Contacts of the helix formed by residues 297 - 317 (chain C) in PDB entry 3QEL
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 297 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C ASN* 3.0 30.8 + - - +
296C LYS* 1.3 74.6 - - - +
298C GLU* 1.3 65.5 + - - +
299C SER* 3.0 14.4 + - - -
300C ALA* 3.1 31.1 + - + +
301C HIS* 3.0 25.9 + - - -
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Residues in contact with GLU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.7 7.6 - - - +
34C SER* 2.6 38.1 + - - -
38C HIS* 3.4 30.2 + - + +
93C SER* 3.2 32.7 + - - -
94C HIS 4.5 4.0 - - - +
121C LEU* 4.6 2.9 - - + -
122C THR* 4.4 16.6 + - + -
296C LYS 2.8 12.8 + - - +
297C ASN* 1.3 70.3 - - - +
299C SER* 1.3 58.2 + - - +
301C HIS* 3.4 3.3 + - - +
302C ILE* 2.9 45.9 + - + +
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Residues in contact with SER 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C HIS* 4.3 6.9 + - - -
41C ILE* 3.1 44.2 - - - +
297C ASN* 3.0 9.8 - - - -
298C GLU* 1.3 80.6 - - - +
300C ALA* 1.3 60.9 + - - +
302C ILE* 3.4 5.9 + - - +
303C SER* 3.1 20.4 + - - -
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Residues in contact with ALA 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ASN* 4.9 2.2 - - - +
297C ASN* 3.1 32.1 + - + +
299C SER* 1.3 75.2 - - - +
301C HIS* 1.3 58.9 + - - +
303C SER* 2.9 22.9 + - - -
304C ASP* 3.1 15.1 + - - -
355C VAL* 3.6 22.1 - - + +
356C THR* 3.6 22.9 - - + -
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Residues in contact with HIS 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 3.5 29.9 - - + +
122C THR* 4.5 1.1 - - + -
140C THR* 3.0 32.5 + - - +
141C VAL* 3.4 26.2 - - + +
292C LEU* 5.7 0.7 - - + -
293C ILE 5.5 0.9 - - - -
294C ASN* 2.8 33.5 + - + -
295C GLY* 3.9 7.2 - - - -
297C ASN 3.0 22.1 + - - +
298C GLU* 3.9 4.5 - - - +
300C ALA* 1.3 76.6 - - - +
302C ILE* 1.3 56.9 + - - +
304C ASP* 3.9 3.8 - - - +
305C ALA* 2.9 30.7 + - - +
356C THR* 4.0 26.9 + - + +
367C ARG* 4.9 0.7 - - - -
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Residues in contact with ILE 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.1 10.8 - - + -
38C HIS* 3.9 33.9 - - + +
41C ILE* 4.2 11.7 - - + +
42C PHE* 3.7 32.5 - - + +
45C ALA* 4.5 0.4 - - + -
91C LEU* 4.6 2.9 - - + -
121C LEU* 3.4 25.8 - - + +
298C GLU* 2.9 41.3 + - + +
299C SER 3.5 4.0 - - - +
301C HIS* 1.3 71.7 - - - +
303C SER* 1.3 69.4 + - - +
306C VAL* 3.1 32.6 + - + +
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Residues in contact with SER 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ILE* 5.4 4.8 - - - +
45C ALA* 4.5 14.2 - - - +
52C ARG* 5.7 0.3 + - - -
299C SER 3.1 9.6 + - - -
300C ALA* 2.9 16.7 + - - -
302C ILE* 1.3 83.7 - - - +
304C ASP* 1.3 59.6 + - - +
306C VAL* 4.0 2.4 - - - +
307C ALA* 3.4 19.6 + - - +
355C VAL* 4.5 17.3 - - - +
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Residues in contact with ASP 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C THR* 5.2 4.9 - - + -
