Contacts of the helix formed by residues 72 - 80 (chain D) in PDB entry 1SA0
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 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D GLU* 1.3 86.3 - - + +
73D GLY* 1.3 69.0 + - - +
74D THR 2.9 0.2 + - - -
75D MET* 2.8 28.9 + - + +
76D ASP* 3.5 19.1 - - - +
94D PHE* 4.6 15.9 - - + -
95D GLY 4.9 0.4 - - - +
96D GLN* 3.2 47.3 - - - +
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Residues in contact with GLY 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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71D GLU* 3.5 6.7 + - - +
72D PRO* 1.3 75.6 - - - +
74D THR* 1.3 57.6 + - - +
76D ASP* 2.9 26.7 + - - +
77D SER* 3.1 12.7 + - - -
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Residues in contact with THR 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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11D GLN* 3.2 42.0 - - + -
14D ASN* 5.0 8.6 - - - +
15D GLN* 5.6 0.7 - - - +
69D ASP* 2.9 29.8 + - - +
71D GLU* 3.6 25.6 + - + +
72D PRO 2.9 0.8 + - - -
73D GLY* 1.3 71.1 - - - +
75D MET* 1.3 59.5 + - - +
77D SER* 3.1 24.1 - - - -
78D VAL* 3.3 12.0 - - - +
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Residues in contact with MET 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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14D ASN* 4.2 16.8 - - - +
67D LEU* 4.2 13.9 - - - +
69D ASP* 4.0 21.1 - - + -
71D GLU 4.3 0.9 - - - +
72D PRO 2.8 21.4 + - - +
74D THR* 1.3 76.8 - - - +
76D ASP* 1.3 63.6 + - - +
77D SER 3.0 5.4 - - - -
78D VAL* 3.0 25.8 + - - +
79D ARG* 3.1 13.5 + - - +
92D PHE* 3.9 19.1 - - + -
93D VAL 3.4 36.3 - - - +
94D PHE* 3.3 35.4 - - + -
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Residues in contact with ASP 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 PRO* 3.5 20.8 - - - +
73D GLY* 2.9 8.8 + - - +
75D MET* 1.3 84.4 - - - +
77D SER* 1.3 59.1 + - - +
78D VAL 3.3 0.2 - - - -
79D ARG* 3.9 25.3 + - + +
80D SER* 3.3 27.5 + - - -
94D PHE* 3.8 15.6 - - - -
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Residues in contact with SER 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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15D GLN* 5.1 10.4 + - - -
73D GLY 3.1 7.5 + - - -
74D THR* 3.1 23.2 - - - -
76D ASP* 1.3 79.2 - - - +
78D VAL* 1.3 63.1 + - - +
80D SER 3.5 15.9 - - - +
81D GLY* 3.6 5.4 - - - -
82D PRO* 4.5 1.7 - - - +
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Residues in contact with VAL 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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8D GLN* 5.6 1.8 - - - +
14D ASN* 4.8 18.6 - - + +
15D GLN* 5.8 1.1 - - - +
18D ALA* 3.9 29.2 - - + -
67D LEU* 5.4 3.6 - - + -
74D THR 3.3 18.4 - - - +
75D MET* 3.3 11.0 - - - +
77D SER* 1.3 75.7 - - - +
79D ARG* 1.3 67.4 + - - +
81D GLY* 2.8 16.5 + - - -
82D PRO* 3.8 11.6 - - + +
84D GLY* 3.3 12.2 - - - -
87D PHE* 3.9 26.5 - - + -
92D PHE* 5.1 7.0 - - + -
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Residues in contact with ARG 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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75D MET* 3.1 8.9 + - - +
76D ASP* 3.9 25.1 + - + +
77D SER 3.6 0.2 - - - -
78D VAL* 1.3 78.0 - - - +
80D SER* 1.3 58.1 + - - +
81D GLY 3.2 4.5 + - - -
84D GLY* 3.3 31.9 - - - +
85D GLN* 4.0 14.9 + - - +
92D PHE* 3.7 42.9 - - + -
94D PHE* 3.2 39.4 - - - -
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Residues in contact with SER 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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76D ASP 3.3 16.2 + - - -
77D SER* 3.5 9.2 - - - +
79D ARG* 1.3 76.1 - - - +
81D GLY* 1.3 54.4 + - - +
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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