Contacts of the helix formed by residues 65 - 79 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B GLY* 1.3 90.7 + - - +
66B PRO* 1.4 76.2 - - + +
67B THR* 3.8 0.9 - - - -
68B ARG* 3.3 11.8 + - - +
69B ASN* 2.7 25.6 + - - +
249B PRO* 6.4 0.9 - - + -
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Residues in contact with PRO 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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65B ASN* 1.4 94.3 - - + +
67B THR* 1.3 62.2 + - - +
69B ASN* 2.6 32.5 + - + +
70B CYS* 3.0 17.4 + - - +
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Residues in contact with THR 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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65B ASN 3.6 0.8 + - - -
66B PRO* 1.3 77.7 - - - +
68B ARG* 1.3 60.0 + - - +
70B CYS* 3.6 6.6 + - - +
71B LEU* 3.2 21.8 + - - +
249B PRO* 3.0 42.4 + - - +
252B CYS* 3.4 4.2 - - + +
253B TYR* 3.3 30.9 - - + +
256B ASN* 5.4 0.7 + - - +
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Residues in contact with ARG 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 GLY* 2.8 43.4 - - - +
65B ASN 3.3 8.0 + - - +
66B PRO 2.8 2.2 + - - -
67B THR* 1.3 75.6 - - - +
69B ASN* 1.3 61.3 + - - +
71B LEU* 3.2 2.3 + - - +
72B GLU* 2.8 48.4 + - - +
86B ALA* 4.2 7.2 - - + -
237B ARG* 3.3 25.3 - - - +
240B GLN* 3.6 15.0 + - - -
241B ASN* 3.5 16.0 + - - -
246B VAL* 2.8 55.3 - - - +
247B PRO* 4.0 7.2 - - - -
249B PRO* 5.8 0.4 - - + +
252B CYS* 3.5 26.2 - - - +
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Residues in contact with ASN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY 4.6 0.7 + - - -
65B ASN* 2.7 34.4 + - - +
66B PRO* 2.6 16.2 + - + +
68B ARG* 1.3 72.9 + - - +
70B CYS* 1.3 58.0 + - - +
72B GLU* 3.4 10.0 + - - +
73B LYS* 2.9 41.1 + - - +
237B ARG* 4.1 22.3 + - - +
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Residues in contact with CYS 70 (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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25B VAL 4.2 3.3 - - - +
26B GLY* 3.2 35.2 - - - +
27B GLN* 5.5 0.7 - - - +
66B PRO* 3.0 15.9 + - - +
67B THR* 4.0 9.2 - - - +
69B ASN* 1.3 76.4 - - - +
71B LEU* 1.3 66.2 + - - +
73B LYS* 3.8 12.0 - - - +
74B ALA* 3.1 24.1 + - - +
256B ASN* 3.5 8.3 + - - +
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Residues in contact with LEU 71 (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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67B THR 3.2 14.9 + - - +
68B ARG 3.2 7.8 + - - +
70B CYS* 1.3 77.0 - - - +
72B GLU* 1.3 59.8 + - - +
74B ALA* 3.4 1.7 - - - +
75B VAL* 2.9 34.8 + - + +
86B ALA* 4.4 4.3 - - + -
222B MET* 3.6 37.2 - - + -
224B LEU* 4.2 12.3 - - + -
252B CYS* 3.7 19.7 - - + +
255B CYS* 4.0 6.7 - - + -
256B ASN* 3.4 42.8 - - + +
259B LEU* 3.8 15.7 - - + -
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Residues in contact with GLU 72 (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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68B ARG* 2.8 33.9 + - - +
69B ASN* 3.7 12.7 + - - +
71B LEU* 1.3 74.5 - - - +
73B LYS* 1.3 64.9 + - - +
76B ALA* 3.0 25.5 + - - +
84B CYS* 3.3 33.5 + - - +
85B LEU* 3.0 5.0 - - - -
86B ALA* 2.6 40.4 + - + +
224B LEU* 5.7 0.2 - - + -
237B ARG* 2.9 25.5 + - - -
240B GLN* 3.1 11.6 - - - +
