Contacts of the helix formed by residues 42 - 60 (chain H) in PDB entry 6O81
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 ILE 42 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H THR* 1.3 74.6 - - - +
43H GLN* 1.3 64.8 + - - +
45H LEU* 4.0 2.4 - - - +
46H ARG* 3.3 31.7 + - - +
80H SER* 5.5 11.2 - - - -
86H TYR* 4.5 13.4 - - + -
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Residues in contact with GLN 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H THR* 4.7 0.2 - - - -
42H ILE* 1.3 77.1 - - - +
44H GLY* 1.3 62.2 + - - +
45H LEU 3.3 0.2 - - - -
46H ARG* 3.7 11.6 - - + +
47H ALA* 2.9 30.7 + - - +
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Residues in contact with GLY 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLY* 6.3 0.9 - - - -
41H THR* 3.7 19.8 - - - -
42H ILE 3.3 1.0 - - - -
43H GLN* 1.3 79.7 - - - +
45H LEU* 1.3 59.5 - - - +
47H ALA* 4.1 7.4 - - - -
48H ASN* 4.4 9.2 - - - -
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Residues in contact with LEU 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ASP* 6.2 4.9 - - + -
39H GLY* 4.6 6.0 + - - +
41H THR* 3.4 21.6 + - - +
42H ILE 4.0 2.7 - - - +
43H GLN 3.3 0.4 - - - -
44H GLY* 1.3 72.8 - - - +
46H ARG* 1.3 60.9 + - + +
47H ALA 3.3 0.2 - - - -
48H ASN* 3.4 8.1 + - - +
49H LEU* 2.9 37.4 + - + +
86H TYR* 3.4 19.7 - - + +
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Residues in contact with ARG 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H ILE* 3.3 18.2 + - - +
43H GLN* 3.3 14.0 + - - +
45H LEU* 1.3 75.9 - - + +
47H ALA* 1.3 59.9 + - - +
49H LEU* 3.4 10.9 + - + +
50H THR* 2.9 29.3 + - - -
76H ILE* 5.3 5.5 + - + -
77H SER* 3.1 48.1 + - - +
80H SER* 4.1 14.3 - - - -
81H LEU* 5.2 2.0 - - - +
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Residues in contact with ALA 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H GLN 2.9 17.2 + - - +
44H GLY* 4.7 5.2 - - - -
46H ARG* 1.3 77.1 - - - +
48H ASN* 1.3 57.7 + - - +
50H THR* 3.3 6.2 + - - -
51H SER* 2.9 28.6 + - - -
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Residues in contact with ASN 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H PHE* 3.3 34.0 - - + -
37H ASP* 5.6 6.1 - - + -
44H GLY 4.4 4.5 - - - -
45H LEU* 3.4 15.2 + - - +
46H ARG 3.4 0.4 - - - -
47H ALA* 1.3 74.8 - - - +
49H LEU* 1.3 60.4 + - - +
51H SER* 3.4 7.6 + - - -
52H ALA 2.9 22.7 + - - -
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Residues in contact with LEU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LEU* 3.8 26.7 - - + +
33H PHE* 4.5 11.0 - - + -
34H LEU* 5.0 9.2 - - + -
45H LEU* 2.9 24.5 + - + +
46H ARG* 3.7 9.4 - - + +
48H ASN* 1.3 76.4 - - - +
50H THR* 1.3 57.0 + - - +
52H ALA* 3.2 4.0 + - - +
53H ILE* 2.9 39.8 + - + +
72H PHE* 3.8 32.1 - - + +
73H LEU* 5.1 8.1 - - + -
76H ILE* 3.9 27.1 - - + -
93H MET* 5.7 2.0 - - - -
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Residues in contact with THR 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ARG 2.9 18.6 + - - -
47H ALA* 3.7 7.4 - - - -
49H LEU* 1.3 75.0 - - - +
51H SER* 1.3 57.9 + - - +
53H ILE* 3.8 10.7 - - - +
54H GLU* 2.9 29.7 + - - +
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Residues in contact with SER 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H PHE* 6.2 0.9 - - - -
47H ALA 2.9 17.1 + - - -
48H ASN* 3.6 8.5 - - - -
49H LEU 3.3 0.2 - - - -
50H THR* 1.3 77.7 - - - +
52H ALA* 1.3 56.6 + - - +
54H GLU* 3.4 6.8 + - - +
