Contacts of the helix formed by residues 235 - 248 (chain T) in PDB entry 3P71
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 235 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232T ASN* 3.4 9.6 - - - +
233T MET 3.0 1.0 + - - +
234T GLY* 1.3 76.4 - - - +
236T ARG* 1.3 64.9 - - - +
237T PHE* 4.0 5.1 - - - +
238T GLY* 3.1 11.3 + - - -
239T GLN* 3.0 28.6 + - - +
314T HIS* 2.8 39.4 + - - -
800T PEG 5.5 1.8 - - - -
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Residues in contact with ARG 236 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C CYS 5.9 0.4 - - - +
270C GLY* 3.6 27.6 - - - -
290C ASP* 6.0 0.2 + - - -
235T ASP* 1.3 73.9 - - - +
237T PHE* 1.3 65.7 - - - +
239T GLN* 3.3 7.6 + - - +
240T ILE* 2.9 39.2 + - + +
800T PEG 3.7 41.3 + - - +
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Residues in contact with PHE 237 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C ARG* 3.4 37.9 - - + +
269C CYS 5.0 2.8 + - - +
307C TYR* 4.0 19.9 + + - -
235T ASP* 3.3 3.2 + - - +
236T ARG* 1.3 79.2 - - - +
238T GLY* 1.3 62.7 + - - +
240T ILE* 3.2 5.9 + - - +
241T MET* 3.1 25.2 + - - +
310T GLN* 3.4 41.5 - - + +
311T LEU* 3.9 35.4 - - + -
314T HIS* 3.3 54.7 - + + +
315T TYR* 5.7 1.3 - + - -
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Residues in contact with GLY 238 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233T MET* 3.4 50.5 - - - +
235T ASP* 3.1 10.3 + - - -
237T PHE* 1.3 82.5 - - - +
239T GLN* 1.3 57.5 + - - +
241T MET* 3.4 2.3 + - - +
242T ILE* 3.0 27.0 + - - +
314T HIS* 4.7 0.2 - - - -
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Residues in contact with GLN 239 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233T MET 4.2 3.8 + - - +
234T GLY 5.9 0.9 - - - -
235T ASP 3.0 21.0 + - - +
236T ARG 3.5 2.2 - - - +
237T PHE 3.2 0.2 - - - -
238T GLY* 1.3 74.7 - - - +
240T ILE* 1.3 63.2 + - - +
242T ILE* 3.4 25.0 + - - +
243T GLU* 3.1 22.7 + - - +
800T PEG 3.5 54.7 + - - +
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Residues in contact with ILE 240 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C ASN* 3.6 19.7 - - + +
267C TYR 3.6 24.2 - - - +
268C ARG 4.0 7.4 - - - +
270C GLY* 3.6 32.5 - - - +
302C ARG* 6.0 0.2 - - - +
307C TYR* 4.0 4.7 - - - +
236T ARG* 2.9 33.8 + - + +
237T PHE 3.7 4.0 - - - +
239T GLN* 1.3 73.2 - - - +
241T MET* 1.3 56.0 + - - +
243T GLU* 3.3 7.5 + - - +
244T ASN* 2.8 38.6 + - - +
800T PEG 4.7 12.6 - - - +
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Residues in contact with MET 241 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C TYR* 3.4 44.9 - - + -
309C LEU* 4.6 1.6 - - + -
230T GLN* 3.0 38.8 - - + +
233T MET* 3.7 23.3 - - + +
237T PHE* 3.1 17.9 + - + +
238T GLY* 3.4 9.9 - - - +
239T GLN 3.2 0.2 - - - -
240T ILE* 1.3 74.6 - - - +
242T ILE* 1.3 66.0 + - - +
244T ASN* 3.1 1.4 + - - +
245T LEU* 2.9 49.7 + - + +
252T LEU* 4.4 2.5 - - + -
314T HIS* 6.1 0.2 - - - -
315T TYR* 3.1 21.8 - - - +
