Contacts of the helix formed by residues 304 - 313 (chain B) in PDB entry 3N2Z
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 TRP 304 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B ASP* 3.5 34.8 - - - +
291B TYR 2.9 19.6 + - - -
292B PRO* 3.6 34.5 + - + +
303B ALA* 1.4 78.0 - - + +
305B PRO* 1.4 70.1 - - - +
306B ILE 3.2 3.4 - - - -
307B LYS* 3.2 48.9 + - + +
308B VAL* 3.3 9.0 + - - +
429B LEU* 3.8 11.2 - - + -
452B GLU* 3.5 48.5 - - + -
467B PRO* 5.7 1.3 - - + -
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Residues in contact with PRO 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.9 20.6 - - + +
289B VAL 3.4 25.4 - - - +
290B ASP* 3.2 11.0 - - - +
291B TYR* 4.0 6.1 - - + +
301B LEU* 4.1 23.6 - - + -
302B PRO* 3.6 20.9 - - + +
303B ALA 3.5 0.9 - - - +
304B TRP* 1.4 87.4 - - - +
306B ILE* 1.3 61.0 + - - +
308B VAL* 3.4 11.1 + - + +
309B VAL* 3.0 27.8 + - - +
333B VAL* 4.6 3.3 - - + +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ASP* 3.9 19.3 - - + +
226B PHE* 3.7 37.0 - - + -
229B SER* 3.2 24.2 - - - +
286B LEU* 4.0 20.4 - - + +
287B ALA* 3.7 28.7 - - - +
290B ASP* 3.2 31.5 + - + +
304B TRP 3.2 0.2 + - - -
305B PRO* 1.3 74.2 - - - +
307B LYS* 1.4 51.2 + - - +
309B VAL* 2.9 10.4 + - - +
310B CYS* 2.8 34.1 + - - +
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LYS 4.8 10.7 + - - -
229B SER* 2.9 34.8 + - - +
290B ASP* 4.7 1.5 + - - +
304B TRP* 3.2 47.3 + - + +
306B ILE* 1.4 72.2 - - - +
308B VAL* 1.3 63.3 + - + +
310B CYS* 3.5 3.3 + - - +
311B GLN* 3.4 29.3 + - - +
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PRO* 3.8 26.5 - - + -
303B ALA 3.6 13.5 - - - +
304B TRP 3.3 15.7 - - - +
305B PRO 3.5 7.0 - - - +
307B LYS* 1.3 78.4 - - + +
309B VAL* 1.4 59.4 + - - +
311B GLN* 3.4 18.6 - - - +
312B TYR* 3.8 12.6 - - + -
333B VAL* 4.3 17.5 - - + -
337B TYR* 5.3 3.4 - - + -
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 3.9 23.1 - - + -
283B TRP* 5.0 1.1 - - + -
286B LEU* 4.4 17.3 - - + -
305B PRO 3.0 17.0 + - - +
306B ILE* 2.9 25.9 + - - +
308B VAL* 1.4 70.5 - - - +
310B CYS* 1.4 57.7 + - - +
311B GLN 3.1 4.7 - - - -
312B TYR* 3.1 27.8 + - - +
313B LEU* 3.4 17.1 - - + +
330B ALA* 3.5 37.1 - - + +
333B VAL* 3.6 19.3 - - + -
334B TYR 5.1 0.4 - - - +
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Residues in contact with CYS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 3.6 14.1 - - - -
229B SER* 3.4 20.6 - - - +
230B GLY* 4.4 4.4 - - - -
231B PRO* 4.8 1.9 - - - +
233B CYS* 2.1 51.9 - - + -
306B ILE* 2.8 32.1 + - - +
307B LYS 3.8 4.0 - - - +
308B VAL 3.4 0.4 - - - -
309B VAL* 1.4 71.6 - - - +
311B GLN* 1.3 60.3 - - - +
312B TYR 3.4 0.4 - - - -
313B LEU* 3.9 2.9 - - - +
314B LYS* 3.5 24.3 + - - +
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Residues in contact with GLN 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 LYS 3.4 14.4 + - - +
308B VAL* 3.4 16.5 - - - +
310B CYS* 1.3 77.7 - - - +
312B TYR* 1.4 66.8 + - + +
313B LEU 3.3 0.4 - - - +
314B LYS* 3.2 56.3 + - - +
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Residues in contact with TYR 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 VAL* 3.8 18.8 - - + -
309B VAL 3.1 10.8 + - - +
311B GLN* 1.4 76.4 - - + +
313B LEU* 1.3 66.8 + - - +
326B ASN* 3.2 40.7 + - - +
329B GLN* 3.3 51.6 + - + -
330B ALA* 4.4 1.1 - - + +
332B ASN* 5.5 1.6 + - - -
333B VAL* 3.7 24.0 - - + +
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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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232B HIS 4.3 2.9 - - - +
233B CYS* 4.0 26.2 - - - +
236B SER* 3.8 32.3 - - - +
237B ILE* 4.6 11.2 - - + -
283B TRP* 5.6 0.2 - - + -
309B VAL* 3.4 26.9 + - + +
310B CYS 3.9 0.6 + - - +
311B GLN 3.3 1.0 - - - +
312B TYR* 1.3 82.6 - - - +
314B LYS* 1.3 60.6 + - - +
315B ASN* 2.6 25.9 + - - +
323B LEU* 4.9 2.0 - - + +
326B ASN* 3.7 34.9 + - + +
327B ILE* 3.9 25.4 - - + -
330B ALA* 4.2 13.5 - - + -
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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