Contacts of the helix formed by residues 63 - 72 (chain B) in PDB entry 6B3I
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 GLU 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B LYS* 5.4 5.5 - - - +
57B LYS* 3.4 38.2 - - + +
62B LYS* 1.3 71.5 - - - +
64B LEU* 1.3 66.8 + - - +
65B GLU* 4.5 3.6 - - + +
66B GLU* 3.0 38.8 + - + +
67B VAL* 3.1 14.4 + - - +
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Residues in contact with LEU 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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23A LEU* 3.8 27.8 - - + -
27A CYS* 4.4 12.1 - - - -
41B LEU* 5.8 0.7 - - + -
52B ILE* 4.9 1.1 - - + -
53B LYS* 4.2 31.6 + - + +
56B TYR* 3.8 45.2 - - + -
62B LYS 3.4 4.0 + - - -
63B GLU* 1.3 72.8 + - - +
65B GLU* 1.3 64.3 + - - +
67B VAL* 3.1 3.4 + - + +
68B LEU* 3.1 36.4 + - + +
84B LEU* 3.9 31.6 - - + -
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Residues in contact with GLU 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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53B LYS* 3.6 25.0 + - + +
63B GLU* 3.3 3.9 - - + +
64B LEU* 1.3 76.0 - - - +
66B GLU* 1.3 64.8 + - + +
68B LEU* 3.4 0.9 + - - -
69B LYS* 3.1 37.9 + - - +
81B LEU* 3.7 22.8 - - + +
84B LEU* 3.6 34.2 - - + +
85B ASP* 3.2 25.0 - - - +
93B ARG* 5.6 2.8 + - - -
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Residues in contact with GLU 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 LYS* 6.2 0.4 - - + -
63B GLU* 3.0 30.9 + - + +
65B GLU* 1.3 76.8 - - + +
67B VAL* 1.3 65.2 + - + +
69B LYS* 3.2 44.6 + - - +
70B SER* 3.4 13.5 + - - -
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Residues in contact with VAL 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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27A CYS* 3.8 35.0 - - + -
28A LYS* 4.5 10.1 - - - +
56B TYR* 4.2 17.0 - - + +
62B LYS* 4.0 30.3 - - + -
63B GLU 3.1 14.8 + - - +
64B LEU* 3.1 7.8 + - - +
66B GLU* 1.3 75.8 - - + +
68B LEU* 1.3 60.1 + - - +
70B SER* 2.8 22.8 + - - +
71B GLU* 3.5 19.2 + - - +
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Residues in contact with LEU 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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23A LEU* 6.3 1.3 - - + -
27A CYS* 3.8 26.0 - - - -
37B ILE* 4.5 15.0 - - + -
41B LEU* 5.2 8.1 - - + -
64B LEU* 3.1 21.1 + - + +
65B GLU 3.9 4.3 - - - +
67B VAL* 1.3 76.1 - - - +
69B LYS* 1.3 58.4 + - - +
71B GLU* 4.6 3.6 - - - +
72B LEU* 2.8 57.7 + - + +
77B GLU* 4.3 2.4 - - + +
80B ALA* 4.4 18.6 - - + -
81B LEU* 4.3 9.0 - - + -
84B LEU* 3.7 30.3 - - + -
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Residues in contact with LYS 69 (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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305A GLY* 4.2 8.4 - - - -
65B GLU* 3.1 28.3 + - - +
66B GLU* 3.2 38.7 + - - +
68B LEU* 1.3 76.2 - - - +
70B SER* 1.3 58.7 + - - +
72B LEU 3.5 12.6 - - - +
77B GLU* 3.8 14.9 - - - +
81B LEU* 3.7 31.4 - - + -
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Residues in contact with SER 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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34A GLU* 4.4 0.5 - - - +
305A GLY* 3.6 14.3 - - - -
306A ASP* 3.1 26.4 + - - +
308A ARG* 6.4 0.2 - - - -
66B GLU 3.4 8.6 + - - -
67B VAL* 2.8 23.0 + - - +
69B LYS* 1.3 77.9 - - - +
71B GLU* 1.3 66.7 + - - +
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Residues in contact with GLU 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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27A CYS* 2.8 42.6 - - - +
28A LYS* 4.7 6.6 + - - -
30A MET* 3.8 14.1 - - + +
31A GLY* 3.5 18.4 + - - -
34A GLU* 2.7 37.7 - - - +
306A ASP* 4.0 6.3 - - - +
37B ILE* 6.1 0.2 - - - +
67B VAL* 3.5 21.6 + - - +
68B LEU* 3.3 4.2 + - + +
70B SER* 1.3 89.2 + - - +
72B LEU* 1.3 70.7 + - + +
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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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30A MET* 3.8 25.6 - - + -
306A ASP* 4.3 1.9 - - - +
34B GLU* 5.4 0.2 - - - +
37B ILE* 4.7 8.1 - - + -
68B LEU* 2.8 42.9 + - + +
69B LYS 3.5 15.6 - - - +
71B GLU* 1.3 86.0 - - + +
73B SER* 1.3 69.6 + - - +
76B PHE* 3.6 37.0 - - + -
77B GLU* 3.6 20.5 - - + +
80B ALA* 4.0 22.7 - - + -
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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