Contacts of the helix formed by residues 301 - 311 (chain B) in PDB entry 2AY6
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 HIS 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 4.9 2.8 + - - -
265A GLU* 3.6 24.0 + - - +
301A HIS* 3.6 35.8 + + + -
57B GLU* 2.9 34.5 + - + +
60B MET* 3.2 26.7 - - + +
265B GLU* 3.3 33.7 - - - +
299B PRO* 3.9 1.2 - - - +
300B PHE* 1.3 84.4 - - - +
302B GLY* 1.3 61.9 + - - +
304B LYS* 3.4 4.1 + - - +
305B ILE* 3.1 38.7 + - + +
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Residues in contact with GLY 302 (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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262B ILE* 4.0 4.4 - - - +
265B GLU* 4.0 16.2 + - - +
267B THR* 3.3 27.5 - - - +
299B PRO* 5.0 2.2 + - - +
300B PHE 3.4 0.6 - - - -
301B HIS* 1.3 75.2 - - - +
303B ALA* 1.3 61.6 + - - +
305B ILE* 2.9 23.5 + - - +
306B VAL* 3.0 17.0 + - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 6.0 4.7 - - + +
79B PHE* 3.4 46.6 - - + +
104B ALA* 5.4 5.2 - - + -
267B THR* 3.7 10.7 + - - +
299B PRO 4.2 13.1 + - - +
300B PHE* 3.2 10.2 + - + +
302B GLY* 1.3 75.7 - - - +
304B LYS* 1.3 57.1 + - - +
306B VAL 3.5 0.2 + - - -
307B SER* 3.0 28.8 + - - -
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B MET* 3.4 34.3 - - + +
63B THR* 5.1 3.2 + - - -
64B GLU* 4.0 17.5 + - - -
76B GLU* 6.1 0.7 - - + -
78B GLU* 5.0 10.5 - - - +
300B PHE* 2.9 51.3 + - + +
301B HIS 3.6 5.4 - - - +
303B ALA* 1.3 75.2 - - - +
305B ILE* 1.3 57.5 + - - +
307B SER* 4.3 9.4 - - - -
308B THR* 2.7 58.0 + - - +
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Residues in contact with ILE 305 (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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68A LYS* 4.6 1.3 - - - -
53B VAL* 3.7 42.4 - - + -
56B ALA* 4.1 6.7 - - + +
57B GLU* 3.6 23.8 - - + +
60B MET* 3.8 18.8 - - - -
260B PHE* 5.4 0.9 - - + -
262B ILE* 4.5 9.6 - - + -
265B GLU* 4.6 9.0 - - + -
301B HIS* 3.1 41.3 + - + +
302B GLY* 2.9 12.4 + - - +
304B LYS* 1.3 77.5 - - - +
306B VAL* 1.3 57.1 + - + +
308B THR* 3.4 1.9 + - - -
309B VAL* 3.0 35.8 + - + +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 4.1 8.7 - - + -
82B ALA* 5.6 0.7 - - + -
83B MET* 4.1 16.2 - - + -
256B CYS* 4.0 17.7 - - + -
260B PHE* 3.7 36.6 - - + -
262B ILE* 3.9 20.6 - - + -
267B THR* 4.1 4.0 - - - +
302B GLY 3.0 12.5 + - - +
303B ALA 3.8 6.5 - - - +
305B ILE* 1.3 74.1 - - + +
307B SER* 1.3 67.3 + - - +
309B VAL* 3.3 1.4 + - - +
310B LEU* 2.9 37.8 + - + +
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Residues in contact with SER 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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78B GLU* 3.1 31.0 + - - +
79B PHE* 4.1 16.1 - - - +
82B ALA* 4.7 11.2 - - - -
303B ALA 3.0 19.4 + - - -
304B LYS* 3.8 13.4 - - - +
306B VAL* 1.3 76.1 - - - +
308B THR* 1.3 58.3 + - - +
310B LEU* 3.9 0.3 - - - -
311B THR* 2.7 39.7 + - - +
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Residues in contact with THR 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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56B ALA* 4.1 24.0 - - + +
59B ARG* 4.5 11.7 - - + -
60B MET* 4.3 2.9 - - + +
304B LYS* 2.7 45.9 + - - +
305B ILE 3.8 3.1 - - - -
307B SER* 1.3 77.7 - - - +
309B VAL* 1.3 62.4 + - - +
311B THR* 4.0 4.3 - - - -
312B THR* 2.6 38.1 + - - +
315B LEU* 4.2 9.6 - - + +
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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
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52B ALA* 4.2 17.9 - - + +
53B VAL* 4.4 2.5 - - + +
56B ALA* 4.1 16.2 - - + -
260B PHE* 4.0 22.4 - - + -
305B ILE* 3.0 30.3 + - + +
306B VAL 3.3 3.1 + - - +
308B THR* 1.3 78.9 - - - +
310B LEU* 1.3 64.6 + - - +
312B THR 3.3 8.0 + - - +
315B LEU* 3.9 16.8 - - + +
316B ARG* 3.3 22.7 + - - +
319B TRP* 3.8 31.2 - - + -
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Residues in contact with LEU 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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82B ALA* 3.8 41.5 - - + +
83B MET* 4.6 1.1 - - - -
86B LEU* 4.2 15.7 - - + -
260B PHE* 3.7 23.3 - - + -
306B VAL* 2.9 32.8 + - + +
307B SER 4.0 0.2 - - - +
309B VAL* 1.3 78.4 - - - +
311B THR* 1.3 59.2 + - - +
312B THR 3.4 0.6 - - - -
316B ARG* 3.7 43.8 + - + +
319B TRP* 3.8 24.5 - - + -
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Residues in contact with THR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 5.2 8.1 - - + +
82B ALA* 4.4 16.6 - - + +
307B SER* 2.7 31.9 + - - +
308B THR* 3.9 5.0 + - - -
310B LEU* 1.3 79.1 - - - +
312B THR* 1.3 62.5 + - - +
313B PRO* 3.3 11.3 - - - +
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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