.3 - - - +
316M GLN 3.4 4.9 - - - +
317M LEU* 1.3 81.8 - - - +
319M GLY* 1.3 67.7 + - - +
320M PHE 4.2 2.1 - - - +
321M GLN 4.3 4.5 - - - +
323M ASN* 5.5 0.2 - - - +
344M ARG* 4.1 14.1 + - - +
346M GLY* 3.2 32.8 - - - +
347M ARG* 3.6 22.8 + - - +
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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