Contacts of the helix formed by residues 65 - 80 (chain H) in PDB entry 5EIG
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H SER 4.6 6.1 - - - +
44H SER 5.2 0.7 - - - +
47H PHE* 4.2 8.1 - - + -
58H PHE* 3.7 8.9 - - - -
61H SER* 2.9 38.6 + - - +
64H GLY* 1.3 74.1 - - - +
66H PRO* 1.3 77.7 - - + +
67H THR 3.8 3.1 + - - -
68H ARG* 3.1 46.4 + - - +
69H ASN* 3.0 26.9 + - - +
247H PRO 5.3 3.0 + - - -
249H PRO* 4.0 20.3 - - - +
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Residues in contact with PRO 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F SER* 3.9 26.0 - - - +
32H TRP* 4.1 26.0 - - + -
40H PRO 5.4 1.8 - - - +
42H SER* 4.0 26.5 - - - +
47H PHE* 4.0 10.5 - - + -
58H PHE* 3.8 17.9 - - + -
65H ASN* 1.3 88.9 - - + +
67H THR* 1.3 58.6 + - - +
69H ASN* 3.3 3.0 + - + +
70H CYS* 3.0 35.6 + - - -
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Residues in contact with THR 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H TRP* 6.0 0.2 - - - -
39H PRO* 5.8 4.0 - - + +
40H PRO 2.9 25.9 + - - +
41H ILE* 4.7 1.1 - - - -
42H SER* 3.0 19.3 + - - -
65H ASN* 3.4 6.4 + - - -
66H PRO* 1.3 76.9 - - - +
68H ARG* 1.3 62.5 + - - +
70H CYS* 3.5 8.8 + - + +
71H LEU* 3.3 20.4 + - - +
249H PRO* 3.3 30.5 - - - +
252H CYS* 4.0 0.8 - - + +
253H TYR* 3.6 28.0 - - + +
256H ASN* 5.2 1.3 - - + +
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Residues in contact with ARG 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H SER 3.6 10.1 + - - -
62H ARG 3.1 19.8 + - - -
63H SER 3.0 29.3 + - - -
64H GLY* 3.5 4.7 - - - -
65H ASN* 3.1 32.0 + - - +
67H THR* 1.3 77.7 - - - +
69H ASN* 1.3 62.6 + - - +
71H LEU* 3.3 2.9 + - - +
72H GLU* 2.9 55.1 + - - +
86H ALA* 4.2 4.9 - - + -
237H ARG* 5.0 1.8 - - - +
240H GLN* 3.3 24.6 + - - +
246H VAL* 3.3 22.0 - - - +
247H PRO* 3.9 23.3 + - - +
249H PRO* 5.7 0.2 - - + -
252H CYS* 3.7 24.8 - - - +
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Residues in contact with ASN 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H PHE* 3.4 25.7 - - + -
64H GLY* 4.1 7.7 - - - -
65H ASN 3.0 27.3 + - - +
66H PRO* 3.6 6.1 - - + +
68H ARG* 1.3 78.7 + - - +
70H CYS* 1.3 60.1 + - - +
72H GLU* 3.8 16.8 - - - +
73H LYS* 2.9 31.1 + - - +
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Residues in contact with CYS 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H GLY* 3.3 34.3 - - - +
27H GLN* 4.7 0.9 - - - +
31H GLN* 4.1 8.3 - - - -
32H TRP* 3.6 30.1 - - - -
39H PRO* 4.3 10.5 - - + -
66H PRO* 3.0 26.2 + - - +
67H THR* 3.7 7.6 - - + +
68H ARG 3.3 0.2 - - - -
69H ASN* 1.3 77.4 - - - +
71H LEU* 1.3 61.1 + - - +
73H LYS* 3.5 3.5 + - - +
74H ALA* 3.1 22.7 + - - +
256H ASN* 3.8 9.7 - - - +
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Residues in contact with LEU 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67H THR 3.3 10.6 + - - +
68H ARG 3.5 6.5 - - - +
69H ASN 3.3 0.2 - - - -
70H CYS* 1.3 80.0 - - - +
72H GLU* 1.3 57.1 + - - +
74H ALA* 3.1 2.9 + - - +
75H VAL* 2.9 51.8 + - + +
86H ALA* 4.4 9.6 - - + -
222H MET* 3.6 30.7 - - - -
224H LEU* 4.4 3.8 - - + -
252H CYS* 3.8 29.2 - - + +
255H CYS* 4.2 8.1 - - + -
256H ASN* 3.5 39.4 + - + +
259H LEU* 4.0 7.2 - - + -
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Residues in contact with GLU 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H ARG* 2.9 31.7 + - - +
69H ASN* 3.8 18.3 - - - +
71H LEU* 1.3 75.8 - - - +
73H LYS* 1.3 62.4 + - - +
75H VAL* 4.7 0.4 - - - -
76H ALA* 3.1 21.0 + - - +
84H CYS* 3.1 41.1 + - - +
85H LEU* 3.4 0.6 - - - -
86H ALA* 2.8 36.8 + - + +
224H LEU* 5.8 0.2 - - - -
237H ARG* 3.1 18.1 + - - +
