Contacts of the helix formed by residues 300 - 313 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B GLY* 4.8 1.4 - - - -
138B LEU 5.4 0.3 + - - -
139B GLU* 4.2 23.4 - - - +
298B LEU 3.3 4.3 + - - +
299B PRO* 1.3 74.5 - - - +
301B LEU* 1.3 68.4 + - - +
302B ALA* 3.8 14.5 + - - +
303B ALA* 2.8 37.9 + - - +
304B ARG* 2.8 12.5 + - - +
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ASP* 1.3 74.0 - - - +
302B ALA* 1.3 57.5 + - - +
304B ARG* 3.0 37.1 + - - +
305B THR* 2.6 38.1 + - - +
325B ARG* 5.2 5.4 - - + +
328B GLY 3.2 3.1 - - - -
329B ALA* 3.1 37.2 - - + +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ASP* 3.2 14.8 + - - +
301B LEU* 1.3 79.5 - - - +
303B ALA* 1.3 63.3 + - - +
305B THR* 3.2 10.0 + - - -
306B THR* 2.9 21.8 + - - -
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ALA 4.8 0.9 - - - -
137B GLY* 4.0 26.7 - - - +
299B PRO* 3.4 21.1 - - + -
300B ASP* 2.8 27.1 + - - +
302B ALA* 1.3 75.1 - - - +
304B ARG* 1.3 54.9 - - - +
306B THR* 2.7 34.9 + - - -
307B MET* 2.9 15.0 + - - +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B PRO* 3.2 48.9 + - + +
300B ASP* 2.8 11.3 + - - +
301B LEU* 3.0 37.7 - - - +
303B ALA* 1.3 71.5 - - - +
305B THR* 1.3 60.8 + - - +
307B MET* 3.6 2.0 + - - -
308B PHE* 3.1 30.7 + - - -
328B GLY* 2.7 34.8 + - - +
329B ALA* 3.6 3.2 - - - +
331B THR* 3.2 25.7 + - - +
332B GLU* 3.4 35.5 - - - +
333B GLY 4.6 1.9 - - - +
334B TYR 4.3 5.8 - - - +
339B ILE* 3.6 20.0 - - + +
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Residues in contact with THR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B LEU* 2.6 25.4 + - - +
302B ALA* 3.4 9.1 + - - -
303B ALA 2.8 5.3 + - - -
304B ARG* 1.3 71.3 - - - +
306B THR* 1.3 67.2 + - - -
308B PHE* 2.9 14.9 + - - +
309B GLU* 3.1 24.0 + - - +
321B LYS 5.5 0.2 - - - +
324B TYR* 3.1 44.9 - - + +
325B ARG* 3.4 12.0 - - + +
328B GLY* 3.8 10.7 - - - -
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ALA* 5.0 10.8 + - - +
302B ALA 2.9 11.1 + - - -
303B ALA* 2.7 18.8 + - - -
305B THR* 1.3 75.0 - - - +
307B MET* 1.3 64.9 + - - -
309B GLU* 2.9 16.4 + - + +
310B ILE* 2.8 42.4 + - + +
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Residues in contact with MET 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ALA* 3.4 35.7 - - + -
176B GLY 5.3 0.2 - - - +
177B THR* 5.5 6.3 - - - +
299B PRO* 3.5 33.4 - - + -
303B ALA 2.9 11.8 + - - +
304B ARG* 3.8 7.6 - - - +
306B THR* 1.3 76.1 - - - +
308B PHE* 1.3 62.4 - - - +
310B ILE* 4.5 8.1 - - + -
311B ASN* 2.8 35.7 + - - +
336B GLY* 3.1 36.8 - - - +
339B ILE* 4.2 18.2 - - + -
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B ARG 3.1 23.6 + - - -
305B THR* 2.9 10.6 + - - +
307B MET* 1.3 77.6 - - - +
309B GLU* 1.3 62.3 + - - +
311B ASN* 3.8 1.2 - - - +
312B VAL* 3.1 29.5 + - - +
324B TYR* 3.9 14.6 - + + +
327B LEU* 3.7 48.9 - - + -
328B GLY 4.5 0.7 - - - -
331B THR* 3.7 24.9 - - + -
339B ILE* 3.8 22.0 - - + -
342B VAL* 3.8 25.6 - - + -
343B VAL* 3.5 27.1 - - + -
406B PHE* 4.4 9.0 - + - -
410B ILE* 4.1 6.3 - - + -
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B THR* 3.3 27.8 - - - +
306B THR* 2.9 14.8 + - + +
308B PHE* 1.3 73.7 - - - +
310B ILE* 1.3 67.8 + - + +
312B VAL* 3.2 3.8 + - - +
313B GLY* 2.8 22.2 + - - +
321B LYS* 5.7 0.9 - - - +
324B TYR* 3.5 41.4 - - + +
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASN* 4.4 1.9 - - - +
134B ASP* 5.4 9.2 - - - +
135B VAL 6.4 0.2 - - - -
136B ALA* 6.0 6.7 - - - +
306B THR* 2.8 36.9 + - + +
307B MET* 3.9 8.3 - - + +
309B GLU* 1.3 72.8 - - + +
311B ASN* 1.3 71.0 + - - +
313B GLY* 2.9 16.0 + - - -
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Residues in contact with ASN 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASN* 2.7 29.9 - - - +
307B MET* 2.8 33.6 + - - +
310B ILE* 1.3 81.4 - - - +
312B VAL* 1.3 58.0 + - - +
336B GLY 5.1 1.6 - - - +
339B ILE* 4.6 0.7 - - - +
340B ALA* 3.0 48.2 + - - +
343B VAL* 3.6 24.6 - - + +
344B LYS 5.4 0.2 - - - +
347B LEU* 4.7 2.4 - - - +
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASN* 3.7 1.5 - - - +
308B PHE 3.1 18.7 + - - +
309B GLU 3.7 1.3 - - - +
311B ASN* 1.3 75.5 - - - +
313B GLY* 1.3 68.7 + - - +
315B THR* 2.6 41.6 + - - +
317B SER* 5.0 2.9 - - - -
324B TYR* 3.6 26.0 - - + +
343B VAL* 3.4 22.7 - - + -
347B LEU* 4.0 15.7 - - + -
401B LEU* 4.9 3.1 - - + -
406B PHE* 3.4 25.4 - - + -
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Residues in contact with GLY 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASN* 4.1 9.4 - - - -
309B GLU 2.8 13.5 + - - +
310B ILE* 2.9 14.4 + - - -
311B ASN 3.0 1.1 + - - -
312B VAL* 1.3 87.1 - - - +
314B ASP* 1.3 58.9 + - - -
315B THR 3.1 4.3 + - - +
324B TYR* 5.2 1.0 + - - -
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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