Contacts of the helix formed by residues 71 - 81 (chain D) in PDB entry 1Y8Q
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 SER 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D ASP 3.9 7.1 + - - -
51D THR* 4.3 4.5 - - - +
70D ARG* 1.3 73.0 - - - +
72D LYS* 1.3 64.3 + - - +
73D ALA* 3.3 4.5 + - - +
74D GLN* 3.0 35.7 + - - +
75D VAL* 2.9 28.2 + - - +
93D HIS* 3.5 37.7 + - - +
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Residues in contact with LYS 72 (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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25D ALA* 3.9 11.2 - - + +
48D ASP* 3.7 17.7 - - - +
50D ASP* 3.2 24.5 + - + +
51D THR 3.7 17.9 - - - -
52D ILE* 4.0 4.5 - - + -
56D ASN* 3.3 24.3 + - - +
60D GLN* 3.2 16.2 + - - +
63D PHE* 3.3 24.0 - - + -
70D ARG 3.5 1.4 + - - -
71D SER* 1.3 70.3 + - - +
73D ALA* 1.3 54.1 + - - +
76D ALA* 2.7 38.8 + - - +
801D ATP 2.8 57.3 + - - +
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Residues in contact with ALA 73 (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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25D ALA* 4.6 2.2 - - - -
46D LEU* 4.2 18.0 - - + +
47D ILE 4.8 0.2 - - - -
48D ASP* 4.2 17.0 - - + +
50D ASP 5.0 0.2 + - - -
71D SER* 3.2 7.5 - - - +
72D LYS* 1.3 78.8 - - - +
74D GLN* 1.3 63.1 + - - +
76D ALA* 3.7 1.4 - - - +
77D LYS* 3.1 17.8 + - - +
91D ALA* 3.4 20.2 - - + +
92D TYR 3.3 31.9 - - - +
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Residues in contact with GLN 74 (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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70D ARG* 4.5 13.5 - - - +
71D SER* 3.0 29.7 + - - +
73D ALA* 1.3 77.3 - - - +
75D VAL* 1.3 64.7 + - + +
77D LYS* 3.3 9.1 + - - +
78D GLU* 3.2 30.8 + - - +
91D ALA* 3.5 35.2 + - - +
93D HIS* 4.4 13.7 - - + +
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Residues in contact with VAL 75 (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 ILE* 3.8 12.1 - - + -
62D LEU 3.7 13.2 - - - +
63D PHE* 3.7 7.6 - - + -
67D HIS* 3.6 34.3 - - + +
70D ARG* 3.7 44.6 - - + +
71D SER 2.9 19.7 + - - +
72D LYS 4.0 0.9 - - - +
74D GLN* 1.3 73.1 - - - +
76D ALA* 1.3 67.3 + - - +
78D GLU* 3.1 10.7 + - + +
79D SER* 2.9 22.7 + - - +
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Residues in contact with ALA 76 (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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25D ALA* 4.6 3.4 - - + -
30D CYS* 5.2 0.4 - - - -
33D LEU* 3.8 11.0 - - + -
46D LEU* 3.6 25.6 - - + -
62D LEU* 3.9 16.6 - - + -
63D PHE* 3.7 12.5 - - + -
72D LYS 2.7 24.3 + - - +
73D ALA 3.7 0.2 - - - +
75D VAL* 1.3 73.9 - - - +
77D LYS* 1.3 63.7 + - - +
79D SER* 3.2 1.7 + - - -
80D VAL* 3.0 27.2 + - - +
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Residues in contact with LYS 77 (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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33D LEU* 4.6 1.1 - - - +
46D LEU* 4.8 0.8 - - + +
73D ALA 3.1 11.1 + - - +
74D GLN* 3.5 13.7 + - - +
76D ALA* 1.3 81.0 - - - +
78D GLU* 1.3 65.0 + - + +
80D VAL* 3.4 2.4 + - - +
81D LEU* 3.1 43.3 + - + +
89D ILE* 3.1 57.7 + - + +
90D VAL* 4.7 3.2 - - - +
91D ALA* 4.1 18.9 - - + +
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Residues in contact with GLU 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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67D HIS* 5.2 3.5 + - - -
70D ARG* 3.0 40.8 + - - -
74D GLN* 3.2 17.2 + - - +
75D VAL* 3.1 9.7 + - + +
77D LYS* 1.3 82.1 - - + +
79D SER* 1.3 62.9 + - - +
81D LEU* 3.3 16.2 + - - +
82D GLN* 3.4 18.9 + - - +
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Residues in contact with SER 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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62D LEU* 2.7 45.8 + - - -
64D GLN* 4.8 2.9 + - - -
67D HIS* 4.4 6.6 - - - -
75D VAL* 2.9 18.1 + - - +
76D ALA 3.7 3.8 - - - -
78D GLU* 1.3 73.8 - - - +
80D VAL* 1.3 65.7 + - - +
82D GLN* 3.2 30.1 + - - +
83D PHE* 3.7 10.2 - - - -
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Residues in contact with VAL 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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33D LEU* 3.2 41.5 - - + -
37D VAL* 3.8 33.9 - - + -
62D LEU* 3.7 13.9 - - + -
76D ALA 3.0 9.8 + - - +
77D LYS 3.8 3.4 - - - +
79D SER* 1.3 75.7 - - - +
81D LEU* 1.3 63.9 + - - +
82D GLN 3.0 1.6 + - - -
83D PHE* 3.2 16.6 + - + -
84D TYR* 3.1 20.7 + - + +
87D ALA* 4.9 1.1 - - + -
89D ILE* 3.7 20.4 - - + -
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Residues in contact with LEU 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 LYS* 3.1 41.9 + - + +
78D GLU* 3.6 10.3 - - + +
79D SER 3.2 0.4 - - - -
80D VAL* 1.3 75.9 - - - +
82D GLN* 1.3 60.4 + - - +
83D PHE 3.4 0.2 - - - -
84D TYR 3.6 16.6 - - - +
85D PRO* 3.4 32.8 - - + +
87D ALA* 3.7 32.5 - - + +
89D ILE* 4.4 9.4 - - + -
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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