Contacts of the helix formed by residues 63 - 77 (chain B) in PDB entry 3A3K
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 THR 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B SER* 3.0 5.1 + - - -
62B ASP* 1.3 89.4 + - - +
64B ALA* 1.3 67.6 + - - +
65B ALA 3.1 3.0 + - - -
66B PRO* 3.2 13.6 - - - +
67B LEU* 3.2 38.8 + - + +
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Residues in contact with ALA 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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52B SER 3.7 4.8 - - - +
53B SER 3.6 12.6 - - - +
54B GLU 3.3 29.8 - - - +
55B ASN* 3.9 6.1 - - + +
61B SER* 3.0 11.0 + - - +
63B THR* 1.3 78.9 - - - +
65B ALA* 1.3 56.8 + - - +
67B LEU* 3.7 9.1 - - - +
68B ALA* 3.1 28.9 + - - +
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Residues in contact with ALA 65 (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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8B VAL* 3.9 9.4 - - + +
53B SER* 3.9 19.0 + - - +
61B SER 3.6 15.4 + - - +
63B THR 3.1 1.4 + - - -
64B ALA* 1.3 75.5 - - - +
66B PRO* 1.4 67.4 - - + +
68B ALA* 3.2 4.4 + - - +
69B ALA* 2.8 28.2 + - - +
89B SER* 3.6 21.8 - - - +
93B VAL* 3.7 14.2 - - + +
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Residues in contact with PRO 66 (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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62B ASP 3.3 23.8 - - - +
63B THR* 3.2 19.7 - - - +
65B ALA* 1.4 86.7 - - + +
67B LEU* 1.3 58.8 + - + +
69B ALA* 3.3 3.7 + - + +
70B VAL* 2.8 36.7 + - - +
92B PRO* 4.0 22.2 - - + -
93B VAL* 3.6 11.6 - - + -
96B PHE* 4.0 26.2 - - + -
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Residues in contact with LEU 67 (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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63B THR* 3.2 40.1 + - + +
64B ALA* 3.7 9.0 - - - +
66B PRO* 1.3 78.1 - - + +
68B ALA* 1.3 58.6 + - - +
70B VAL* 3.3 6.9 + - + +
71B ASP* 2.9 36.6 + - - +
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Residues in contact with ALA 68 (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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8B VAL* 4.7 4.0 - - + -
51B GLY* 4.6 7.2 - - - -
52B SER 3.6 28.5 - - - +
64B ALA 3.1 16.2 + - - +
65B ALA* 3.2 4.5 + - - +
67B LEU* 1.3 76.0 - - - +
69B ALA* 1.3 59.4 + - - +
71B ASP* 3.2 10.5 + - - +
72B LEU* 2.8 35.5 + - + +
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.1 6.4 - - + +
65B ALA 2.8 16.7 + - - +
66B PRO* 3.5 10.8 - - + +
68B ALA* 1.3 72.9 - - - +
70B VAL* 1.3 57.6 + - - +
72B LEU* 3.3 2.3 + - - +
73B LYS* 2.9 30.1 + - - +
81B PHE* 3.6 28.5 - - + -
93B VAL* 4.0 22.4 - - + -
96B PHE* 5.6 1.8 - - + -
100B TRP* 4.0 10.5 - - + -
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Residues in contact with VAL 70 (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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66B PRO 2.8 23.9 + - - +
67B LEU* 3.6 7.0 - - + +
69B ALA* 1.3 71.4 - - - +
71B ASP* 1.3 66.7 + - - +
73B LYS* 3.2 2.0 + - - +
74B TRP* 2.9 60.9 + - + +
96B PHE* 3.8 33.7 - - + -
100B TRP* 4.0 17.0 - - + -
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Residues in contact with ASP 71 (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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67B LEU* 2.9 23.8 + - - +
68B ALA* 3.2 11.1 + - - +
70B VAL* 1.3 75.7 - - - +
72B LEU* 1.3 65.9 + - + +
74B TRP* 3.5 27.0 + - - +
75B GLU* 3.1 27.0 + - - +
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Residues in contact with LEU 72 (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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6B ALA* 3.9 27.1 - - + -
7B VAL 3.6 24.0 - - - +
8B VAL* 4.2 9.2 - - + -
49B VAL* 4.1 12.8 - - + +
50B LEU 4.2 13.2 - - - +
51B GLY* 3.7 15.0 - - - +
68B ALA 2.8 22.2 + - - +
69B ALA 3.6 4.3 - - - +
71B ASP* 1.3 73.6 - - + +
73B LYS* 1.3 57.3 + - - +
75B GLU* 5.7 1.3 - - - +
76B HIS* 2.9 56.2 + - + +
78B PRO* 3.6 4.3 - - - +
81B PHE* 4.5 1.8 - - + -
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Residues in contact with LYS 73 (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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69B ALA 2.9 17.0 + - - +
70B VAL 3.6 4.5 - - - +
72B LEU* 1.3 76.1 - - - +
74B TRP* 1.3 65.1 + - + +
77B SER* 3.2 32.6 + - - +
78B PRO* 3.8 13.0 - - + +
81B PHE* 4.4 7.4 - - + -
100B TRP* 3.5 62.4 + - + +
102B VAL* 4.8 11.1 - - - +
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Residues in contact with TRP 74 (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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70B VAL* 2.9 37.7 + - + +
71B ASP* 3.7 27.1 - - - +
73B LYS* 1.3 82.7 - - + +
75B GLU* 1.3 64.8 + - - +
77B SER* 4.6 4.5 + - - -
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Residues in contact with GLU 75 (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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71B ASP 3.1 15.8 + - - +
72B LEU* 5.7 1.0 - - - +
74B TRP* 1.3 82.1 - - + +
76B HIS* 1.3 92.4 + - + +
77B SER* 5.4 0.2 - - - -
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Residues in contact with HIS 76 (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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4B THR* 4.2 16.8 + - + +
49B VAL* 3.5 47.8 - - + +
72B LEU* 2.9 27.4 + - + +
75B GLU* 1.3 114.7 + - + +
77B SER* 1.3 73.7 + - - +
78B PRO* 3.3 2.5 - - + +
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Residues in contact with SER 77 (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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4B THR* 4.9 2.3 - - - -
73B LYS* 3.2 23.7 + - - +
74B TRP 4.7 4.2 + - - -
75B GLU 5.4 0.3 - - - -
76B HIS* 1.3 80.1 - - - +
78B PRO* 1.4 73.3 - - - +
79B ALA* 3.7 1.0 + - - -
343B THR* 6.1 0.9 - - - +
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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