Contacts of the helix formed by residues 306 - 313 (chain B) in PDB entry 2AXT
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 PRO 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B LEU* 4.6 10.1 - - + -
287B ARG* 3.5 28.0 - - - +
304B ALA 3.1 9.1 - - - +
305B ILE* 1.3 93.1 - - + +
307B GLU* 1.3 66.6 + - - +
308B LYS* 4.4 5.8 - - + +
309B LEU* 3.3 26.3 + - + +
310B ALA* 3.3 14.9 + - - +
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Residues in contact with GLU 307 (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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51B VAL* 4.3 14.1 - - + +
52B LEU* 4.0 17.8 - - + +
305B ILE 3.5 2.1 + - - +
306B PRO* 1.3 71.6 - - - +
308B LYS* 1.3 66.6 + - - +
310B ALA* 2.9 9.8 + - - +
311B PHE* 2.8 23.4 + - - +
339B ALA* 3.9 2.9 - - - +
340B TRP* 2.9 52.3 + - + +
404B GLY* 5.2 1.0 - - - -
430B PHE* 4.5 1.6 - - - -
5085o LYS* 3.3 27.3 - - - +
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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
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50B PRO* 3.6 25.4 + - - +
51B VAL* 3.9 29.7 - - + +
54B PRO* 6.0 2.2 - - - -
173B GLY 3.6 18.8 - - - +
174B LEU* 4.0 28.2 + - + +
266B GLU* 3.2 21.9 + - - +
306B PRO* 3.2 4.6 - - + +
307B GLU* 1.3 80.4 - - - +
309B LEU* 1.3 63.4 + - - +
311B PHE* 3.3 14.5 + - + +
312B TYR* 3.4 27.5 + - + +
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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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172B TYR* 5.2 2.9 - - + -
174B LEU* 3.7 20.0 - - + +
280B PHE* 4.1 24.9 - - + +
283B GLU* 4.3 13.9 - - + -
284B ILE* 3.5 31.4 - - + +
287B ARG* 4.0 31.2 - - - +
305B ILE* 4.5 3.4 - - + -
306B PRO* 3.3 29.9 + - + +
307B GLU 3.1 0.6 - - - -
308B LYS* 1.3 75.2 - - - +
310B ALA* 1.3 69.5 + - - +
312B TYR* 3.1 15.6 + - - +
313B ASP* 3.5 5.4 + - - +
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Residues in contact with ALA 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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284B ILE* 4.1 12.8 - - + -
305B ILE* 4.4 4.8 - - + +
306B PRO 3.3 7.6 + - - +
307B GLU 2.9 8.2 + - - +
309B LEU* 1.3 78.4 - - - +
311B PHE* 1.3 54.3 + - - +
313B ASP* 2.7 34.0 + - - +
340B TRP* 3.9 34.8 - - + -
428B GLU* 3.7 13.4 - - + +
430B PHE* 3.7 10.3 - - + -
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Residues in contact with PHE 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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51B VAL 4.1 7.9 - - - -
52B LEU* 3.3 38.8 - - + -
54B PRO* 4.5 1.1 - - + -
56B TRP* 4.4 11.4 - + - -
57B ARG* 4.0 25.8 - - + -
307B GLU 2.8 6.5 + - - +
308B LYS* 3.4 11.7 - - + +
309B LEU 3.1 0.2 - - - -
310B ALA* 1.3 75.6 - - - +
312B TYR* 1.3 63.2 + + + +
313B ASP 3.1 0.7 + - - -
314B TYR* 3.3 23.4 - + - +
317B ASN* 3.1 40.3 + - - -
337B ALA* 3.4 29.8 - - + -
430B PHE* 3.2 29.9 - + + -
432B PHE* 4.5 3.4 - + - -
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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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56B TRP* 3.9 21.8 + + - -
172B TYR 3.2 23.1 - - - -
173B GLY* 2.7 22.4 + - - -
174B LEU* 4.4 4.0 - - + -
265B ILE* 3.9 13.4 + - + -
266B GLU* 3.4 18.0 - - - +
270B PRO* 3.4 35.8 - - + +
275B TRP* 5.3 4.0 - - - +
280B PHE* 3.3 52.4 - + + -
308B LYS* 3.4 28.2 + - + -
309B LEU* 3.1 9.6 + - + +
311B PHE* 1.3 78.0 - + + +
313B ASP* 1.3 57.2 + - - +
314B TYR 3.1 9.3 + - - +
317B ASN* 4.7 2.6 - - - +
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Residues in contact with ASP 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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275B TRP* 4.1 7.9 - - - -
278B SER* 5.5 0.9 - - - -
280B PHE* 4.0 11.1 - - + +
281B GLN* 3.7 20.8 + - - +
284B ILE* 3.8 23.0 - - + +
309B LEU 3.5 0.6 + - - +
310B ALA 2.7 13.9 + - - +
312B TYR* 1.3 77.8 - - - +
314B TYR* 1.3 56.4 + - - +
358B ARG* 2.8 42.6 + - - -
427B GLY* 3.7 4.0 - - - -
428B GLU* 3.0 33.2 + - + +
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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