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Residues in contact with LYS 73 (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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25B VAL* 3.8 17.0 - - + +
26B GLY* 5.3 8.1 - - - +
69B ASN* 2.9 29.9 + - - +
70B CYS* 3.8 11.8 - - - +
71B LEU 3.3 0.2 - - - -
72B GLU* 1.3 76.3 - - - +
74B ALA* 1.3 63.7 - - - +
76B ALA* 3.4 5.8 + - - +
77B ALA* 3.1 21.7 + - - +
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Residues in contact with ALA 74 (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 GLN* 4.9 5.1 - - - +
22B ALA* 5.4 4.9 - - - +
25B VAL* 3.7 28.2 - - + +
70B CYS 3.1 14.9 + - - +
71B LEU 3.4 4.3 - - - +
73B LYS* 1.3 80.0 - - - +
75B VAL* 1.3 63.3 + - - +
77B ALA* 2.9 15.2 + - - +
78B LEU* 3.0 18.5 + - + +
256B ASN* 3.8 13.2 - - - +
259B LEU* 4.5 10.1 - - + -
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Residues in contact with VAL 75 (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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71B LEU* 2.9 27.0 + - + +
74B ALA* 1.3 72.5 - - - +
76B ALA* 1.3 63.1 + - - +
78B LEU* 3.1 10.3 + - + -
79B ASP* 2.9 41.0 + - - +
84B CYS* 3.7 21.1 - - - -
193B PRO* 5.7 3.1 - - + -
208B TYR* 5.6 4.5 - - + -
224B LEU* 3.7 33.2 - - + -
259B LEU* 3.5 26.5 - - + -
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Residues in contact with ALA 76 (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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72B GLU 3.0 21.0 + - - +
73B LYS* 3.4 7.6 - - - +
74B ALA 3.1 0.2 - - - -
75B VAL* 1.3 76.8 - - - +
77B ALA* 1.3 60.6 + - - +
79B ASP 3.3 1.0 + - - -
80B GLY 3.2 3.1 + - - -
81B ALA* 2.8 42.9 + - - +
82B LYS 4.2 3.4 - - - +
83B TYR* 3.7 24.7 - - - +
84B CYS* 3.7 7.9 - - - +
226B SER* 4.0 4.5 - - - -
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Residues in contact with ALA 77 (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 GLN* 3.4 40.6 + - + +
25B VAL* 4.4 10.1 - - + -
73B LYS 3.1 8.1 + - - +
74B ALA 2.9 9.3 + - - +
76B ALA* 1.3 76.9 - - - +
78B LEU* 1.3 60.3 + - - +
80B GLY* 2.8 21.0 + - - +
81B ALA 4.6 3.1 - - - +
197B ARG* 4.0 3.8 + - - -
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Residues in contact with LEU 78 (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 PHE* 3.4 71.0 - - + +
21B GLN* 4.1 10.1 - - + +
22B ALA* 3.8 22.2 - - + +
74B ALA 3.0 17.4 + - - +
75B VAL* 3.1 10.5 + - + +
77B ALA* 1.3 75.7 - - - +
79B ASP* 1.3 58.7 + - - +
80B GLY 3.2 0.2 - - - -
193B PRO* 3.9 16.3 - - + +
197B ARG* 3.2 19.2 + - - -
259B LEU* 4.1 28.0 - - + -
262B LEU* 4.6 6.5 - - + -
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Residues in contact with ASP 79 (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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75B VAL* 2.9 23.6 + - - +
76B ALA 3.9 2.2 - - - +
78B LEU* 1.3 75.9 - - - +
80B GLY* 1.3 63.2 + - - +
81B ALA* 3.4 1.5 + - + -
188B ASN* 4.4 2.9 + - - -
193B PRO* 3.0 28.1 - - - +
196B GLN 5.2 0.7 - - - +
197B ARG* 3.4 23.2 - - - +
198B PRO* 5.6 1.3 - - + +
199B LEU* 4.0 11.4 - - + +
206B SER* 4.2 18.6 + - - +
208B TYR* 5.0 7.7 - - - +
224B LEU* 5.5 0.9 - - - +
226B SER* 2.5 40.5 + - - +
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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