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Residues in contact with ILE 242 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233T MET* 4.2 8.5 - - + +
238T GLY 3.0 24.0 + - - +
239T GLN* 3.4 30.5 + - + +
241T MET* 1.3 77.1 - - - +
243T GLU* 1.3 62.7 + - - +
245T LEU* 3.5 2.8 + - - +
246T ARG* 3.3 55.4 + - - +
250T CYS 4.9 0.2 - - - +
251T ASP* 5.1 0.9 - - - +
252T LEU* 4.1 19.6 + - + +
255T VAL* 4.1 37.5 - - + -
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Residues in contact with GLU 243 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C ARG* 4.5 1.0 + - - -
239T GLN 3.1 16.6 + - - +
240T ILE* 3.7 7.0 - - - +
242T ILE* 1.3 77.4 - - + +
244T ASN* 1.3 67.5 + - - +
246T ARG* 3.3 22.1 + - + +
247T ARG* 2.8 56.7 + - - +
800T PEG 5.5 6.3 - - - +
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Residues in contact with ASN 244 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C TYR 2.7 29.7 + - - -
302C ARG* 3.3 27.7 + - - +
304C THR* 3.4 26.9 + - + -
305C PRO* 3.4 16.0 - - - +
307C TYR* 3.3 18.8 + - + -
240T ILE* 2.8 23.9 + - - +
241T MET 3.1 4.7 + - - +
243T GLU* 1.3 76.6 + - - +
245T LEU* 1.3 60.4 + - - +
247T ARG* 3.3 28.5 + - - +
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Residues in contact with LEU 245 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C THR* 4.1 17.7 - - + -
307C TYR* 4.3 9.2 - - + -
309C LEU* 4.1 32.1 - - + -
29T THR* 6.2 0.2 - - + -
203T TYR* 5.5 0.2 - - - +
241T MET* 2.9 37.4 + - + +
242T ILE 4.1 2.7 - - - +
244T ASN* 1.3 76.1 - - - +
246T ARG* 1.3 58.4 + - - +
248T ARG* 3.1 23.4 + - - +
250T CYS* 2.9 43.7 + - + +
252T LEU* 3.6 40.6 - - + -
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Residues in contact with ARG 246 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242T ILE* 3.3 37.0 + - + +
243T GLU* 3.5 13.6 - - + +
244T ASN 3.2 0.4 - - - -
245T LEU* 1.3 74.6 - - - +
247T ARG* 1.3 62.6 + - - +
248T ARG 3.1 1.8 - - - -
249T GLN* 3.1 13.2 + - - +
250T CYS 4.0 12.1 - - - +
251T ASP* 2.8 34.7 + - + +
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Residues in contact with ARG 247 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C HIS 3.2 28.7 + - - +
300C VAL* 3.7 15.0 + - - +
302C ARG* 3.1 52.4 + - - +
303C ARG* 5.6 0.9 - - - -
304C THR* 4.5 9.0 - - - +
243T GLU* 2.8 43.3 + - - +
244T ASN* 3.3 25.4 + - - +
245T LEU 3.3 0.4 - - - -
246T ARG* 1.3 78.2 - - - +
248T ARG* 1.3 57.1 + - - +
249T GLN* 3.1 19.3 + - - -
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Residues in contact with ARG 248 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C THR* 3.5 28.4 - - - +
309C LEU* 4.2 9.9 - - - +
25T GLY* 4.1 8.8 + - - +
28T GLY* 3.2 21.2 + - - -
29T THR* 4.1 11.0 - - - +
31T GLU* 5.5 0.6 + - - +
32T ASP* 3.0 50.5 + - - +
244T ASN 4.3 0.2 - - - +
245T LEU* 3.1 23.9 + - - +
246T ARG 3.1 0.6 - - - -
247T ARG* 1.3 76.2 - - - +
249T GLN* 1.3 78.2 + - - +
250T CYS* 3.1 16.8 + - - +
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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