Contacts of the helix formed by residues 302 - 308 (chain E) in PDB entry 1QRP
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 GLY 302 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215E ASP 3.5 10.8 - - - -
218E THR 3.1 14.4 - - - -
219E SER 4.1 0.2 - - - -
220E LEU 3.3 13.6 + - - -
221E LEU* 3.9 3.0 - - - +
300E ILE* 3.2 11.7 + - - -
301E LEU* 1.3 77.4 - - - +
303E ASP* 1.3 58.9 + - - -
304E VAL 3.3 2.0 - - - -
305E PHE 3.0 19.3 + - - -
306E ILE* 3.2 12.4 + - - +
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Residues in contact with ASP 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ASP 4.6 0.7 - - - +
12E MET 3.7 16.6 - - - +
13E GLU* 4.7 0.7 - - - -
14E TYR* 3.5 24.1 - - + -
155E LEU* 3.3 15.3 - - + +
216E THR* 2.8 30.5 - - - +
217E GLY 5.0 0.3 - - - -
218E THR 2.8 19.2 + - - +
219E SER* 3.1 11.8 + - - +
302E GLY* 1.3 70.7 - - - -
304E VAL* 1.3 62.7 + - - +
306E ILE* 4.4 5.3 - - - +
307E ARG* 2.9 49.8 + - - +
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Residues in contact with VAL 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E SER 3.2 14.8 + - - +
220E LEU* 4.0 21.1 - - + -
221E LEU* 3.8 30.7 - - + +
269E VAL* 4.3 5.9 - - + +
273E ALA* 3.6 31.3 - - - +
274E TYR* 4.1 7.4 - - - -
276E LEU* 4.3 5.2 - - + -
285E GLY* 4.2 9.4 - - - +
302E GLY 3.1 0.2 + - - -
303E ASP* 1.3 76.5 - - - +
305E PHE* 1.3 60.1 + - - +
307E ARG* 3.7 23.5 + - - +
308E GLN* 3.6 18.5 + - - +
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Residues in contact with PHE 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E VAL* 5.7 3.6 - - + -
221E LEU* 3.7 15.2 - - + +
260E PHE* 4.2 24.0 - + + -
262E ILE* 3.9 21.1 - - + -
267E TYR* 3.9 20.6 - + + -
269E VAL* 4.0 19.3 - - + -
301E LEU* 4.1 31.2 - - + -
302E GLY 3.0 10.2 + - - +
304E VAL* 1.3 78.2 - - - +
306E ILE* 1.3 68.1 + - + +
308E GLN* 3.0 24.9 + - - +
309E TYR* 3.3 34.7 + + + -
311E THR* 5.6 0.4 - - - -
322E LEU* 4.1 24.2 - - + -
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Residues in contact with ILE 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E VAL* 4.5 15.4 - - + +
154E TYR* 6.0 0.3 - - - -
155E LEU* 3.7 32.6 + - + +
214E VAL* 4.0 21.1 - - + -
215E ASP 3.7 29.8 - - - +
216E THR* 3.8 16.4 - - + +
301E LEU 3.9 7.6 - - - +
302E GLY 3.2 16.4 + - - +
303E ASP* 3.3 2.4 + - - +
305E PHE* 1.3 82.3 - - + +
307E ARG* 1.3 62.2 + - - +
309E TYR 2.8 25.7 + - - +
310E PHE* 4.2 0.7 + - - -
311E THR* 4.0 16.4 - - - +
325E VAL* 4.7 1.4 - - - +
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Residues in contact with ARG 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ASP* 2.9 42.7 + - - +
14E TYR* 3.0 18.1 + - - +
154E TYR* 5.2 0.2 - - - -
155E LEU* 3.7 20.6 - - + +
156E SER 3.3 27.6 - - - +
157E ALA* 3.8 20.2 - - + +
219E SER 4.7 0.8 + - - -
273E ALA* 5.1 1.8 + - - +
276E LEU* 4.0 17.4 - - - +
303E ASP* 2.9 27.7 + - - +
304E VAL* 3.7 34.4 + - - +
305E PHE 3.3 0.2 - - - -
306E ILE* 1.3 75.1 - - - +
308E GLN* 1.3 72.4 + - - +
325E VAL* 3.3 23.2 - - - +
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Residues in contact with GLN 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E PRO 5.0 0.7 - - - +
269E VAL* 4.7 6.3 - - + -
270E PRO* 3.5 26.3 - - + +
273E ALA* 3.7 25.6 - - + +
304E VAL 3.6 15.9 + - - +
305E PHE* 3.0 9.9 + - - +
307E ARG* 1.3 90.5 + - - +
309E TYR* 1.3 84.4 + - + +
324E PRO* 3.6 2.8 - - - +
325E VAL* 3.1 26.8 + - - +
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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
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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