Contacts of the helix formed by residues 72 - 87 (chain D) in PDB entry 2AMT
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 ASP 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D ILE* 6.0 3.6 - - + -
36D ASP* 3.5 18.4 - - + +
70D GLY 3.8 2.0 + - - -
71D ALA* 1.3 77.5 - - - +
73D SER* 1.3 61.3 + - - +
74D ARG* 3.1 15.4 + - + +
75D GLU* 2.8 61.6 + - - +
76D LEU* 3.2 11.8 + - - +
78D ARG* 4.5 1.4 + - - -
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Residues in contact with SER 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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35D SER* 5.2 0.2 - - - -
36D ASP* 2.4 37.1 + - - -
38D ASP* 3.3 17.0 - - - +
41D LEU* 3.8 18.5 - - - +
42D HIS* 2.7 26.3 + - - -
45D THR* 4.8 1.4 + - - -
72D ASP* 1.3 70.0 - - - +
74D ARG* 1.3 60.6 + - - +
76D LEU* 3.7 11.1 - - - +
77D LEU* 2.8 29.1 + - - +
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Residues in contact with ARG 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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19D ILE* 6.0 2.0 - - + -
22D GLY* 4.2 19.7 + - - -
41D LEU* 3.7 19.5 - - + -
72D ASP* 3.1 11.8 + - + +
73D SER* 1.3 76.2 - - - +
75D GLU* 1.3 58.4 + - - +
77D LEU* 3.4 2.5 + - - +
78D ARG* 3.0 50.6 + - - +
115D PHE* 3.2 52.4 + - + +
118D GLU* 3.3 22.0 + - - +
119D ASP* 2.9 38.2 + - - +
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Residues in contact with GLU 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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68D PHE* 4.5 10.6 - - + -
71D ALA* 3.4 27.5 - - + +
72D ASP* 2.8 41.7 + - - +
74D ARG* 1.3 73.8 - - - +
76D LEU* 1.3 56.3 + - - +
78D ARG* 3.4 23.7 + - - +
79D GLU* 3.1 28.6 + - - +
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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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35D SER* 5.1 2.9 - - - -
42D HIS* 4.2 15.5 - - - +
45D THR* 4.4 2.4 - - - +
57D ILE* 4.3 16.2 - - + -
61D PHE* 3.5 45.5 - - + -
68D PHE* 3.8 30.3 - - + +
71D ALA* 4.2 11.9 - - + +
72D ASP 3.2 14.5 + - - +
73D SER* 3.7 15.5 - - - +
74D ARG 3.3 0.2 - - - -
75D GLU* 1.3 73.8 - - - +
77D LEU* 1.3 60.3 + - - +
79D GLU* 4.7 0.2 - - - -
80D ALA* 3.0 30.3 + - - +
4901E 1AA 4.3 17.3 - - + -
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Residues in contact with LEU 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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41D LEU* 3.9 25.8 - - + +
44D LEU* 4.2 17.5 - - + -
45D THR* 3.6 23.3 + - + +
48D LEU* 3.7 28.5 - - + -
73D SER 2.8 18.3 + - - +
74D ARG 3.6 4.5 - - - +
76D LEU* 1.3 76.7 - - - +
78D ARG* 1.3 56.6 + - - +
80D ALA* 3.4 3.7 + - + +
81D TRP* 2.8 30.5 + - - +
116D ILE* 4.8 4.3 - - + -
119D ASP* 3.7 30.5 - - + +
120D LEU* 3.9 13.5 - - + -
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Residues in contact with ARG 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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72D ASP* 4.5 1.4 + - - -
74D ARG* 3.0 40.2 + - - +
75D GLU* 3.4 34.8 - - - +
76D LEU 3.4 0.2 - - - -
77D LEU* 1.3 76.0 - - - +
79D GLU* 1.3 58.0 + - - +
81D TRP* 3.5 7.1 + - - +
82D ARG* 2.9 28.9 + - - +
118D GLU 5.6 0.2 - - - -
119D ASP* 2.8 63.7 + - + +
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Residues in contact with GLU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D PHE* 3.6 21.1 - - + -
68D PHE* 3.4 35.7 - - + -
75D GLU 3.1 16.4 + - - +
78D ARG* 1.3 74.7 - - - +
80D ALA* 1.3 63.6 + - - +
82D ARG* 2.8 42.3 + - - +
