Contacts of the helix formed by residues 77 - 88 (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 PRO 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D GLY 3.3 9.9 - - - +
76D LEU* 1.3 93.5 - - + +
78D SER* 1.3 61.5 + - - +
80D THR* 3.2 8.1 + - - +
81D SER* 3.0 30.5 + - - -
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Residues in contact with SER 78 (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* 3.3 11.9 - - - +
77D PRO* 1.3 79.4 - - - +
79D LEU* 1.3 62.9 + - - +
81D SER* 4.1 4.0 - - - -
82D ASN* 2.8 31.2 + - - +
307D ALA* 3.7 13.4 - - - +
311D GLU* 3.2 34.6 + - - -
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Residues in contact with LEU 79 (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* 3.2 15.0 + - + +
78D SER* 1.3 80.8 - - - +
80D THR* 1.3 57.6 + - - +
82D ASN* 4.2 0.8 - - - +
83D ALA* 3.0 33.6 + - - +
104D GLN* 3.7 23.1 - - + +
256D PHE* 4.3 9.6 - - + -
267D VAL* 3.6 18.6 - - + -
268D GLY 4.6 0.2 - - - +
269D CYS* 4.0 11.4 - - - -
303D ALA* 3.6 36.8 - - + +
306D VAL* 3.5 37.0 - - + -
307D ALA* 3.7 7.4 - - + +
310D LEU* 4.5 3.0 - - + +
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Residues in contact with THR 80 (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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74D THR 4.1 8.7 - - - +
76D LEU 3.1 13.5 + - - +
77D PRO* 3.2 14.0 + - - +
79D LEU* 1.3 77.1 - - + +
81D SER* 1.3 61.7 + - - +
84D ALA* 3.3 23.2 + - - +
102D SER* 3.9 23.8 + - - +
103D VAL* 3.9 6.1 - - - -
104D GLN* 3.6 36.1 - - + +
269D CYS* 3.8 17.8 - - - -
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Residues in contact with SER 81 (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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77D PRO 3.0 18.5 + - - -
78D SER* 3.6 6.6 + - - -
80D THR* 1.3 77.5 + - - +
82D ASN* 1.3 68.2 + - - +
84D ALA* 3.7 5.7 + - - +
85D LYS* 3.1 37.6 + - - +
102D SER* 5.7 0.9 - - - -
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Residues in contact with ASN 82 (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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78D SER* 2.8 25.0 + - - +
81D SER* 1.3 85.5 + - - +
83D ALA* 1.3 64.2 + - - +
84D ALA 3.2 0.4 - - - -
85D LYS* 3.5 19.5 + - - +
86D ILE* 3.1 27.2 + - - +
310D LEU* 3.7 35.8 + - + -
311D GLU* 3.4 27.3 - - - +
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Residues in contact with ALA 83 (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 3.0 19.4 + - - +
80D THR 4.0 2.2 - - - +
82D ASN* 1.3 76.2 - - - +
84D ALA* 1.3 63.2 + - - +
86D ILE* 3.3 3.0 + - - +
87D ILE* 3.3 12.8 + - - +
254D GLN* 3.2 41.1 + - - +
256D PHE* 3.7 17.5 - - + -
269D CYS* 3.8 16.2 - - - -
310D LEU* 3.9 7.6 - - + +
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Residues in contact with ALA 84 (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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80D THR 3.3 16.8 + - - +
81D SER* 3.9 7.2 - - - +
82D ASN 3.2 0.2 - - - -
83D ALA* 1.3 79.4 - - - +
85D LYS* 1.3 57.6 + - - +
87D ILE* 4.7 0.2 - - - -
88D PHE* 2.8 47.2 + - + +
95D LEU* 4.2 15.0 - - + -
102D SER* 3.8 9.0 - - - +
269D HIS* 3.5 21.5 - - - +
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Residues in contact with LYS 85 (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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398A GLU* 4.5 15.4 + - - +
81D SER* 3.1 26.7 - - - +
82D ASN* 3.5 22.4 + - - +
83D ALA 3.3 0.4 - - - -
84D ALA* 1.3 74.9 - - - +
86D ILE* 1.3 64.1 + - + +
87D ILE 3.4 0.2 - - - -
89D GLY* 2.9 31.2 + - - +
90D THR* 3.6 17.1 + - - +
91D GLN* 4.7 13.9 + - - +
95D LEU* 4.3 20.5 - - + +
241D ARG* 4.2 0.5 + - - -
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Residues in contact with ILE 86 (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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82D ASN 3.1 15.7 - - - +
83D ALA* 3.5 10.3 - - - +
84D ALA 3.2 0.6 - - - -
85D LYS* 1.3 80.7 - - + +
87D ILE* 1.3 56.1 + - - +
226D GLN* 3.0 38.8 + - - +
233D LEU* 4.2 27.8 - - + +
234D ASP* 4.8 1.2 - - - +
241D ARG* 3.0 19.6 + - - -
254D GLN* 4.2 8.3 - - - +
256D PHE* 5.4 1.8 - - + -
259D ASN* 6.1 0.2 - - - +
310D LEU* 3.7 27.1 - - + -
316D THR* 5.8 3.8 - - + -
319D TRP* 4.3 8.1 - - + -
320D HIS* 5.5 2.2 - - + -
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Residues in contact with ILE 87 (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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83D ALA 3.3 9.7 + - - +
84D ALA 3.9 0.9 - - - +
86D ILE* 1.3 79.2 - - - +
88D PHE* 1.3 93.9 + - + +
89D GLY 3.5 0.2 - - - -
223D THR* 4.3 15.7 - - + +
226D GLN* 3.9 15.9 - - - +
237D ALA* 3.9 11.5 - - + +
240D VAL* 3.6 37.5 - - + +
241D ARG* 2.9 22.9 + - - +
252D VAL* 4.2 20.2 - - + -
254D GLN* 4.3 10.8 - - - +
269D HIS* 4.4 6.5 - - - +
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Residues in contact with PHE 88 (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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84D ALA* 2.8 35.1 + - + +
87D ILE* 1.3 92.8 - - + +
89D GLY* 1.3 60.7 + - - +
92D SER* 3.5 17.1 + - - -
94D ALA* 4.8 2.2 - - + -
95D LEU* 3.8 23.1 - - + -
100D VAL* 3.7 24.5 - - + -
240D VAL* 5.2 1.8 - - + -
241D ARG* 3.4 20.6 + - + +
242D VAL* 3.6 38.8 - - - -
252D VAL* 3.9 16.2 - - + -
269D ALA* 3.6 48.9 - + - -
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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