Contacts of the helix formed by residues 65 - 79 (chain A) in PDB entry 3ELP
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLY* 1.3 87.2 + - - +
66A PRO* 1.3 84.2 - - + +
67A THR* 3.3 2.2 - - - +
68A ARG* 2.8 16.3 + - - +
69A ASN* 3.0 23.5 + - - +
237A ARG* 5.6 0.4 - - - +
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Residues in contact with PRO 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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65A ASN* 1.3 96.5 - - + +
67A THR* 1.3 67.7 + - - +
69A ASN* 3.2 7.2 + - + +
70A CYS* 2.9 35.3 + - - -
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Residues in contact with THR 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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64A GLY 5.3 1.4 + - - -
65A ASN* 2.9 4.7 + - - +
66A PRO* 1.3 77.2 - - - +
68A ARG* 1.3 62.3 + - - -
70A CYS* 3.5 5.7 + - - +
71A LEU* 3.1 21.5 + - - +
249A PRO* 3.3 44.3 - - + +
252A CYS* 3.8 4.5 - - + +
253A TYR* 3.7 28.3 - - + +
256A ASN* 5.0 1.2 - - - +
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Residues in contact with ARG 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 GLY* 3.0 38.8 + - - +
65A ASN 2.8 13.4 + - - +
67A THR* 1.3 72.5 - - - +
69A ASN* 1.3 59.4 + - - +
71A LEU* 3.1 2.6 + - - +
72A GLU* 2.8 44.8 + - - +
86A ALA* 4.1 12.1 - - + -
237A ARG* 2.8 33.1 - - - +
240A GLN* 3.3 18.5 + - - -
241A ASN* 3.2 21.0 + - - -
246A VAL* 3.1 46.9 - - - +
247A PRO* 4.4 4.0 - - - -
252A CYS* 3.8 25.4 - - - +
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Residues in contact with ASN 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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65A ASN* 3.0 31.2 + - - +
66A PRO* 3.6 8.8 - - + +
68A ARG* 1.3 75.9 - - - +
70A CYS* 1.3 52.7 + - - +
72A GLU* 3.2 12.5 + - - +
73A LYS* 2.7 57.7 + - - +
237A ARG* 4.3 15.0 + - - +
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Residues in contact with CYS 70 (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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25A VAL 4.6 2.8 - - - +
26A GLY* 3.3 31.9 - - - +
27A GLN* 5.0 0.9 - - - +
66A PRO* 2.9 25.7 + - - +
67A THR* 3.7 5.4 - - - +
69A ASN* 1.3 73.5 - - - +
71A LEU* 1.3 66.7 + - - +
73A LYS* 3.3 15.4 + - - +
74A ALA* 3.0 25.8 + - - +
256A ASN* 3.9 9.7 - - - +
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Residues in contact with LEU 71 (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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67A THR 3.1 14.0 + - - +
68A ARG* 3.1 8.5 + - - +
70A CYS* 1.3 76.5 - - - +
72A GLU* 1.3 58.5 + - - +
74A ALA* 3.7 1.4 - - - +
75A VAL* 2.9 46.8 + - + +
86A ALA* 4.4 5.2 - - + -
222A MET* 3.8 37.5 - - + -
224A LEU* 4.4 8.1 - - + -
252A CYS* 3.8 21.1 - - - +
255A CYS* 3.9 12.3 - - - -
256A ASN* 3.6 43.5 + - + +
259A LEU* 4.2 2.9 - - + -
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Residues in contact with GLU 72 (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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68A ARG* 2.8 29.5 + - - +
69A ASN* 3.6 11.4 - - - +
71A LEU* 1.3 74.6 - - + +
73A LYS* 1.3 67.2 + - - +
75A VAL* 3.1 3.1 + - - -
76A ALA* 2.8 27.4 + - - +
84A CYS* 3.4 28.3 - - + +
85A LEU* 3.1 4.8 - - - -
86A ALA* 2.7 40.7 + - + +
224A LEU* 5.5 0.4 - - + -
237A ARG* 2.9 26.9 + - - -
240A GLN* 3.1 13.9 - - - +
