Contacts of the helix formed by residues 65 - 74 (chain E) in PDB entry 3J41
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 PHE 65 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E PHE 4.7 5.4 - - - -
13E LYS* 4.1 34.5 - - + -
16E PHE* 3.2 55.5 - + + -
17E SER* 5.3 3.6 - - - -
20E ASP* 5.6 1.6 - - + -
23E GLY 5.8 1.6 - - - -
25E GLY* 2.9 28.2 + - - +
64E ASP* 1.3 70.8 - - - +
66E PRO* 1.4 67.8 - - + +
68E PHE* 3.9 6.9 + - - +
69E LEU* 3.7 19.5 - - + +
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Residues in contact with PRO 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E ASP* 3.6 10.3 - - + +
65E PHE* 1.4 94.1 - - + +
67E GLU* 1.3 60.0 + - + +
69E LEU* 2.9 28.6 + - + +
70E THR* 2.9 15.7 + - - +
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Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E VAL* 4.9 1.9 - - - +
56E ASP* 3.5 9.7 - - - -
57E ALA* 2.8 40.7 + - - +
58E ASP* 4.0 10.4 - - - +
63E ILE* 3.7 24.8 - - + +
64E ASP* 2.9 29.9 + - - +
66E PRO* 1.3 77.3 - - + +
68E PHE* 1.3 58.7 + - - +
70E THR* 3.1 27.6 + - - +
71E MET* 2.9 29.1 + - - +
202E CA 4.5 0.2 - - - -
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Residues in contact with PHE 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 3.7 30.5 - - + -
15E ALA* 3.5 24.0 - - + -
16E PHE* 3.6 38.4 - + + -
19E PHE* 5.3 11.2 - + + -
27E ILE* 3.8 31.4 - - + -
63E ILE* 3.4 17.6 - - + +
64E ASP 2.9 8.0 + - - +
65E PHE 3.9 2.0 - - - +
66E PRO 3.3 0.2 - - - -
67E GLU* 1.3 76.4 - - - +
69E LEU* 1.3 65.3 + - + +
71E MET* 3.3 5.0 + - + +
72E MET* 3.2 55.6 + - + +
146E THR* 5.8 1.1 - - + -
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Residues in contact with LEU 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 3.8 58.8 - - + +
15E ALA* 6.4 1.6 - - + -
16E PHE* 5.8 2.0 - - + -
65E PHE* 3.7 17.7 - - + +
66E PRO* 2.9 13.4 + - + +
68E PHE* 1.3 83.5 - - + +
70E THR* 1.3 56.9 + - - +
72E MET* 3.2 7.2 + - + +
73E ALA* 2.9 38.2 + - + +
74E ARG* 5.2 2.2 - - - -
146E THR* 6.0 2.2 - - + -
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Residues in contact with THR 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E VAL* 5.8 0.4 - - + -
57E ALA* 5.1 4.3 - - + -
66E PRO* 2.9 13.9 + - - +
67E GLU* 3.1 31.5 + - - +
69E LEU* 1.3 72.7 - - - +
71E MET* 1.3 56.1 + - - -
74E ARG* 2.9 35.3 + - + +
75E LYS* 2.8 26.8 + - - -
76E MET 3.8 20.9 - - - +
78E ASP 5.2 2.5 - - - +
79E THR* 4.8 8.3 - - - +
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Residues in contact with MET 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A LYS* 6.0 0.2 - - - +
234B LEU* 5.0 11.9 - - + -
237B LEU* 6.0 4.3 - - + -
51E MET 4.0 21.3 - - - +
52E ILE* 4.1 19.7 - - + +
55E VAL* 4.0 33.7 - - + +
56E ASP 5.8 0.2 - - - -
63E ILE* 4.3 28.5 - - + -
67E GLU* 2.9 19.7 + - - +
68E PHE* 3.3 11.1 + - - +
70E THR* 1.3 74.1 - - - +
72E MET* 1.3 78.7 + - + +
75E LYS* 4.1 16.2 - - - +
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Residues in contact with MET 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B LEU* 6.0 4.9 - - + -
241B ARG* 4.0 22.7 - - + +
12E PHE* 6.5 0.7 - - + -
68E PHE* 3.2 46.6 + - + +
69E LEU* 3.2 9.4 + - + +
71E MET* 1.3 102.0 - - + +
73E ALA* 1.3 59.5 + - + +
74E ARG 4.0 0.2 - - - -
75E LYS* 5.0 3.3 - - - +
85E ILE* 5.9 1.2 - - - +
141E PHE* 5.3 6.6 - - - -
142E VAL* 3.8 23.3 - - + +
145E MET* 3.8 33.8 - - + +
146E THR* 3.9 15.5 - - + +
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Residues in contact with ALA 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 5.7 5.8 - - + -
69E LEU* 2.9 17.1 + - + +
72E MET* 1.3 78.9 - - + +
74E ARG* 1.3 66.9 - - - +
75E LYS* 5.3 0.2 - - - -
82E GLU* 4.0 7.1 - - - +
85E ILE* 3.9 14.4 - - - +
138E TYR* 3.6 21.5 + - - +
142E VAL* 4.1 23.7 - - + +
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Residues in contact with ARG 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LEU 4.8 1.1 - - - -
70E THR* 2.9 33.3 + - + +
73E ALA* 1.3 83.0 - - - +
75E LYS* 1.3 66.4 + - - +
76E MET 3.1 3.3 + - - +
78E ASP 4.7 1.3 - - - +
79E THR 2.8 25.6 + - - +
80E ASP* 2.7 34.4 + - - +
81E SER* 3.1 48.5 - - - +
82E GLU* 2.7 38.7 + - + +
85E ILE* 3.8 4.4 + - - +
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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