Contacts of the helix formed by residues 300 - 311 (chain D) in PDB entry 1YAA
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 ALA 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264C GLY* 2.7 23.4 + - - +
265C GLU* 4.0 9.8 + - - +
67D ASN 5.7 0.2 - - - +
68D HIS 5.7 0.4 - - - -
69D GLU 4.4 4.7 - - - +
71D LEU* 3.8 26.9 - - + -
299D PRO* 1.3 72.9 - - - +
301D TYR* 1.3 67.9 + - - +
303D ALA* 3.2 4.7 + - - +
304D LYS* 2.9 43.2 + - - +
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Residues in contact with TYR 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C HIS* 3.4 1.9 + - - -
66C TYR* 3.9 5.6 - - - -
68C HIS* 4.4 2.0 - + - -
265C GLU* 3.1 27.1 + - - +
301C TYR* 3.3 40.8 - + + -
57D GLU* 2.7 30.9 + - + +
60D ILE* 3.7 15.5 - - + -
61D HIS* 2.9 29.2 + + - -
66D TYR* 3.5 32.1 - + - -
265D GLU* 4.7 6.1 - - - +
299D PRO 3.9 0.2 - - - -
300D ALA* 1.3 74.4 - - - +
302D GLY* 1.3 64.6 + - - +
304D LYS* 3.1 18.6 + - + +
305D ILE* 3.3 36.0 + - + +
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Residues in contact with GLY 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D MET* 4.2 3.7 - - - +
265D GLU* 4.0 31.2 + - - +
267D VAL* 4.2 11.0 - - - -
299D PRO* 4.8 3.0 + - - +
300D ALA 3.5 0.4 - - - -
301D TYR* 1.3 79.6 - - - +
303D ALA* 1.3 62.2 + - - +
305D ILE* 3.4 11.4 + - - +
306D VAL* 3.3 27.0 + - - +
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Residues in contact with ALA 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LEU* 4.6 1.8 - - + -
76D LEU* 3.7 12.7 - - + +
79D LEU* 3.6 23.6 - - + +
104D GLN* 3.4 30.7 - - - +
267D VAL* 4.1 6.4 - - + +
299D PRO 3.9 5.3 + - - +
300D ALA 3.2 10.0 + - - +
301D TYR 3.2 0.4 - - - -
302D GLY* 1.3 76.8 - - - +
304D LYS* 1.3 61.2 + - - +
306D VAL 3.7 0.3 + - - -
307D ALA* 3.2 26.2 + - - +
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Residues in contact with LYS 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C GLU* 5.1 1.4 + - - -
60D ILE* 3.7 24.4 - - + +
66D TYR* 4.9 9.1 - - + -
67D ASN* 3.3 33.3 + - - +
68D HIS* 5.3 0.2 - - - +
69D GLU 5.5 1.5 + - - -
71D LEU* 4.3 15.3 - - - -
76D LEU* 4.0 17.0 - - + +
300D ALA* 2.9 46.2 + - - +
301D TYR* 3.1 12.4 + - + +
303D ALA* 1.3 76.3 - - - +
305D ILE* 1.3 57.1 + - - +
307D ALA* 3.9 2.0 - - - +
308D LYS* 3.0 30.3 + - - +
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Residues in contact with ILE 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C HIS* 4.4 3.6 - - + -
53D VAL* 3.8 26.9 - - + +
56D ALA* 3.6 19.8 - - + +
57D GLU* 3.5 24.9 - - + -
60D ILE* 4.4 7.9 - - + -
262D MET* 3.9 23.8 - - + -
265D GLU* 5.6 0.2 - - + -
301D TYR* 3.3 46.2 + - + +
302D GLY* 3.7 5.6 - - - +
303D ALA 3.4 0.2 - - - -
304D LYS* 1.3 73.3 - - - +
306D VAL* 1.3 60.9 + - + +
308D LYS* 3.2 8.3 + - - +
309D LEU* 2.9 27.1 + - + +
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Residues in contact with VAL 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LEU* 3.5 26.0 - - + -
256D PHE* 4.0 24.5 - - + -
260D ALA* 4.8 7.4 - - + -
262D MET* 3.8 28.3 - - + -
267D VAL* 3.9 11.4 - - + -
302D GLY 3.3 16.1 + - - +
303D ALA 4.2 0.2 - - - +
305D ILE* 1.3 75.8 - - - +
307D ALA* 1.3 57.3 + - - +
309D LEU* 3.1 12.1 + - + +
310D LEU* 2.8 42.9 + - + +
319D TRP* 6.3 0.4 - - + -
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Residues in contact with ALA 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D LEU* 4.4 4.9 - - + -
78D SER* 3.7 16.8 - - - -
79D LEU* 3.7 32.5 - - + +
303D ALA 3.2 17.5 + - - +
304D LYS* 3.9 3.8 - - - +
306D VAL* 1.3 78.4 - - - +
308D LYS* 1.3 58.2 + - - +
310D LEU* 3.7 5.7 - - - +
311D GLU* 2.8 39.4 + - - +
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Residues in contact with LYS 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ALA* 4.0 10.5 - - + +
59D LEU* 3.7 40.6 - - + +
60D ILE* 3.5 23.6 - - + -
63D ASP* 5.8 2.8 + - - -
304D LYS 3.0 19.1 + - - +
305D ILE 3.3 5.2 - - - +
307D ALA* 1.3 76.2 - - - +
309D LEU* 1.3 57.4 + - - +
311D GLU* 4.6 7.6 - - + +
312D THR* 2.5 44.5 + - - +
315D LEU* 4.0 1.2 - - - +
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D SER* 3.2 26.5 - - - +
53D VAL* 3.8 28.3 - - + +
56D ALA* 4.4 5.6 - - + +
260D ALA* 5.0 6.1 - - + -
305D ILE 2.9 12.5 + - - +
306D VAL* 3.4 14.8 - - + +
308D LYS* 1.3 78.1 - - - +
310D LEU* 1.3 54.9 + - + +
312D THR 3.5 2.6 - - - +
315D LEU* 4.0 12.1 - - + +
316D THR* 2.7 33.0 + - - -
319D TRP* 3.3 55.9 - - + +
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LEU* 4.5 6.5 - - + +
82D ASN* 3.7 36.4 + - + +
83D ALA* 3.9 17.7 - - - +
86D ILE* 3.7 20.2 - - + -
256D PHE* 4.3 5.8 - - + -
306D VAL* 2.8 38.9 + - + +
307D ALA* 3.2 4.2 + - - +
309D LEU* 1.3 80.3 - - + +
311D GLU* 1.3 60.5 + - - +
312D THR 4.9 0.2 - - - -
316D THR* 3.5 13.8 + - + +
319D TRP* 3.5 36.6 - - + -
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Residues in contact with GLU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A GLN* 4.9 15.1 - - - +
78D SER* 3.2 32.9 + - - -
82D ASN* 3.4 23.0 - - - +
307D ALA* 2.8 25.0 + - - +
308D LYS* 4.3 8.1 + - + +
310D LEU* 1.3 78.8 - - - +
312D THR* 1.3 59.6 + - - +
313D PRO* 3.3 11.7 - - - +
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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