Contacts of the helix formed by residues 306 - 317 (chain B) in PDB entry 2F37
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 LYS 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B LYS* 5.4 2.0 - - - +
253B VAL* 3.3 19.3 - - + +
254B MSE 3.6 24.2 + - - +
256B SER* 2.9 42.8 + - - +
257B ASP* 4.5 7.5 - - - +
258B ASN* 3.7 4.3 - - - +
301B ALA* 2.9 14.9 + - - +
304B GLU* 3.9 26.7 + - + +
305B GLY* 1.3 76.4 - - - +
307B ILE* 1.3 57.8 + - - +
308B GLU 3.4 2.5 - - - -
309B ILE* 3.5 10.9 - - + +
310B PHE* 2.9 27.9 + - - +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ASN* 3.0 11.8 + - - +
301B ALA 4.8 1.6 - - - +
302B ALA* 4.8 11.4 - - - +
305B GLY* 3.0 29.5 + - - +
306B LYS* 1.3 71.4 - - - +
308B GLU* 1.3 65.1 + - - +
310B PHE* 3.3 13.0 + - + +
311B ARG* 3.0 56.1 + - + +
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASP 3.7 15.3 - - - +
258B ASN* 3.1 35.5 + - + +
259B SER 5.1 2.5 - - - +
260B ALA* 6.0 2.5 - - - -
263B ILE* 3.9 20.8 - - + +
307B ILE* 1.3 76.9 - - - +
309B ILE* 1.3 61.6 + - - +
311B ARG* 2.6 34.2 + - - +
312B HIS* 2.8 47.8 + - - -
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Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU 4.1 0.4 - - - +
253B VAL* 4.0 26.9 - - + -
256B SER* 3.6 21.0 + - - +
257B ASP 5.0 0.2 + - - -
263B ILE* 3.8 15.3 - - + +
266B VAL* 3.8 27.4 - - + -
267B THR* 5.1 4.0 - - - +
270B TYR* 3.9 24.9 - - + -
301B ALA* 3.9 11.0 - - + -
306B LYS* 3.5 17.8 + - + +
308B GLU* 1.3 77.3 - - - +
310B PHE* 1.3 67.8 + - - +
312B HIS* 3.1 8.4 + - + +
313B ILE* 2.9 35.4 + - + +
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Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LEU* 3.5 43.8 - - + +
299B LYS* 5.7 2.0 - - + -
301B ALA* 3.9 10.5 - - + -
302B ALA* 3.7 27.1 - - + -
306B LYS 2.9 19.8 + - - +
307B ILE* 3.4 19.5 - - + +
308B GLU 3.2 0.2 - - - -
309B ILE* 1.3 78.1 - - - +
311B ARG* 1.3 67.4 + - + +
313B ILE* 4.7 0.4 - - - -
314B LEU* 2.8 60.3 + - + +
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Residues in contact with ARG 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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307B ILE* 3.0 44.3 + - + +
308B GLU* 2.6 38.5 + - - +
309B ILE 3.2 0.4 - - - -
310B PHE* 1.3 87.0 - - + +
312B HIS* 1.3 62.3 + - + +
314B LEU* 3.7 7.0 - - + +
315B GLN* 3.0 30.1 + - - +
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Residues in contact with HIS 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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263B ILE* 4.2 18.1 - - + +
267B THR* 3.5 33.1 + - + +
308B GLU* 2.8 39.0 + - - +
309B ILE* 3.1 12.6 + - + +
311B ARG* 1.3 78.1 - - + +
313B ILE* 1.3 64.2 + - + +
315B GLN* 3.5 17.6 + - - +
316B ARG* 3.3 33.4 + - - +
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Residues in contact with ILE 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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253B VAL* 3.9 24.5 - - + -
270B TYR* 3.5 21.3 - - + +
287B GLU* 3.5 21.0 - - + +
297B PRO* 4.1 11.9 - - + +
298B LEU* 3.7 33.0 - - + +
301B ALA* 4.6 1.3 - - + -
309B ILE* 2.9 31.3 + - + +
312B HIS* 1.3 73.4 - - + +
314B LEU* 1.3 66.6 + - - +
316B ARG* 3.2 31.9 + - - +
317B GLU* 3.2 15.1 + - - +
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Residues in contact with LEU 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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298B LEU* 3.7 19.9 - - + +
310B PHE* 2.8 47.8 + - + +
311B ARG* 3.7 9.2 - - + +
313B ILE* 1.3 73.0 - - - +
315B GLN* 1.3 63.3 + - - +
317B GLU* 3.2 18.3 + - + +
318B PHE* 3.3 36.2 - - + -
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Residues in contact with GLN 315 (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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311B ARG 3.0 17.8 + - - +
312B HIS* 3.7 21.0 - - - +
313B ILE 3.2 0.2 - - - -
314B LEU* 1.3 77.0 - - - +
316B ARG* 1.3 62.5 + - - +
318B PHE* 3.1 29.4 + - - +
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Residues in contact with ARG 316 (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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270B TYR* 2.9 32.5 - - - -
271B ASP* 3.3 26.2 + - - -
274B LEU* 3.3 14.7 - - - +
287B GLU* 2.7 37.5 + - - +
312B HIS* 3.3 15.5 + - - +
313B ILE* 3.2 23.2 + - - +
315B GLN* 1.3 78.7 - - + +
317B GLU* 1.3 57.5 + - - +
318B PHE* 2.8 15.5 + - - -
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 5.8 0.6 + - - -
298B LEU* 3.5 28.2 - - - +
313B ILE* 3.2 12.5 + - + +
314B LEU* 3.2 19.1 + - + +
316B ARG* 1.3 73.8 - - - +
318B PHE* 1.3 73.3 + - + +
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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