Contacts of the helix formed by residues 301 - 314 (chain B) in PDB entry 2P2N
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 THR 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ASN 4.1 4.1 + - - +
160B ARG* 4.0 25.4 - - - +
161B THR 4.0 10.4 + - - +
162B THR* 4.9 1.1 - - - -
175B PRO* 5.0 4.3 - - + -
176B ASN* 5.6 0.4 - - - +
270B LEU* 4.1 0.4 - - - -
299B ASP 3.6 1.5 + - - +
300B MET* 1.3 73.6 - - - +
302B VAL* 1.3 62.1 + - - +
303B GLU* 3.4 15.4 + - - +
304B ALA* 2.9 27.0 + - - +
305B THR* 3.0 27.4 + - - -
8002B ASN* 3.5 15.0 - - - +
9004B EDO 3.7 18.8 - - - +
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 4.7 9.2 - - + +
214B VAL* 4.6 19.3 - - + -
238B ILE* 4.7 10.3 - - + -
240B ARG* 3.9 16.4 - - + -
270B LEU* 3.8 23.3 - - + +
300B MET 4.1 0.2 + - - -
301B THR* 1.3 70.8 - - - +
303B GLU* 1.3 54.9 + - - +
305B THR* 3.9 0.2 - - - -
306B LEU* 2.7 37.4 + - + +
8002B ASN* 2.8 38.6 + - - +
216D THR* 5.2 1.3 - - + -
218D TYR* 5.7 0.9 - - + -
9012D EDO 3.7 26.2 - - - +
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA* 4.0 11.3 - - + +
96B TYR* 3.7 48.4 - - + +
99B SER* 3.7 14.9 - - - +
161B THR 3.9 5.6 - - - +
162B THR* 2.6 31.8 + - - -
163B LYS 4.3 1.2 + - - -
301B THR* 3.2 7.6 - - - +
302B VAL* 1.3 76.8 - - - +
304B ALA* 1.3 59.6 + - - +
306B LEU* 4.1 0.7 - - - +
307B THR* 2.8 32.7 + - - +
8002B ASN* 2.4 27.7 + - - -
272D GLN* 4.9 0.5 - - - +
9012D EDO 3.8 13.6 - - - -
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Residues in contact with ALA 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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99B SER* 3.9 6.2 + - - -
103B PHE* 3.6 4.1 - - + -
159B ASN* 3.5 22.0 - - + +
300B MET* 4.4 7.6 - - + -
301B THR* 2.9 26.3 + - - +
303B GLU* 1.3 77.0 - - - +
305B THR* 1.3 52.2 + - - +
307B THR* 3.0 7.4 + - - -
308B LYS* 2.8 37.6 + - - +
333B GLU* 4.1 17.9 - - + +
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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
----------------------------------------------------------
238B ILE* 3.8 18.6 - - + -
268B VAL* 3.9 18.8 - - + -
270B LEU* 3.3 30.0 - - + +
300B MET* 3.3 14.4 - - - +
301B THR 3.0 17.7 + - - -
302B VAL 3.9 1.3 - - - -
304B ALA* 1.3 72.8 - - - +
306B LEU* 1.3 65.7 + - - +
308B LYS* 3.8 5.7 - - - +
309B LEU* 3.0 26.9 + - + +
326B MET* 3.7 18.8 - - + -
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Residues in contact with LEU 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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68B TRP* 4.6 8.3 - - + -
96B TYR* 3.8 19.5 - - + -
212B ILE* 3.9 35.4 - - + +
214B VAL* 4.5 3.4 - - + -
238B ILE* 3.7 12.9 - - + +
302B VAL* 2.7 25.9 + - + +
303B GLU 4.1 2.7 - - - +
305B THR* 1.3 73.5 - - - +
307B THR* 1.3 58.2 + - - +
309B LEU* 3.4 4.1 + - - +
310B HIS* 3.1 40.9 + - + +
218D TYR* 3.7 45.8 - - + -
219D PRO* 4.2 10.3 - - + +
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Residues in contact with THR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TRP* 3.6 19.5 - - + -
96B TYR* 3.5 27.6 - - + +
99B SER* 3.4 12.0 - - - -
100B ALA* 3.5 27.6 - - + +
103B PHE* 3.5 7.6 - - - -
207B ILE* 3.7 3.3 - - - +
303B GLU 2.8 19.9 + - - +
304B ALA 3.0 9.7 + - - -
306B LEU* 1.3 76.3 - - + +
308B LYS* 1.3 53.7 + - - +
310B HIS* 3.3 8.1 + - - +
311B TYR* 2.8 33.8 + - - +
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Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 3.5 24.8 - - + -
300B MET* 3.7 22.8 - - - -
304B ALA 2.8 20.7 + - - +