300C ALA 3.1 11.3 + - - +
301C HIS* 3.9 7.0 - - - +
302C ILE 3.1 0.2 - - - -
303C SER* 1.3 75.4 - - - +
305C ALA* 1.3 67.3 + - - +
306C VAL 3.2 1.3 - - - -
307C ALA* 3.1 5.5 + - - +
308C VAL* 2.8 27.4 + - - +
351C TYR* 4.7 4.4 - - - -
354C GLY* 3.7 4.7 - - - -
355C VAL* 3.1 25.5 + - - +
356C THR* 2.6 43.8 + - - +
359C ILE* 3.3 25.7 - - + +
367C ARG* 5.4 0.2 - - - +
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Residues in contact with ALA 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 3.6 17.0 - - + -
119C ILE* 4.0 15.9 - - + -
121C LEU* 3.4 33.0 - - + -
140C THR* 4.3 9.7 - - + +
301C HIS 2.9 8.6 + - - +
304C ASP* 1.3 75.1 - - - +
306C VAL* 1.3 57.5 + - - +
308C VAL* 3.4 5.1 + - - +
309C VAL* 2.8 36.4 + - - +
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Residues in contact with VAL 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 5.0 6.0 - - + +
42C PHE* 3.7 24.0 - - + -
45C ALA* 3.6 40.4 - - + +
46C VAL* 3.8 13.9 - - + +
49C ALA* 4.4 8.7 - - + -
60C LEU* 5.9 0.2 - - + -
91C LEU* 3.7 19.7 - - + -
302C ILE* 3.1 19.1 + - + +
303C SER 4.0 1.6 - - - +
305C ALA* 1.3 76.3 - - - +
307C ALA* 1.3 58.2 + - - +
309C VAL* 3.2 5.7 + - - +
310C ALA* 2.8 30.7 + - + +
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Residues in contact with ALA 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ARG* 3.9 27.2 + - - +
53C HIS* 4.9 0.5 + - - -
303C SER 3.4 12.9 + - - +
304C ASP* 3.1 8.8 + - - +
306C VAL* 1.3 78.5 - - - +
308C VAL* 1.3 63.9 + - - +
310C ALA* 3.8 1.9 - - - +
311C GLN* 3.0 25.3 + - - +
351C TYR* 3.8 36.8 - - + +
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Residues in contact with VAL 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ILE* 6.2 3.1 - - + -
140C THR* 6.2 0.4 - - + -
304C ASP 2.8 18.5 + - - +
305C ALA* 3.8 7.4 - - - +
307C ALA* 1.3 77.2 - - - +
309C VAL* 1.3 67.0 + - + +
311C GLN* 3.5 5.6 - - - +
312C ALA* 2.9 22.3 + - - +
346C LEU* 4.4 10.1 - - + -
349C SER* 4.4 15.1 + - - -
350C LYS 5.4 1.1 - - - -
351C TYR* 3.7 30.1 - - + +
359C ILE* 3.9 25.4 - - + +
361C PHE* 4.2 23.8 - - + -
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Residues in contact with VAL 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 3.5 29.8 - - + -
88C TYR* 6.3 0.2 - - + -
89C ALA* 4.5 16.6 - - + -
91C LEU* 4.4 7.6 - - + -
119C ILE* 3.8 34.1 - - + -
305C ALA 2.8 25.9 + - - +
306C VAL* 3.7 3.8 - - - +
308C VAL* 1.3 74.8 - - + +
310C ALA* 1.3 52.7 + - - +
312C ALA* 3.2 3.1 + - - +
313C ILE* 2.7 48.6 + - + +
342C PHE* 4.5 3.9 - - + -
346C LEU* 4.2 12.3 - - + -
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Residues in contact with ALA 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 3.7 17.7 - - + -
53C HIS* 4.1 11.4 - - + +
60C LEU* 3.3 33.7 - - + -
306C VAL* 2.8 21.0 + - + +
307C ALA* 3.8 3.6 - - - +
309C VAL* 1.3 70.8 - - - +
311C GLN* 1.3 67.0 + - - +
313C ILE* 3.0 7.3 + - - +
314C HIS* 3.0 26.0 + - - -
