Contacts of the helix formed by residues 55 - 69 (chain B) in PDB entry 2FE3
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 SER 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B TYR* 3.9 10.3 - - - -
53B ASN 3.6 3.0 + - - -
54B MET* 1.3 75.5 - - - +
56B VAL* 1.3 63.8 + - - +
57B ALA* 3.4 12.1 + - - +
58B THR* 2.9 41.3 + - - +
59B VAL* 3.2 10.9 + - - +
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Residues in contact with VAL 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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40B ALA* 4.8 5.2 - - + -
41B ASP* 4.2 19.1 - - - +
44B TYR* 3.7 38.5 - - + -
55B SER* 1.3 73.6 - - - +
57B ALA* 1.3 62.8 + - - +
59B VAL* 3.2 7.2 + - - +
60B TYR* 3.0 47.0 + - + -
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Residues in contact with ALA 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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55B SER* 3.1 11.9 + - - +
56B VAL* 1.3 78.9 - - - +
58B THR* 1.3 58.6 + - + +
60B TYR* 3.2 8.3 + - - +
61B ASN* 2.8 42.5 + - - +
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Residues in contact with THR 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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23B GLN* 2.8 30.0 + - - +
53B ASN 4.1 13.9 - - - +
54B MET* 3.4 1.9 - - - +
55B SER* 2.9 36.3 + - - +
57B ALA* 1.3 77.8 - - + +
59B VAL* 1.3 62.2 + - - +
61B ASN* 3.7 10.8 - - - +
62B ASN* 3.0 30.4 + - - +
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Residues in contact with VAL 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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23B GLN* 4.1 4.5 - - - +
27B ILE* 4.3 7.3 - - + +
40B ALA* 4.0 18.4 - - + +
43B ILE* 3.9 26.0 - - + -
44B TYR* 4.2 18.6 - - + +
54B MET* 3.9 24.5 - - + -
55B SER 3.2 13.4 + - - +
56B VAL* 3.5 8.5 - - - +
58B THR* 1.3 78.1 + - - +
60B TYR* 1.3 63.7 + - - +
62B ASN* 3.3 3.5 + - - +
63B LEU* 2.9 38.8 + - + +
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Residues in contact with TYR 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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40B ALA* 3.3 31.9 + - + +
41B ASP* 5.5 2.4 + - - -
56B VAL* 3.0 41.3 + - + -
57B ALA* 3.6 9.0 - - - +
59B VAL* 1.3 76.0 - - - +
61B ASN* 1.3 67.9 + - - +
63B LEU* 3.2 7.2 + - + +
64B ARG* 3.0 23.0 + - - +
74B GLU* 6.4 0.2 - - - -
81B SER* 4.4 16.6 + - - -
82B SER* 5.1 7.3 + - - -
84B PHE* 4.1 24.1 - + - -
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Residues in contact with ASN 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 ALA* 2.8 38.1 + - - +
58B THR* 3.7 11.6 - - - +
59B VAL 3.3 0.2 - - - -
60B TYR* 1.3 76.0 - - - +
62B ASN* 1.3 66.9 + - - +
64B ARG* 3.3 10.1 + - - +
65B VAL* 3.1 26.1 + - + +
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Residues in contact with ASN 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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21B THR* 5.2 0.3 + - - -
23B GLN* 3.2 36.0 + - - +
24B ARG* 2.9 51.2 - - + +
27B ILE* 3.6 18.8 - - + -
58B THR* 3.0 15.7 + - - +
59B VAL 3.8 0.2 - - - +
61B ASN* 1.3 78.5 - - - +
63B LEU* 1.3 59.4 + - - +
65B VAL* 3.2 5.7 + - - +
66B PHE* 2.9 37.3 + - + -
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Residues in contact with LEU 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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27B ILE* 4.2 8.3 - - + -
31B LEU* 4.1 21.5 - - + -
40B ALA* 4.3 5.8 - - + -
43B ILE* 4.1 19.3 - - + -
59B VAL* 2.9 37.3 + - + +
60B TYR* 3.2 10.5 + - + +
62B ASN* 1.3 74.3 - - - +
64B ARG* 1.3 57.9 + - - +
66B PHE* 3.3 8.1 + - + +
67B ARG* 2.8 30.2 + - - +
72B VAL* 4.5 7.3 - - + +
84B PHE* 3.7 56.0 - - + -
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Residues in contact with ARG 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 TYR 3.0 12.6 + - - +
61B ASN* 3.5 12.6 - - - +
63B LEU* 1.3 76.8 - - - +
65B VAL* 1.3 57.5 + - + +
67B ARG* 3.2 34.9 + - - +
68B GLU* 2.9 57.3 + - - +
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Residues in contact with VAL 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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18B VAL* 3.7 40.2 - - + -
24B ARG* 4.1 20.4 - - - +
61B ASN* 3.1 16.0 + - + +
62B ASN* 3.2 9.2 + - - +
64B ARG* 1.3 79.2 - - + +
66B PHE* 1.3 69.5 + - + +
68B GLU* 3.3 13.9 + - - +
69B SER* 3.0 25.8 + - - +
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Residues in contact with PHE 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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13B LEU* 4.0 28.5 - - + -
24B ARG* 3.5 49.4 - - + -
27B ILE* 3.7 29.6 - - + -
28B LEU* 3.7 28.3 - - + -
31B LEU* 4.5 1.6 - - + -
62B ASN* 2.9 27.1 + - + -
63B LEU* 3.7 8.1 - - - +
65B VAL* 1.3 79.3 - - + +
67B ARG* 1.3 61.6 + - - +
69B SER* 3.3 5.0 + - - -
70B GLY 3.1 3.6 + - - -
71B LEU* 2.8 34.5 + - + +
72B VAL* 3.6 24.5 - - + -
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Residues in contact with ARG 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 LEU 2.8 20.1 + - - +
64B ARG* 3.2 46.6 + - - +
66B PHE* 1.3 72.3 - - - +
68B GLU* 1.3 68.7 + - - +
70B GLY* 3.0 18.5 + - - -
72B VAL* 3.4 25.7 - - + +
73B LYS* 5.0 1.3 - - + +
74B GLU* 4.2 37.5 + - - +
84B PHE* 6.2 0.6 - - - -
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Residues in contact with GLU 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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64B ARG* 2.9 58.5 + - + +
65B VAL* 3.6 14.0 - - - +
67B ARG* 1.3 87.8 + - - +
69B SER* 1.3 57.6 + - - +
70B GLY 3.2 1.7 + - - -
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Residues in contact with SER 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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12B THR* 3.7 21.4 - - - +
13B LEU* 4.2 5.2 - - - +
16B THR* 3.8 25.9 + - - +
18B VAL* 3.9 14.7 - - - +
65B VAL 3.0 17.3 + - - -
66B PHE* 3.7 8.5 - - - -
67B ARG 3.2 0.4 - - - -
68B GLU* 1.3 74.6 - - - +
70B GLY* 1.3 60.1 + - - +
71B LEU* 3.3 13.3 + - - -
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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