Contacts of the helix formed by residues 300 - 313 (chain C) in PDB entry 2QPA
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 ASP 300 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C GLY* 5.2 0.9 - - - -
138C LEU 5.8 0.3 + - - -
139C GLU* 4.5 10.4 - - - +
298C LEU 3.4 3.0 + - - +
299C PRO* 1.3 71.7 - - - +
301C LEU* 1.3 60.4 + - - +
302C ALA* 3.5 16.2 + - - +
303C ALA* 3.0 18.3 + - - +
304C ARG* 2.7 42.9 + - - +
332C GLU* 5.4 2.2 - - - +
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Residues in contact with LEU 301 (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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300C ASP* 1.3 74.7 + - - +
302C ALA* 1.3 84.1 + - + +
304C ARG* 2.8 38.8 + - - +
305C THR* 2.9 23.6 + - - +
325C ARG* 4.7 12.3 - - + +
328C GLY* 4.1 9.4 - - - -
329C ALA* 4.0 24.2 - - + -
332C GLU* 4.9 4.3 + - + +
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Residues in contact with ALA 302 (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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300C ASP* 3.5 11.3 + - - +
301C LEU* 1.3 89.3 - - + +
303C ALA* 1.3 58.8 + - - +
305C THR* 3.9 5.9 - - - -
306C THR* 3.1 26.7 + - - -
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Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ALA* 4.4 1.7 - - - +
137C GLY* 3.9 25.6 - - - +
139C GLU* 5.5 0.2 - - - +
299C PRO* 3.5 14.1 - - + -
300C ASP* 3.0 34.2 + - - +
301C LEU 3.0 0.8 - - - -
302C ALA* 1.3 78.9 - - - +
304C ARG* 1.3 65.4 + - - +
306C THR* 3.4 7.0 + - - -
307C MET* 3.1 25.8 + - - +
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Residues in contact with ARG 304 (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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299C PRO* 2.7 44.2 + - + +
300C ASP* 2.7 24.1 + - - +
301C LEU* 2.8 39.0 - - - +
303C ALA* 1.3 70.4 - - - +
305C THR* 1.3 65.2 + - - +
307C MET* 3.1 6.7 + - - +
308C PHE* 3.0 27.0 + - - -
328C GLY* 3.0 18.1 + - - +
329C ALA* 5.0 0.2 - - - +
331C THR* 2.8 41.0 + - - +
332C GLU* 3.5 40.3 + - - +
333C GLY 4.2 3.4 - - - +
334C TYR 4.2 6.1 - - - -
339C ILE* 3.5 18.9 - - + +
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Residues in contact with THR 305 (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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301C LEU* 2.9 17.6 + - - +
302C ALA* 3.9 8.3 - - - +
304C ARG* 1.3 75.1 - - - +
306C THR* 1.3 68.7 + - - +
308C PHE* 2.9 17.8 + - - +
309C GLU* 3.2 21.1 + - - +
324C TYR* 3.4 32.8 + - + -
325C ARG* 3.7 10.8 - - + +
328C GLY* 3.1 25.8 - - - +
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Residues in contact with THR 306 (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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136C ALA* 5.6 9.6 - - - -
302C ALA 3.1 13.7 + - - -
303C ALA* 3.7 9.4 - - - -
304C ARG 3.4 0.2 - - - -
305C THR* 1.3 80.1 - - - +
307C MET* 1.3 57.3 + - - +
309C GLU* 3.2 12.7 + - + +
310C ILE* 3.0 51.8 + - + +
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Residues in contact with MET 307 (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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136C ALA* 3.4 28.9 - - + -
177C THR* 6.3 2.2 - - - -
299C PRO* 3.6 31.2 - - + -
303C ALA 3.1 16.1 + - - +
304C ARG 3.1 7.8 + - - +
305C THR 3.0 0.6 - - - -
306C THR* 1.3 74.9 - - - +
308C PHE* 1.3 63.1 - - - +
309C GLU 3.1 1.8 - - - -
310C ILE* 4.2 8.6 - - + +
311C ASN* 3.1 32.6 + - - +
336C GLY* 3.4 31.6 - - - +
339C ILE* 3.9 19.5 - - + -
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Residues in contact with PHE 308 (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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304C ARG 3.0 21.4 + - - -
305C THR* 2.9 9.0 + - - +
307C MET* 1.3 76.2 - - - +
309C GLU* 1.3 62.9 + - - +
311C ASN* 4.2 1.0 - - - +
312C VAL* 3.5 20.4 + - - +
324C TYR* 3.3 23.9 - - + -
327C LEU* 3.9 41.5 - - + -
328C GLY 4.3 0.7 - - - -
331C THR* 3.5 39.0 - - + -
339C ILE* 3.8 17.0 - - + -
342C VAL* 4.1 22.4 - - + -
343C VAL* 3.4 28.7 - - + +
406C PHE* 4.3 12.1 - + - -
410C ILE* 4.5 1.1 - - + -
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Residues in contact with GLU 309 (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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305C THR* 3.3 22.3 - - - +
306C THR* 3.2 11.4 + - + +
307C MET 3.1 0.6 - - - -
308C PHE* 1.3 75.6 - - - +
310C ILE* 1.3 68.2 + - + +
311C ASN 3.0 0.7 + - - -
312C VAL* 3.0 6.1 + - - +
313C GLY* 2.9 19.8 + - - +
321C LYS* 5.1 6.0 - - - +
324C TYR* 3.4 51.5 + - + +
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Residues in contact with ILE 310 (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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134C ASP 5.4 7.4 - - - +
135C VAL 6.1 0.9 - - - +
136C ALA* 5.6 7.0 - - + +
306C THR* 3.0 36.3 - - + +
307C MET* 4.2 9.0 - - + +
309C GLU* 1.3 74.4 - - + +
311C ASN* 1.3 68.9 + - - +
313C GLY* 3.1 14.4 + - - +
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Residues in contact with ASN 311 (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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307C MET* 3.1 23.5 + - - +
308C PHE 4.2 0.2 - - - +
310C ILE* 1.3 78.9 - - - +
312C VAL* 1.3 71.3 + - - +
313C GLY* 3.0 1.9 + - - -
336C GLY 4.7 0.7 - - - +
339C ILE* 3.3 8.3 - - - +
340C ALA* 3.0 43.4 + - - +
343C VAL* 3.4 23.7 - - + +
347C LEU* 4.7 5.0 - - - +
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Residues in contact with VAL 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PHE 3.5 14.4 + - - +
309C GLU 3.0 7.9 + - - +
311C ASN* 1.3 79.2 - - - +
313C GLY* 1.3 70.7 + - - +
315C THR* 2.8 43.8 + - - +
317C SER* 5.3 8.3 - - - +
324C TYR* 3.7 16.2 - - + +
343C VAL* 3.4 9.6 - - + +
347C LEU* 4.0 12.2 - - + +
401C LEU* 6.0 2.5 - - + -
406C PHE* 3.4 37.0 - - + -
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Residues in contact with GLY 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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309C GLU 2.9 13.2 + - - +
310C ILE* 3.4 13.9 - - - -
311C ASN 3.0 2.5 + - - -
312C VAL* 1.3 83.0 - - - +
314C ASP* 1.3 58.5 + - - -
315C THR 2.9 13.0 + - - +
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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