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Residues in contact with GLN 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C HIS* 3.7 24.2 + - + +
307C ALA 3.0 18.6 + - - +
308C VAL* 3.5 5.2 + - - +
310C ALA* 1.3 73.9 - - - +
312C ALA* 1.3 64.4 + - - +
314C HIS* 2.9 14.6 + - - +
315C GLU* 3.0 14.4 + - + +
349C SER* 3.6 20.0 + - - +
350C LYS 3.1 32.4 + - - +
351C TYR* 3.5 22.2 - - + +
352C PRO* 5.8 0.2 - - - +
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Residues in contact with ALA 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C VAL 2.9 20.8 + - - +
309C VAL 3.6 1.3 - - - +
311C GLN* 1.3 73.8 - - - +
313C ILE* 1.3 60.4 + - - +
315C GLU* 3.9 2.7 - - - -
316C LEU* 3.1 19.8 + - - +
342C PHE* 3.8 3.8 - - + -
345C VAL* 3.2 27.7 - - + +
346C LEU* 3.6 29.6 - - + -
349C SER* 3.4 19.2 + - - +
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Residues in contact with ILE 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 4.4 3.8 - - + -
29C ILE* 5.1 3.1 - - + -
58C ILE* 3.7 26.0 - - + -
60C LEU* 3.9 19.5 - - + -
88C TYR* 3.8 35.2 - - + -
309C VAL* 2.7 34.5 + - + +
310C ALA* 3.0 11.6 + - - +
312C ALA* 1.3 73.3 - - - +
314C HIS* 1.3 60.6 + - + +
316C LEU* 2.8 24.6 + - + +
317C PHE* 3.0 13.8 + - + -
342C PHE* 3.5 26.0 - - + -
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Residues in contact with HIS 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA 5.3 0.4 - - - -
50C ASN* 5.8 2.9 - - - -
53C HIS* 3.1 53.4 + + + +
54C PHE 5.0 6.0 + - - -
55C THR* 5.7 0.7 - - - -
58C ILE* 3.4 51.6 + - + +
60C LEU* 5.0 16.6 - - + +
310C ALA 3.0 13.6 + - - -
311C GLN 2.9 7.8 + - - +
313C ILE* 1.3 73.7 - - + +
315C GLU* 1.3 63.3 + - - +
316C LEU 3.0 2.4 + - - -
317C PHE* 3.4 11.8 + - + +
318C GLU* 3.4 11.8 + - - +
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Residues in contact with GLU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C GLN* 3.0 13.8 + - + +
312C ALA* 3.9 8.5 - - - +
314C HIS* 1.3 76.1 - - - +
316C LEU* 1.3 62.0 + - - +
318C GLU* 3.7 16.5 + - - +
319C MET* 3.8 18.5 - - + +
345C VAL* 4.1 14.6 - - + -
349C SER* 5.9 0.4 - - - +
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C TYR* 4.5 11.0 - - + -
312C ALA 3.1 12.8 + - - +
313C ILE* 2.8 16.2 + - + +
315C GLU* 1.3 80.1 - - - +
317C PHE* 1.3 68.7 + - + +
318C GLU 3.1 4.8 + - - -
319C MET* 3.2 21.6 + - - +
322C ILE* 3.6 42.7 - - + +
336C TRP* 5.1 0.2 - - + -
338C THR* 4.1 11.9 - - + -
341C LEU* 3.9 23.8 - - + -
342C PHE* 4.1 33.9 - - + +
345C VAL* 4.1 10.5 - - + -
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Residues in contact with PHE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LYS* 5.6 7.9 - - + -
27C VAL* 3.6 21.1 - - + -
58C ILE* 3.1 42.0 - - + -
88C TYR* 3.6 35.0 - + - -
313C ILE* 3.0 26.5 + - + +
314C HIS* 3.4 5.9 + - - +
316C LEU* 1.3 78.9 - - + +
318C GLU* 1.3 64.8 + - - +
319C MET 3.4 7.4 - - - +
322C ILE* 3.6 25.8 - - + -
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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