Contacts of the helix formed by residues 305 - 317 (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 ASN 305 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137L GLY 5.1 2.6 + - - -
138L LEU* 6.3 0.4 - - - +
303L LEU 3.3 4.2 + - - +
304L PRO* 1.3 73.4 - - - +
306L GLU* 1.3 59.7 + - - +
307L GLN* 3.0 10.1 + - + +
308L ALA* 2.7 23.9 - - - +
309L ARG* 2.2 42.7 + - - +
171h LYS* 5.9 1.4 + - - -
206h LEU* 3.7 11.3 - - - +
207h SER* 3.5 21.4 + - - +
208h ILE* 4.8 8.2 - - + +
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Residues in contact with GLU 306 (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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305L ASN* 1.3 72.8 - - - +
307L GLN* 1.3 57.2 + - - +
309L ARG* 3.1 32.5 + - - +
310L LEU* 2.8 27.8 + - - +
329L GLU* 4.2 10.6 - - - +
332L VAL* 3.1 27.2 - - + +
333L LYS* 3.9 42.4 + - - +
336L ASP* 5.0 3.8 - - - +
55h LYS* 6.2 0.2 - - - +
208h ILE* 4.9 11.4 - - + +
214h GLU* 4.1 15.1 - - - +
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Residues in contact with GLN 307 (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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305L ASN* 3.7 10.1 + - + +
306L GLU* 1.3 74.5 - - - +
308L ALA* 1.3 56.8 + - - +
310L LEU* 3.2 8.6 + - + +
311L ASP* 2.5 57.0 + - - +
207h SER* 2.6 30.6 + - - +
208h ILE* 2.9 18.4 + - + +
209h ASP* 2.6 32.7 + - - +
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Residues in contact with ALA 308 (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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137L GLY* 3.5 25.8 - - - +
138L LEU* 5.5 1.3 - - + -
304L PRO* 3.1 15.5 - - + -
305L ASN* 2.7 39.5 + - + +
307L GLN* 1.3 75.8 - - - +
309L ARG* 1.3 50.0 + - - -
311L ASP* 3.5 8.7 - - - +
312L ILE* 2.7 40.2 + - - +
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Residues in contact with ARG 309 (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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304L PRO* 3.1 37.2 + - + +
305L ASN* 2.2 30.4 + - - +
306L GLU* 3.1 47.3 + - - +
308L ALA* 1.3 65.4 - - - +
310L LEU* 1.3 54.4 + - - +
312L ILE* 2.7 3.8 + - - +
313L LEU* 2.4 40.5 + - - +
332L VAL* 3.7 8.5 + - + -
335L SER* 2.5 29.9 + - - -
336L ASP* 3.1 25.7 + - - -
337L GLY* 3.9 10.3 - - - +
338L PHE* 3.8 15.3 - - - +
343L LEU* 3.9 30.0 - - + +
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Residues in contact with LEU 310 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306L GLU 2.8 22.9 + - - +
307L GLN* 3.5 6.7 - - + +
309L ARG* 1.3 72.4 - - - +
311L ASP* 1.3 72.8 + - - +
313L LEU* 3.5 1.3 - - + +
314L LYS* 3.1 58.4 + - + +
328L TYR* 4.0 12.8 - - + +
329L GLU* 4.9 14.1 - - - +
332L VAL* 3.4 28.8 - - + +
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Residues in contact with ASP 311 (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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137L GLY* 4.5 14.7 - - - +
307L GLN* 2.5 46.5 + - - +
308L ALA* 3.5 9.4 + - - +
310L LEU* 1.3 83.4 - - - +
312L ILE* 1.3 57.2 + - - +
314L LYS* 4.0 5.3 + - - +
315L ILE* 3.0 26.8 - - + +
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Residues in contact with ILE 312 (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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136L GLY 3.2 32.5 - - - +
137L GLY* 4.2 2.9 - - - -
138L LEU* 6.0 2.0 - - + -
304L PRO* 3.8 26.0 - - + -
308L ALA* 2.7 20.7 + - + +
309L ARG 2.7 4.4 + - - +
311L ASP* 1.3 71.5 - - - +
313L LEU* 1.3 62.8 + - - +
314L LYS 3.2 0.7 - - - -
315L ILE* 3.1 23.9 + - + +
316L HIS* 3.4 10.1 + - - +
340L GLY* 4.5 6.1 - - - +
343L LEU* 4.3 16.2 - - + -
344L ARG 6.2 0.2 - - - +
401L ADP 3.3 44.6 - - + +
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Residues in contact with LEU 313 (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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309L ARG 2.4 30.8 + - - +
310L LEU* 3.2 6.9 + - - +
312L ILE* 1.3 71.4 - - - +
314L LYS* 1.3 57.9 + - - +
316L HIS* 3.6 0.6 + - - -
317L ALA* 3.1 39.0 + - + +
328L TYR* 3.9 24.0 - - + +
331L ILE* 3.9 26.7 - - + -
332L VAL* 2.9 32.3 - - + +
343L LEU* 5.1 24.2 - - + +
346L VAL* 5.3 2.5 - - + -
347L CYS* 4.1 21.3 - - - -
367L PHE* 4.8 4.9 - - + -
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Residues in contact with LYS 314 (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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310L LEU* 3.1 34.2 + - + +
311L ASP* 4.0 4.7 + - - +
312L ILE 3.2 0.2 - - - -
313L LEU* 1.3 77.0 - - - +
315L ILE* 1.3 59.1 + - + +
318L GLY* 3.4 22.5 + - - +
319L PRO* 5.1 0.2 - - - +
328L TYR* 3.1 61.9 - - + +
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Residues in contact with ILE 315 (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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134L GLU* 3.5 40.5 - - - +
135L ILE* 4.7 13.2 - - - +
136L GLY* 5.1 2.7 - - - +
137L GLY 5.5 0.9 - - - +
311L ASP* 3.0 25.4 - - + +
312L ILE* 3.3 23.1 - - + +
313L LEU 3.0 0.8 - - - -
314L LYS* 1.3 80.9 - - + +
316L HIS* 1.3 69.4 + - + +
317L ALA 3.5 0.2 - - - -
318L GLY 4.4 0.4 - - - -
319L PRO* 3.7 14.6 - - - +
401L ADP 5.7 5.8 - - + +
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Residues in contact with HIS 316 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134L GLU* 5.2 8.7 + - - -
182L LEU* 5.6 0.9 - - + -
312L ILE* 3.4 9.5 + - + +
313L LEU* 4.7 0.7 - - - +
315L ILE* 1.3 82.9 - - + +
317L ALA* 1.3 62.3 + - - +
318L GLY 3.5 0.2 - - - -
319L PRO* 3.6 12.6 - - + +
320L ILE* 3.8 4.9 - - - +
340L GLY 4.9 0.8 + - - -
344L ARG* 3.9 37.7 + - + +
347L CYS* 4.1 15.4 - - + +
401L ADP 3.3 55.9 + + - -
218M GLN* 4.9 11.9 + - - -
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Residues in contact with ALA 317 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313L LEU* 3.1 23.4 + - + +
316L HIS* 1.3 71.9 - - - +
318L GLY* 1.3 61.1 + - - +
319L PRO 3.2 1.1 - - - -
320L ILE* 1.4 55.0 - - + +
322L LYS* 3.4 4.8 - - - +
328L TYR* 4.2 13.5 - - + +
347L CYS* 3.0 23.6 - - - -
367L PHE* 4.5 7.9 - - + -
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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