Contacts of the helix formed by residues 68 - 80 (chain D) in PDB entry 1A4Y
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 GLY 68 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D GLU 3.7 1.2 - - - -
67D LEU* 1.3 76.7 - - - +
69D ASP* 1.3 61.6 + - - -
70D VAL* 3.0 7.9 - - - -
72D VAL* 2.9 34.0 + - - +
94D CYS 3.1 8.6 + - - -
95D CYS* 3.7 21.0 - - - +
96D LEU* 4.8 1.1 - - - -
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Residues in contact with ASP 69 (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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68D GLY* 1.3 71.9 - - - -
70D VAL* 1.3 59.2 + - + +
72D VAL* 4.1 0.9 - - - +
73D HIS* 3.1 26.7 + - - +
95D CYS 4.2 0.4 + - - -
96D LEU* 3.0 19.4 - - - +
97D THR* 2.7 56.5 + - - +
99D ALA* 3.9 7.3 - - + +
100D GLY* 3.5 19.4 + - - -
103D VAL* 5.2 4.2 - - - +
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Residues in contact with VAL 70 (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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41D GLU* 3.4 31.0 - - + +
67D LEU 3.7 11.2 - - - +
68D GLY* 4.2 4.7 - - - -
69D ASP* 1.3 77.4 - - + +
71D GLY* 1.3 65.3 + - - +
73D HIS* 2.8 23.4 + - - +
74D CYS* 3.0 14.5 + - - +
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Residues in contact with GLY 71 (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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41D GLU* 3.6 11.4 - - - +
44D CYS* 3.6 23.2 - - - -
67D LEU* 3.2 16.2 + - - -
70D VAL* 1.3 84.3 - - - +
72D VAL* 1.3 60.7 + - - +
74D CYS* 3.4 3.5 + - - +
75D VAL* 3.1 29.7 + - - +
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Residues in contact with VAL 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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67D LEU* 3.9 24.2 - - + +
68D GLY 2.9 21.7 + - - +
69D ASP 4.3 1.6 - - - +
71D GLY* 1.3 75.0 - - - +
73D HIS* 1.3 64.9 + - - +
75D VAL* 4.0 5.1 - - + +
76D LEU* 3.0 42.2 + - + +
91D LEU* 3.9 27.4 - - + -
94D CYS* 4.5 7.6 - - + +
96D LEU* 4.2 29.2 - - + -
100D GLY 5.7 1.1 - - - +
103D VAL* 6.2 0.2 - - + -
104D LEU* 5.2 2.5 - - + -
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Residues in contact with HIS 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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69D ASP 3.1 16.2 + - - +
70D VAL* 2.8 13.2 + - - +
72D VAL* 1.3 79.0 - - - +
74D CYS* 1.3 66.6 + - - +
76D LEU* 3.8 2.0 - - - +
77D GLN* 3.3 45.3 + - + +
103D VAL* 3.1 46.2 - - + +
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Residues in contact with CYS 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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41D GLU* 5.1 7.0 - - - -
44D CYS* 4.1 15.3 - - + +
45D LYS* 4.5 31.9 - - - -
48D SER* 2.5 29.1 + - - -
70D VAL 3.0 11.5 + - - +
71D GLY* 3.5 10.8 - - - +
73D HIS* 1.3 80.6 - - - +
75D VAL* 1.3 59.6 + - - +
77D GLN* 3.2 21.3 + - - +
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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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44D CYS* 3.9 22.4 - - + +
47D ILE* 4.0 18.2 - - + -
48D SER* 3.9 7.4 + - - +
51D LEU* 4.3 9.6 - - + +
60D LEU* 4.0 17.5 - - + -
62D LEU* 3.7 30.1 - - + -
67D LEU* 4.6 2.2 - - + -
71D GLY 3.1 16.7 + - - +
72D VAL* 4.0 5.6 - - - +
74D CYS* 1.3 79.3 - - - +
76D LEU* 1.3 67.4 + - + +
78D GLY* 3.2 15.1 + - - -
79D LEU* 3.8 9.8 - - + +
89D LEU* 5.7 1.6 - - + -
91D LEU* 5.4 5.4 - - + -
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Residues in contact with LEU 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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72D VAL* 3.0 43.1 + - + +
73D HIS* 3.8 4.5 - - - +
75D VAL* 1.3 80.7 - - + +
77D GLN* 1.3 62.3 - - - +
79D LEU* 3.0 39.7 + - + +
80D GLN* 3.5 12.0 + - - +
89D LEU* 4.4 17.7 - - + -
91D LEU* 4.8 4.7 - - + -
100D GLY 5.7 0.2 - - - +
103D VAL* 4.1 25.6 - - + -
104D LEU* 4.3 22.0 - - + +
107D THR* 4.1 26.2 - - + +
111D LEU* 5.9 0.2 - - + -
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Residues in contact with GLN 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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48D SER* 4.0 2.0 + - - +
52D ARG* 4.4 24.1 + - - +
73D HIS* 3.3 36.9 + - + +
74D CYS* 3.2 20.9 + - - +
76D LEU* 1.3 76.6 - - - +
78D GLY* 1.3 56.1 + - - +
79D LEU 3.0 0.2 - - - -
80D GLN* 2.7 49.0 + - + +
81D THR 4.7 0.2 + - - -
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Residues in contact with GLY 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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48D SER* 2.9 39.5 + - - -
51D LEU* 3.9 3.6 - - - +
52D ARG* 3.2 36.0 + - - +
75D VAL 3.2 5.8 + - - -
77D GLN* 1.3 75.1 - - - +
79D LEU* 1.3 60.5 + - - +
80D GLN 3.1 2.7 + - - -
81D THR* 3.9 4.2 + - - -
84D CYS* 5.3 0.3 - - - -
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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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51D LEU* 3.9 25.8 - - + -
57D LEU* 3.9 20.2 - - + -
60D LEU* 4.3 5.2 - - + -
75D VAL* 3.8 7.6 - - + +
76D LEU* 3.0 39.5 + - + +
78D GLY* 1.3 76.0 - - - +
80D GLN* 1.3 62.3 + - - +
81D THR 3.4 2.9 - - - +
84D CYS* 3.5 34.6 - - - +
86D ILE* 4.4 15.5 - - + -
89D LEU* 4.6 12.8 - - + -
111D LEU* 3.6 31.0 - - + +
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Residues in contact with GLN 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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52D ARG* 5.9 1.1 - - - +
76D LEU* 3.5 7.1 + - - +
77D GLN* 2.7 43.5 + - + +
78D GLY 3.1 0.6 - - - -
79D LEU* 1.3 79.9 - - - +
81D THR* 1.3 62.8 + - + +
82D PRO* 3.7 4.5 - - - +
103D VAL* 6.0 2.2 - - - +
107D THR* 3.7 29.6 + - - +
110D THR* 3.7 15.0 + - - +
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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