Contacts of the helix formed by residues 53 - 64 (chain B) in PDB entry 3AEV
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 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B ILE* 3.2 20.4 - - - -
50B GLY 2.8 7.4 + - - -
52B LYS* 1.3 76.5 - - - +
54B GLN* 1.3 58.8 + - - +
55B THR 3.1 0.5 + - - -
56B LYS* 3.3 5.6 + - - +
57B LYS* 2.9 34.1 + - - +
11C C 3.5 25.7 + - - -
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Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE 3.6 0.8 + - - -
50B GLY* 5.5 0.2 - - - -
51B LYS* 3.2 23.9 + - - +
52B LYS* 3.1 13.6 + - + +
53B GLY* 1.3 76.5 - - - +
55B THR* 1.3 57.5 + - - +
57B LYS* 3.7 9.4 - - + +
58B GLU* 2.9 32.3 + - + +
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL 3.8 6.2 + - - +
48B LEU 3.3 13.7 - - - +
49B ILE 3.1 12.2 + - - -
50B GLY* 3.6 12.0 - - - -
54B GLN* 1.3 74.9 - - - +
56B LYS* 1.3 67.6 + - - +
58B GLU* 2.9 16.0 + - - +
59B ILE* 3.0 25.7 + - + +
100B ILE* 4.5 2.2 - - + -
106B PRO* 3.6 37.2 - - + +
110B PHE* 5.5 2.5 - - + -
8C C 4.9 2.8 + - - -
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.2 15.4 + - + +
49B ILE* 3.1 8.7 + - - +
53B GLY* 3.8 6.3 - - - +
55B THR* 1.3 77.4 - - - +
57B LYS* 1.3 68.3 + - - +
59B ILE* 3.2 10.1 + - - +
60B GLU* 2.9 51.4 + - - +
66B LYS* 6.0 1.6 - - - +
67B ILE* 2.7 32.6 + - + +
68B THR* 4.6 3.8 - - - +
69B ILE* 3.7 24.4 - - + +
11C C 3.0 33.1 + - + +
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS 4.5 8.1 + - - +
53B GLY* 2.9 23.2 + - - +
54B GLN* 3.7 9.6 - - + +
55B THR 3.1 0.2 - - - -
56B LYS* 1.3 82.4 - - + +
58B GLU* 1.3 55.9 + - - +
60B GLU* 3.7 15.8 - - - +
61B LYS* 2.8 29.3 + - - +
11C C 4.0 20.2 + - - +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLN* 2.9 14.0 + - + +
55B THR* 2.9 11.5 + - - +
57B LYS* 1.3 73.2 - - - +
59B ILE* 1.3 58.3 + - - +
61B LYS* 3.6 32.0 + - + +
62B ARG* 2.7 75.3 + - - +
110B PHE* 3.9 16.8 - - + -
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.7 30.3 - - + -
55B THR* 3.0 21.2 + - + +
56B LYS* 3.6 6.3 - - - +
58B GLU* 1.3 75.6 - - - +
60B GLU* 1.3 57.0 + - - +
62B ARG* 3.7 1.3 - - - -
63B THR* 2.9 39.7 + - + +
67B ILE* 3.3 24.5 - - + -
93B ALA* 4.2 21.5 - - + +
96B ILE* 4.0 21.5 - - + -
97B VAL* 5.2 1.1 - - + -
100B ILE* 4.0 7.9 - - + -
110B PHE* 3.8 25.1 - - + -
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LYS* 2.9 46.9 + - - +
57B LYS* 3.7 15.7 - - - +
59B ILE* 1.3 75.4 - - - +
61B LYS* 1.3 57.1 + - - +
64B LYS* 2.8 33.8 + - - -
65B THR* 3.3 26.8 + - - +
66B LYS* 3.8 7.3 - - - +
67B ILE* 2.8 36.2 + - + +
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LYS 2.8 22.1 + - - +
58B GLU* 3.6 28.0 + - - +
60B GLU* 1.3 74.7 - - - +
62B ARG* 1.3 70.8 + - - +
63B THR 3.3 0.3 + - - -
64B LYS* 3.4 18.1 + - - +
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLU* 2.7 55.9 + - - +
59B ILE* 4.1 2.7 - - - +
61B LYS* 1.3 79.8 - - - +
63B THR* 1.3 61.8 + - + +
64B LYS* 3.6 2.5 - - - +
110B PHE* 3.7 37.7 + - + +
113B LEU* 3.4 38.5 - - + +
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Residues in contact with THR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 2.9 24.6 + - + +
62B ARG* 1.3 82.9 - - + +
64B LYS* 1.3 70.2 + - - +
65B THR* 2.8 33.0 + - - +
84B THR* 4.1 1.4 - - - +
86B ASP* 5.5 1.5 + - - +
89B ALA* 3.3 30.6 - - + +
92B LYS* 4.8 3.1 - - + -
93B ALA* 3.8 24.1 - - + +
96B ILE* 4.8 1.6 - - + -
113B LEU* 3.7 25.6 - - + -
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLU 2.8 11.7 + - - -
61B LYS* 3.4 13.2 + - - +
62B ARG 5.4 2.0 - - - +
63B THR* 1.3 79.7 - - - +
65B THR* 1.3 56.0 + - - +
81B THR* 3.4 6.0 + - - -
83B GLU* 4.2 32.3 - - + +
84B THR* 2.6 44.5 + - + +
85B GLU* 3.5 31.1 + - + +
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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