Contacts of the helix formed by residues 46 - 60 (chain B) in PDB entry 3F8F
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 ASN 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B THR* 5.7 1.1 + - - +
44B GLU 3.5 4.3 + - - +
45B LEU* 1.3 72.4 - - - +
47B GLU* 1.3 64.6 + - - +
48B ALA* 2.8 34.8 + - - +
49B THR* 2.9 37.5 + - - +
50B LEU* 2.9 15.1 + - - +
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Residues in contact with GLU 47 (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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28B VAL* 4.2 3.4 - - + -
29B TYR* 3.6 24.2 + - - -
32B ILE* 4.0 24.0 - - + +
45B LEU 3.3 6.7 + - - -
46B ASN* 1.3 71.9 + - - +
48B ALA* 1.3 63.4 + - - +
50B LEU* 3.1 14.9 + - - +
51B TYR* 2.7 58.4 + - + +
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Residues in contact with ALA 48 (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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46B ASN* 2.8 24.5 + - - +
47B GLU* 1.3 74.1 - - - +
49B THR* 1.3 59.7 + - - +
51B TYR* 3.5 11.1 + - - +
52B THR* 3.2 29.5 + - + +
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Residues in contact with THR 49 (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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10B ARG* 4.6 15.3 - - + +
13B THR* 4.4 14.1 - - + +
46B ASN* 2.9 32.7 + - - +
48B ALA* 1.3 76.4 - - - +
50B LEU* 1.3 65.9 + - - +
52B THR* 2.9 24.3 + - - +
53B ILE* 3.0 29.9 + - + +
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Residues in contact with LEU 50 (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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13B THR* 4.0 16.6 - - + -
17B LEU* 2.6 41.5 - - + +
28B VAL* 3.7 25.1 - - + +
31B ILE* 4.6 6.7 - - + -
32B ILE* 3.4 36.3 - - + -
45B LEU* 4.1 9.9 - - + -
46B ASN 2.9 14.5 + - - +
47B GLU* 3.3 8.5 - - - +
49B THR* 1.3 77.1 - - - +
51B TYR* 1.3 52.5 + - - +
53B ILE* 3.2 5.1 + - + +
54B PHE* 2.7 46.0 + - + +
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Residues in contact with TYR 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.5 39.2 - - + +
29B TYR* 4.6 3.8 - - - -
47B GLU* 2.7 55.1 + - + +
48B ALA* 3.7 9.9 - - - +
50B LEU* 1.3 75.6 - - - +
52B THR* 1.3 65.6 + - + +
54B PHE* 3.9 9.5 - + + +
55B LYS* 3.0 25.8 + - - +
79B TYR* 5.0 5.6 - - - -
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Residues in contact with THR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ARG* 2.8 37.9 + - - -
48B ALA* 3.2 17.2 + - + +
49B THR* 2.9 18.7 + - - -
51B TYR* 1.3 78.1 - - + +
53B ILE* 1.3 60.6 + - - +
55B LYS* 3.6 8.6 + - - +
56B ARG* 3.3 16.8 + - - +
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Residues in contact with ILE 53 (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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10B ARG* 3.7 28.9 - - + +
13B THR* 3.7 26.7 - - + -
14B ASN* 3.5 40.6 - - - +
17B LEU* 4.4 11.7 - - + -
49B THR* 3.0 38.1 + - + +
50B LEU* 3.6 4.5 - - + +
52B THR* 1.3 76.5 + - - +
54B PHE* 1.3 60.6 + - - +
56B ARG* 3.2 4.2 + - + +
57B LEU* 2.8 42.1 + - + +
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Residues in contact with PHE 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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17B LEU* 2.8 39.7 - - + -
21B LEU* 4.4 5.4 - - + -
28B VAL* 3.9 16.6 - - + -
31B ILE* 3.6 25.1 - - + -
50B LEU* 2.7 33.1 + - + +
51B TYR* 3.9 8.3 - + - +
53B ILE* 1.3 70.5 - - - +
55B LYS* 1.3 56.7 + - - +
57B LEU* 3.7 0.8 - - + -
58B GLU* 2.8 42.0 + - - +
63B ILE* 3.0 27.0 - - + +
79B TYR* 3.6 47.8 - + + +
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Residues in contact with LYS 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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51B TYR 3.0 18.6 + - - +
52B THR* 3.7 8.1 - - - +
54B PHE* 1.3 76.8 - - - +
56B ARG* 1.3 60.5 + - - +
58B GLU* 4.0 9.0 + - - +
59B LYS* 3.3 21.1 + - - +
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Residues in contact with ARG 56 (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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5A PRO* 4.1 14.6 - - - +
6A LYS* 5.3 7.5 - - - +
7A GLU* 3.3 35.2 + - - -
10B ARG* 4.5 11.6 - - - +
52B THR 3.3 9.7 + - - +
53B ILE* 3.2 10.4 + - + +
55B LYS* 1.3 78.9 - - - +
57B LEU* 1.3 69.4 + - + +
58B GLU 3.2 0.2 - - - -
59B LYS* 3.3 14.7 + - - +
60B ASP* 2.4 66.0 + - - +
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Residues in contact with LEU 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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14B ASN* 4.1 14.4 - - - +
17B LEU* 4.2 12.6 - - + -
18B LEU* 3.9 28.3 - - + -
53B ILE* 2.8 40.6 + - + +
56B ARG* 1.3 77.5 - - + +
58B GLU* 1.3 58.0 + - - +
60B ASP* 3.4 4.6 + - - +
61B GLY 3.1 6.1 + - - -
62B ILE* 2.9 58.4 + - + +
63B ILE* 3.4 29.2 + - + -
88B ASN* 5.6 0.7 - - - +
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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 PHE* 2.8 20.9 + - - +
55B LYS* 4.0 6.8 + - - +
57B LEU* 1.3 75.2 - - - +
59B LYS* 1.3 64.6 + - - +
61B GLY* 3.1 12.8 + - - -
63B ILE* 3.6 30.6 - - + +
64B SER* 4.3 1.6 - - - -
65B SER* 2.8 31.4 + - - -
77B LYS* 4.5 3.5 - - - -
79B TYR* 3.8 20.7 + - - -
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Residues in contact with LYS 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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1A MET 5.2 0.5 + - - -
55B LYS 3.3 11.9 + - - +
56B ARG* 3.3 19.4 + - - +
58B GLU* 1.3 78.4 - - - +
60B ASP* 1.3 69.8 + - - +
61B GLY* 3.5 0.5 + - - -
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Residues in contact with ASP 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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1A MET* 2.6 43.2 + - - +
5A PRO* 5.7 1.2 - - - +
56B ARG* 2.4 55.0 + - - +
57B LEU* 3.9 3.6 - - - +
58B GLU 3.2 0.4 - - - -
59B LYS* 1.3 87.1 + - - +
61B GLY* 1.3 59.4 + - - +
62B ILE* 3.2 29.6 + - + +
84B ILE* 4.0 3.8 - - - +
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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