Contacts of the helix formed by residues 300 - 311 (chain A) 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 PHE 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A MET* 4.6 7.2 - - + -
64A GLU* 4.4 17.3 - - + -
68A LYS* 6.0 1.8 - - - -
71A ALA* 4.9 2.9 - - + -
76A GLU* 4.2 29.6 - - + -
298A PRO 3.2 5.7 + - - +
299A PRO* 1.3 73.2 - - - +
301A HIS* 1.3 72.9 + - - +
303A ALA* 3.2 9.1 + - + +
304A LYS* 3.1 59.2 + - + -
264B ARG* 3.2 72.3 + - + +
265B GLU* 4.6 8.6 + - - -
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Residues in contact with HIS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 2.8 35.4 + - + +
60A MET* 3.6 30.7 - - + +
68A LYS* 5.7 0.2 + - - -
265A GLU* 3.2 35.2 - - - +
299A PRO* 3.8 1.4 - - - +
300A PHE* 1.3 85.8 - - - +
302A GLY* 1.3 63.0 + - - +
304A LYS 3.3 6.8 + - - -
305A ILE* 3.3 19.5 + - + +
57B GLU* 4.9 2.8 + - - -
265B GLU* 3.4 23.9 + - - +
301B HIS* 3.6 36.3 + + + -
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Residues in contact with GLY 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ILE* 3.8 5.6 - - - +
265A GLU* 3.9 25.4 + - - +
267A THR* 3.1 21.0 + - - -
299A PRO 4.9 1.4 + - - -
300A PHE 3.6 0.6 - - - -
301A HIS* 1.3 77.9 - - - +
303A ALA* 1.3 62.3 + - - +
305A ILE* 3.1 17.8 + - - +
306A VAL* 3.1 18.4 + - - +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLU* 6.4 1.6 - - + -
79A PHE* 3.3 38.4 - - + -
104A ALA* 5.5 4.9 - - + -
267A THR* 3.3 19.2 + - + -
299A PRO 4.1 12.0 + - - +
300A PHE* 3.2 12.9 + - + +
302A GLY* 1.3 75.6 - - - +
304A LYS* 1.3 56.8 + - - +
306A VAL 3.3 1.9 + - - -
307A SER* 3.1 24.7 + - - -
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Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A MET* 3.5 31.6 - - + -
64A GLU* 3.9 21.2 + - - +
76A GLU* 6.2 1.6 - - + -
78A GLU* 3.5 20.1 + - - +
300A PHE* 3.1 39.4 + - + +
301A HIS 3.7 2.0 - - - +
302A GLY 3.2 0.2 - - - -
303A ALA* 1.3 74.6 - - - +
305A ILE* 1.3 58.8 + - - +
307A SER* 3.2 10.7 + - - +
308A THR* 2.4 45.5 + - - +
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Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL* 3.7 33.4 - - + -
56A ALA* 3.8 15.0 - - + -
57A GLU* 3.3 36.6 - - + +
60A MET* 3.5 21.8 - - + -
260A PHE* 5.4 1.3 - - + -
262A ILE* 4.5 11.7 - - + -
265A GLU* 5.1 0.4 - - - -
301A HIS* 3.3 22.6 + - + +
302A GLY* 3.1 12.9 + - - +
304A LYS* 1.3 76.0 - - - +
306A VAL* 1.3 66.9 + - + +
308A THR* 3.4 2.9 + - - -
309A VAL* 3.1 31.6 + - + +
68B LYS* 4.7 2.0 - - - +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE* 3.7 18.6 - - + -
83A MET* 4.0 7.9 - - - -
256A CYS* 4.1 16.6 - - + -
260A PHE* 3.7 36.6 - - + -
262A ILE* 3.7 20.9 - - + -
267A THR* 4.1 3.4 - - + -
302A GLY 3.1 15.0 + - - +
303A ALA 3.3 7.2 + - - +
305A ILE* 1.3 76.3 - - - +
307A SER* 1.3 62.6 + - - +
309A VAL* 3.3 3.5 + - - +
310A LEU* 3.0 37.1 + - + +
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLU* 3.1 32.5 + - - +
79A PHE* 3.9 20.6 - - - +
82A ALA* 4.7 6.5 - - - -
303A ALA 3.1 13.3 + - - -
304A LYS* 3.2 20.4 + - - +
306A VAL* 1.3 76.2 - - - +
308A THR* 1.3 53.8 + - - +
310A LEU* 3.9 4.2 - - - -
311A THR* 2.7 42.0 + - - +
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 3.9 26.0 - - + +
59A ARG* 5.0 9.9 - - + -
60A MET* 4.4 5.9 - - + +
78A GLU* 4.7 2.5 - - - -
304A LYS* 2.4 37.6 + - - +
305A ILE* 3.4 5.7 - - - -
307A SER* 1.3 77.9 + - - +
309A VAL* 1.3 58.0 + - - +
311A THR* 3.9 4.7 - - - -
312A THR* 2.7 42.0 + - - +
315A LEU* 4.0 13.2 - - + -
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 3.8 26.9 - - + +
53A VAL* 4.6 2.0 - - + +
56A ALA* 4.1 8.1 - - + -
260A PHE* 4.1 14.6 - - + -
305A ILE* 3.1 23.0 + - + +
306A VAL 3.7 3.8 - - - +
308A THR* 1.3 75.0 - - - +
310A LEU* 1.3 66.8 + - + +
312A THR 3.1 8.1 - - - +
315A LEU* 3.8 11.9 - - + -
316A ARG* 3.0 32.5 + - - +
319A TRP* 3.6 36.1 - - + -
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA* 3.7 38.8 - - + +
83A MET* 4.5 2.9 - - - -
86A LEU* 4.3 14.6 - - + -
260A PHE* 3.4 27.1 - - + -
306A VAL* 3.0 33.0 + - + +
307A SER 4.0 2.5 - - - +
309A VAL* 1.3 79.5 - - - +
311A THR* 1.3 59.1 + - - +
316A ARG* 3.2 44.0 + - + +
319A TRP* 3.9 23.8 - - + -
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Residues in contact with THR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLU* 3.7 34.2 + - + +
82A ALA* 4.5 12.3 - - + -
307A SER 2.7 27.0 + - - +
308A THR* 3.6 6.4 + - - -
310A LEU* 1.3 76.5 - - - +
312A THR* 1.3 63.1 + - - +
313A PRO* 3.2 12.1 - - - +
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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