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Residues in contact with LYS 73 (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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25A VAL* 3.9 12.9 - - + +
26A GLY* 4.9 11.4 - - - +
69A ASN* 2.7 43.4 + - - +
70A CYS* 3.6 15.0 - - - +
72A GLU* 1.3 73.9 - - - +
74A ALA* 1.3 62.6 + - - +
76A ALA* 3.2 7.3 + - - +
77A ALA* 3.2 18.9 + - - +
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Residues in contact with ALA 74 (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 GLN 4.7 4.4 - - - +
22A ALA* 5.4 5.6 - - - +
25A VAL* 3.5 33.6 - - + +
70A CYS 3.0 15.0 + - - +
71A LEU 3.7 3.4 - - - +
73A LYS* 1.3 78.3 - - - +
75A VAL* 1.3 65.4 + - - +
77A ALA* 3.3 5.2 + - - +
78A LEU* 3.1 26.9 + - - +
256A ASN* 4.6 14.1 - - - +
259A LEU* 5.0 6.7 - - + -
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Residues in contact with VAL 75 (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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71A LEU* 2.9 34.3 + - + +
72A GLU 3.9 0.2 - - - +
74A ALA* 1.3 72.6 - - - +
76A ALA* 1.3 68.5 + - - +
78A LEU* 3.2 10.2 + - + +
79A ASP* 3.0 39.8 + - - +
84A CYS* 3.6 20.0 - - - -
193A PRO* 5.9 3.4 - - + -
208A TYR* 5.8 3.1 - - + -
224A LEU* 3.8 39.3 - - + -
259A LEU* 3.8 20.0 - - + -
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Residues in contact with ALA 76 (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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72A GLU 2.8 12.5 + - - +
73A LYS* 3.2 13.5 - - - +
75A VAL* 1.3 77.7 - - - +
77A ALA* 1.3 61.1 + - - +
79A ASP 3.2 0.7 + - - -
80A GLY 3.1 2.9 + - - -
81A ALA* 2.8 42.0 + - - +
82A LYS 4.3 4.0 - - - +
83A TYR* 3.9 25.1 - - - -
84A CYS* 3.8 8.0 - - - +
226A SER* 4.2 5.2 - - - -
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Residues in contact with ALA 77 (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 GLN* 3.4 42.6 + - + +
25A VAL* 4.4 10.8 - - + -
73A LYS 3.2 8.3 + - - +
74A ALA 3.5 9.4 - - - +
76A ALA* 1.3 79.8 - - - +
78A LEU* 1.3 58.1 + - - +
80A GLY* 2.8 20.9 + - - -
81A ALA 4.4 3.6 - - - -
197A ARG* 3.9 3.1 + - - -
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Residues in contact with LEU 78 (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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18A PHE* 3.2 72.7 - - + +
21A GLN* 4.1 5.8 - - + +
22A ALA* 3.8 27.6 - - + +
74A ALA 3.1 14.2 + - - +
75A VAL* 3.2 8.7 + - + +
77A ALA* 1.3 75.0 - - - +
79A ASP* 1.3 57.4 + - - +
80A GLY 3.1 0.2 - - - -
193A PRO* 3.8 15.0 - - + +
197A ARG* 2.8 23.7 + - - +
259A LEU* 4.1 28.9 - - + -
262A LEU* 5.2 2.7 - - + -
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Residues in contact with ASP 79 (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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75A VAL* 3.0 28.0 + - - +
76A ALA 3.6 4.5 - - - +
78A LEU* 1.3 74.8 - - - +
80A GLY* 1.3 61.0 + - - +
81A ALA* 2.9 4.7 + - + +
188A ASN* 4.9 2.1 + - - +
193A PRO* 3.2 26.7 - - - +
196A GLN 5.4 0.2 - - - +
197A ARG* 3.5 23.9 - - - +
198A PRO* 5.8 0.3 - - - +
199A LEU* 3.7 13.0 - - + +
206A SER* 4.2 19.5 + - - +
208A TYR* 5.3 7.8 - - - +
224A LEU* 5.5 1.0 - - - +
226A SER* 2.6 37.2 + - - +
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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