240H GLN* 3.0 19.1 + - - -
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Residues in contact with LYS 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H VAL* 3.3 24.2 - - + +
26H GLY* 3.9 25.3 - - - +
31H GLN* 5.8 2.7 - - - +
69H ASN 2.9 18.4 + - - +
70H CYS* 3.9 5.6 - - - +
72H GLU* 1.3 76.7 - - - +
74H ALA* 1.3 61.3 + - - +
76H ALA* 3.7 6.1 - - - +
77H ALA* 3.4 13.3 + - - +
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Residues in contact with ALA 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H GLN 5.0 4.3 - - - +
22H ALA* 5.0 4.3 - - - +
25H VAL* 3.3 30.6 - - + +
27H GLN* 4.1 9.4 - - - +
70H CYS 3.1 10.3 + - - +
71H LEU 3.1 8.2 + - - +
73H LYS* 1.3 76.6 - - - +
75H VAL* 1.3 63.0 + - - +
77H ALA* 3.1 14.7 + - - +
78H LEU* 3.2 18.5 + - - +
256H ASN* 4.4 2.7 - - - +
259H LEU* 4.3 14.8 - - + -
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Residues in contact with VAL 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H LEU* 2.9 29.5 + - + +
74H ALA* 1.3 72.8 - - - +
76H ALA* 1.3 65.6 + - - +
78H LEU* 3.2 10.1 + - + +
79H ASP* 3.1 27.7 + - - +
84H CYS* 3.6 23.3 - - - -
193H PRO* 5.9 0.2 - - + -
208H TYR* 5.0 1.1 - - + -
214H MET* 4.0 10.5 - - + -
224H LEU* 3.7 35.4 - - + -
226H SER* 3.8 7.4 - - - +
259H LEU* 3.6 21.3 - - + -
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Residues in contact with ALA 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H GLU 3.1 19.7 + - - +
73H LYS* 3.7 8.3 - - - +
75H VAL* 1.3 76.9 - - - +
77H ALA* 1.3 57.6 + - - +
79H ASP 3.3 1.7 + - - -
80H GLY 3.1 2.9 + - - -
81H ALA* 2.6 49.9 + - - +
82H LYS 4.3 3.1 - - - +
83H TYR* 3.8 17.7 - - - +
84H CYS* 3.8 14.7 - - + +
226H SER* 4.2 1.3 - - - -
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Residues in contact with ALA 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H GLN* 3.7 28.6 + - + +
25H VAL* 3.9 27.1 - - + -
73H LYS 3.4 9.7 + - - +
74H ALA 3.1 10.6 + - - +
76H ALA* 1.3 80.0 - - - +
78H LEU* 1.3 57.6 + - - +
80H GLY* 3.0 18.1 + - - -
81H ALA 4.7 2.9 - - - +
197H ARG* 3.8 4.7 + - - -
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Residues in contact with LEU 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H PHE* 3.6 58.9 - - + +
21H GLN* 4.4 6.1 - - + +
22H ALA* 3.7 24.7 - - + +
74H ALA 3.2 11.4 + - - +
75H VAL* 3.2 9.5 + - - +
77H ALA* 1.3 77.0 - - - +
79H ASP* 1.3 57.3 + - - +
193H PRO* 3.2 21.7 - - + +
197H ARG* 3.0 24.5 + - - +
214H MET* 4.9 1.6 - - + -
259H LEU* 3.8 34.8 - - + -
262H LEU* 4.3 6.5 - - + -
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Residues in contact with ASP 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H VAL* 3.1 17.8 + - - +
76H ALA 3.7 3.8 - - - +
77H ALA 3.1 0.2 - - - -
78H LEU* 1.3 76.7 - - - +
80H GLY* 1.3 62.2 + - - +
81H ALA* 3.5 3.5 + - + -
193H PRO* 3.6 6.7 - - - +
196H GLN 4.9 0.5 - - - +
197H ARG* 3.8 20.8 - - - +
198H PRO* 4.7 4.0 - - - +
199H LEU* 4.2 15.0 - - + +
200H ALA* 5.3 1.2 + - - +
206H SER* 3.2 9.3 + - - -
208H TYR* 2.2 46.7 + - - -
226H SER* 2.6 36.2 + - - +
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Residues in contact with GLY 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77H ALA* 3.0 17.8 + - - -
78H LEU 3.2 1.0 + - - -
79H ASP* 1.3 79.0 - - - +
81H ALA* 1.3 61.2 + - - +
197H ARG* 4.0 14.3 - - - +
199H LEU* 4.9 1.4 - - - +
228H ASN* 4.0 11.3 + - - +
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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
------------------------------------------------------------
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