305B THR 3.8 4.5 - - - +
307B THR* 1.3 69.0 + - - +
309B LEU* 1.3 61.4 + - - +
311B TYR* 3.3 4.0 + - - +
312B LEU* 2.9 39.0 + - + +
325B ALA 3.3 15.6 + - - -
326B MET* 2.9 39.4 + - + +
328B GLN 2.7 26.5 + - - -
330B LEU* 3.8 13.9 - - + -
333B GLU* 2.8 20.2 + - - +
334B LEU* 4.1 2.2 - - - +
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Residues in contact with LEU 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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212B ILE* 3.8 13.9 - - + -
236B ALA* 3.9 23.3 - - + -
237B LEU 5.2 0.4 - - - +
238B ILE* 3.8 28.3 - - + -
266B VAL* 3.8 27.8 - - + +
268B VAL* 4.3 6.7 - - + -
305B THR* 3.0 26.9 + - + +
306B LEU 3.6 3.6 - - - +
308B LYS* 1.3 74.6 - - - +
310B HIS* 1.3 59.8 + - - +
312B LEU* 3.2 2.1 + - - -
313B LEU* 2.8 42.8 + - + +
322B ILE* 4.6 7.9 - - + -
326B MET* 3.6 25.4 - - + -
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Residues in contact with HIS 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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65B PRO* 3.4 29.9 - - + +
68B TRP* 3.9 13.4 - + + -
207B ILE* 3.5 17.2 - - + +
208B THR 3.0 25.1 - - - -
209B PRO* 4.3 0.2 - - - +
210B GLN* 3.6 30.6 + - + +
212B ILE* 3.5 19.5 - - + +
306B LEU* 3.1 38.6 + - + -
307B THR 3.3 8.9 + - - +
309B LEU* 1.3 72.7 - - - +
311B TYR* 1.3 61.1 + - - +
313B LEU 4.2 0.2 - - - -
314B SER* 2.7 32.1 + - - -
218D TYR* 6.0 1.3 - + - -
219D PRO 4.7 5.2 - - - -
220D GLY* 5.8 0.6 - - - -
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Residues in contact with TYR 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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103B PHE* 3.4 44.9 - + + -
104B MET* 4.5 1.8 - - - -
205B HIS* 3.4 38.0 + + + -
206B PRO 4.9 0.9 - - - -
207B ILE* 3.7 14.8 - - + +
307B THR 2.8 17.6 + - - +
308B LYS 3.5 4.0 - - - +
309B LEU 3.2 0.2 - - - -
310B HIS* 1.3 79.2 - - - +
312B LEU* 1.3 97.0 + - + +
314B SER 3.2 1.9 + - - -
315B GLN* 2.8 44.0 + - + +
330B LEU* 4.1 15.0 - - + +
331B ARG* 3.4 22.2 + - - -
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Residues in contact with LEU 312 (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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308B LYS* 2.9 22.1 + - + +
309B LEU* 4.1 1.6 - - - +
311B TYR* 1.3 98.0 - - + +
313B LEU* 1.3 58.6 + - - +
315B GLN* 3.0 27.0 + - - +
317B LEU* 3.6 25.0 - - + +
322B ILE* 3.8 32.0 - - + +
325B ALA* 3.5 34.1 - - + -
326B MET* 3.7 30.1 - - - +
330B LEU* 4.2 6.5 - - + -
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Residues in contact with LEU 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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210B GLN* 3.5 42.3 + - + +
212B ILE* 4.3 3.8 - - + -
235B LYS* 4.1 44.3 + - + +
236B ALA* 4.2 18.4 - - + -
266B VAL* 4.7 7.9 - - + -
309B LEU* 2.8 32.0 + - + +
312B LEU* 1.3 74.5 - - - +
314B SER* 1.3 58.6 + - - +
315B GLN 3.2 5.6 + - - +
322B ILE* 3.9 28.3 - - + +
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Residues in contact with SER 314 (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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206B PRO* 3.3 32.3 - - - +
208B THR* 2.9 39.6 + - - +
210B GLN* 3.2 7.6 + - - +
310B HIS 2.7 22.9 + - - -
311B TYR 3.6 1.1 - - - -
312B LEU 3.2 1.0 - - - -
313B LEU* 1.3 74.5 - - - +
315B GLN* 1.3 65.8 + - - +
316B GLU* 4.8 3.3 - - - +
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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