Contacts of the helix formed by residues 55 - 69 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TYR* 3.7 12.1 - - - -
53A ASN 4.9 2.1 + - - -
54A MET* 1.3 74.6 - - - +
56A VAL* 1.3 65.3 + - - +
57A ALA* 3.3 12.5 + - - +
58A THR* 3.1 27.2 + - - +
59A VAL* 3.0 23.7 + - - +
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA* 4.4 3.6 - - + -
41A ASP* 3.8 25.6 - - - +
44A TYR* 3.7 33.9 - - + -
55A SER* 1.3 73.2 - - - +
57A ALA* 1.3 57.1 + - - +
59A VAL* 3.2 7.8 + - - +
60A TYR* 2.9 54.0 + - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A SER* 3.1 11.5 + - - +
56A VAL* 1.3 79.6 - - - +
58A THR* 1.3 57.2 + - - +
60A TYR* 3.3 7.0 + - - +
61A ASN* 2.9 44.1 + - - +
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Residues in contact with THR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 2.5 47.4 + - - +
53A ASN 3.9 8.7 + - - -
54A MET* 3.5 4.7 - - + -
55A SER* 3.1 31.8 + - - +
57A ALA* 1.3 78.2 - - - +
59A VAL* 1.3 63.8 + - - +
61A ASN* 3.4 10.1 + - - +
62A ASN* 3.0 30.0 + - - +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 4.1 6.5 - - - +
27A ILE* 4.2 6.9 - - + +
40A ALA* 3.8 22.9 - - + +
43A ILE* 3.8 22.2 - - + -
44A TYR* 4.3 13.2 - - + -
54A MET* 3.9 28.5 - - + -
55A SER 3.0 14.9 + - - +
56A VAL* 3.5 7.9 - - - +
58A THR* 1.3 75.9 - - - +
60A TYR* 1.3 63.5 + - - +
62A ASN* 3.2 3.6 + - - +
63A LEU* 2.9 44.6 + - + +
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR* 5.8 0.2 - - - -
40A ALA* 3.4 28.0 + - + +
41A ASP* 5.1 3.2 + - - -
56A VAL* 2.9 38.6 + - + -
57A ALA* 3.6 9.6 - - - +
59A VAL* 1.3 76.8 - - - +
61A ASN* 1.3 67.0 + - - +
63A LEU* 3.2 5.8 + - + +
64A ARG* 2.9 23.7 + - - +
74A GLU* 5.5 1.8 - - - -
81A SER* 4.2 21.7 + - - -
82A SER* 4.5 9.4 + - - -
84A PHE* 3.9 26.5 - + - -
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Residues in contact with ASN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA* 2.9 33.1 + - - +
58A THR* 3.6 9.7 + - - +
59A VAL 3.3 0.2 - - - -
60A TYR* 1.3 78.4 - - - +
62A ASN* 1.3 65.9 + - - +
64A ARG* 3.4 9.7 + - - +
65A VAL* 3.2 26.4 + - - +
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Residues in contact with ASN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 5.2 0.2 + - - -
23A GLN* 3.1 34.0 + - - +
24A ARG* 2.8 53.4 - - + +
27A ILE* 3.6 20.5 - - + +
58A THR* 3.0 12.3 + - - +
59A VAL 3.7 0.2 - - - +
61A ASN* 1.3 77.5 - - - +
63A LEU* 1.3 60.3 + - - +
65A VAL* 3.2 3.9 + - - +
66A PHE* 2.9 39.1 + - + -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 4.2 12.1 - - + -
31A LEU* 4.0 27.1 - - + -
40A ALA* 4.3 5.6 - - + -
43A ILE* 3.9 11.4 - - + -
59A VAL* 2.9 39.3 + - + +
60A TYR* 3.2 7.2 + - - +
62A ASN* 1.3 75.6 - - - +
64A ARG* 1.3 58.1 + - - +
66A PHE* 3.3 8.8 + - + +
67A ARG* 2.9 29.6 + - - +
72A VAL* 4.5 7.1 - - + +
84A PHE* 3.6 56.7 - - + -
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR 2.9 12.9 + - - +
61A ASN* 3.5 12.8 - - - +
63A LEU* 1.3 74.0 - - - +
65A VAL* 1.3 60.1 + - - +
67A ARG* 3.2 40.1 + - - +
68A GLU* 2.9 54.4 + - - +
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.5 42.8 - - + -
24A ARG* 4.0 19.5 - - - +
61A ASN 3.2 13.9 + - - +
62A ASN* 3.2 9.5 + - - +
64A ARG* 1.3 76.2 - - + +
66A PHE* 1.3 69.7 + - + +
68A GLU* 3.2 15.3 + - + +
69A SER* 3.0 25.7 + - - +
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.0 31.6 - - + -
24A ARG* 3.5 48.7 - - + -
27A ILE* 3.7 24.9 - - + -
28A LEU* 3.7 25.4 - - + -
31A LEU* 4.4 0.9 - - + -
62A ASN* 2.9 25.9 + - + -
63A LEU* 3.6 14.4 - - + +
65A VAL* 1.3 80.3 - - + +
67A ARG* 1.3 60.8 + - - +
69A SER* 3.1 13.0 + - - -
71A LEU* 2.9 30.4 + - + -
72A VAL* 3.7 24.0 - - + -
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU 2.9 20.1 + - - +
64A ARG* 3.2 53.3 + - - +
66A PHE* 1.3 73.2 - - - +
68A GLU* 1.3 67.4 + - - +
70A GLY* 3.1 18.4 + - - -
72A VAL* 3.4 27.7 - - + +
73A LYS* 5.1 7.0 - - + +
74A GLU* 3.8 39.1 + - - +
84A PHE* 6.0 1.5 - - + -
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Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 2.9 55.8 + - + +
65A VAL* 3.2 16.0 + - - +
67A ARG* 1.3 85.5 - - - +
69A SER* 1.3 56.9 + - - +
70A GLY 3.3 1.1 + - - -
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Residues in contact with SER 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 3.5 19.8 - - - +
13A LEU* 4.1 8.7 - - - +
16A THR* 3.3 34.0 + - - +
18A VAL* 3.6 14.6 - - - +
65A VAL 3.0 14.0 + - - -
66A PHE 3.1 8.3 + - - -
68A GLU* 1.3 75.8 - - - +
70A GLY* 1.3 60.0 + - - +
71A LEU* 4.3 10.8 - - - -
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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