83D ARG* 2.6 55.3 + - - +
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Residues in contact with ALA 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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45D THR* 3.6 26.7 - - + -
48D LEU* 6.1 0.9 - - + -
49D LEU* 3.9 15.3 - - + +
60D LEU* 3.8 17.5 - - + -
61D PHE* 4.2 1.1 - - + -
76D LEU 3.0 18.6 + - - +
77D LEU* 3.6 3.6 - - + +
79D GLU* 1.3 77.1 - - - +
81D TRP* 1.3 57.4 + - - +
83D ARG* 3.1 4.5 + - - +
84D ILE* 2.9 35.7 + - + +
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Residues in contact with TRP 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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48D LEU* 4.1 10.7 - - + +
77D LEU* 2.8 21.3 + - + +
78D ARG* 3.7 6.1 - - - +
80D ALA* 1.3 72.4 - - - +
82D ARG* 1.3 57.4 + - - +
84D ILE* 3.4 23.6 + - + +
85D GLN* 2.9 69.3 + - + +
89D TYR 4.3 2.7 - - - -
90D THR* 3.6 10.1 - - - -
91D LEU* 3.4 42.0 - - + -
119D ASP 3.6 7.2 - - - -
120D LEU* 3.0 59.1 + - + -
154D LEU* 3.5 23.1 - - + -
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Residues in contact with ARG 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 ARG 2.9 19.1 + - - +
79D GLU* 2.8 44.7 + - - +
80D ALA 3.1 0.2 - - - -
81D TRP* 1.3 78.3 - - - +
83D ARG* 1.3 80.5 + - - +
85D GLN* 3.5 14.1 + - - +
86D ALA* 3.1 32.8 + - - +
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Residues in contact with ARG 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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54D LEU* 4.0 14.2 - - + +
60D LEU* 3.5 49.7 + - + +
61D PHE* 4.6 0.8 - - - -
65D ASP* 5.0 5.5 + - - -
68D PHE* 4.3 12.3 - - - -
79D GLU* 2.6 41.0 + - - +
80D ALA 3.1 6.0 + - - +
82D ARG* 1.3 94.2 - - - +
84D ILE* 1.3 64.8 + - - +
86D ALA* 3.5 9.9 + - - +
87D LYS* 3.4 24.8 + - - +
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Residues in contact with ILE 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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48D LEU* 3.5 39.7 - - + +
49D LEU* 3.7 8.3 - - + +
52D ALA* 3.8 6.7 - - + -
54D LEU* 3.8 20.6 - - + -
80D ALA* 2.9 28.3 + - + +
81D TRP* 3.6 22.4 - - + +
83D ARG* 1.3 75.4 - - - +
85D GLN* 1.3 64.7 + - - +
87D LYS* 3.1 10.1 + - - +
89D TYR* 3.3 29.4 + - + -
154D LEU* 3.7 27.1 - - + -
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Residues in contact with GLN 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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81D TRP* 2.9 61.8 + - + +
82D ARG* 3.8 14.8 + - - +
84D ILE* 1.3 74.7 - - - +
86D ALA* 1.3 57.7 + - - +
88D GLY* 2.9 20.8 + - - -
89D TYR 3.4 21.6 + - - +
90D THR* 5.3 3.6 - - + +
120D LEU 4.7 0.7 - - - +
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Residues in contact with ALA 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 ARG* 3.1 22.8 + - - +
83D ARG* 3.5 14.6 - - - +
84D ILE 3.2 0.4 - - - -
85D GLN* 1.3 76.5 - - - +
87D LYS* 1.3 61.0 + - + +
88D GLY* 3.5 0.5 + - - -
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Residues in contact with LYS 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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52D ALA 2.8 26.4 + - - +
53D ALA 4.5 5.1 + - - -
54D LEU* 3.7 29.6 - - + +
83D ARG 3.4 10.5 + - - +
84D ILE 3.1 12.2 + - - +
86D ALA* 1.3 78.1 - - + +
88D GLY* 1.3 56.1 + - - +
89D TYR* 3.7 22.4 + - + -
156D LYS 5.3 1.7 - - - +
125E ASP* 2.8 30.7 + - - -
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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