55H THR* 2.9 29.5 + - - -
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Residues in contact with ALA 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 5.6 8.6 - - + +
30H LEU* 3.8 20.0 - - + -
33H PHE* 3.9 25.5 - - + -
48H ASN 2.9 17.4 + - - +
49H LEU 3.2 5.1 + - - +
51H SER* 1.3 74.4 - - - +
53H ILE* 1.3 58.5 + - - +
55H THR* 3.3 6.8 + - - -
56H LEU* 2.9 34.9 + - + +
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Residues in contact with ILE 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LEU* 4.0 24.0 - - + -
49H LEU* 2.9 28.3 + - + +
50H THR* 3.8 8.3 - - - +
52H ALA* 1.3 74.6 - - - +
54H GLU* 1.3 58.3 + - - +
56H LEU* 3.8 5.9 - - - +
57H CYS* 2.9 31.7 + - + +
65H VAL 5.4 1.1 - - - +
66H SER* 5.1 12.1 - - - +
69H GLY* 3.3 37.7 - - - +
70H GLU* 5.2 0.4 - - - +
72H PHE* 5.8 0.7 - - + -
73H LEU* 4.3 13.9 - - + +
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Residues in contact with GLU 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H THR 2.9 17.4 + - - +
51H SER* 3.7 7.2 - - - +
53H ILE* 1.3 76.1 - - - +
55H THR* 1.3 58.2 + - - +
57H CYS* 3.8 4.7 - - - +
58H GLY* 2.9 25.3 + - - -
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Residues in contact with THR 55 (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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6H LEU* 5.7 8.5 - - - -
7H ILE* 5.6 6.4 - - - +
51H SER 2.9 17.6 + - - -
52H ALA* 3.3 7.2 + - - -
54H GLU* 1.3 76.2 - - - +
56H LEU* 1.3 61.8 + - - +
58H GLY* 3.6 1.5 + - - -
59H VAL* 3.4 22.0 + - - +
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Residues in contact with LEU 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 4.7 9.9 - - + +
7H ILE* 5.2 4.0 - - + -
10H PHE* 3.7 45.1 - - + -
26H ALA* 4.0 34.1 - - + +
29H THR* 4.5 12.3 - - + -
30H LEU* 4.2 18.2 - - + -
52H ALA* 2.9 22.1 + - + +
53H ILE* 3.8 6.1 - - - +
54H GLU 3.3 0.2 - - - -
55H THR* 1.3 77.5 - - - +
57H CYS* 1.3 58.0 + - - +
59H VAL* 4.0 3.2 - - + +
60H ASP* 2.9 34.5 + - - +
65H VAL* 4.7 7.8 - - + +
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Residues in contact with CYS 57 (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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53H ILE* 2.9 20.4 + - + +
54H GLU* 4.0 5.6 - - - +
56H LEU* 1.3 75.1 - - - +
58H GLY* 1.3 63.1 + - - +
59H VAL 3.3 0.2 - - - -
60H ASP 2.9 20.2 - - - +
61H SER* 4.5 2.9 - - - -
62H SER 6.0 0.7 - - - +
65H VAL* 5.1 4.3 - - + -
66H SER* 5.2 16.2 - - - -
249H LYS* 5.6 15.2 - - + +
250H PHE* 6.0 2.5 - - + -
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Residues in contact with GLY 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H GLU 2.9 17.3 + - - -
55H THR* 3.6 2.9 + - - -
56H LEU 3.3 0.2 - - - -
57H CYS* 1.3 78.5 - - - +
59H VAL* 1.3 59.2 + - - +
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Residues in contact with VAL 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H ILE* 5.2 13.7 - - + -
10H PHE* 5.8 7.9 - - + -
55H THR 3.4 15.5 + - - +
56H LEU* 4.0 4.5 - - + +
57H CYS 3.3 0.4 - - - -
58H GLY* 1.3 79.2 - - - +
60H ASP* 1.3 62.9 + - + +
61H SER* 3.6 4.3 + - - -
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Residues in contact with ASP 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H PHE* 4.2 24.0 - - + -
22H SER* 5.7 1.6 - - - +
56H LEU* 2.9 18.4 + - + +
57H CYS* 2.9 24.0 - - - +
59H VAL* 1.3 72.4 - - - +
61H SER* 1.3 57.4 + - - +
62H SER* 3.3 10.1 + - - +
65H VAL* 3.8 23.9 - - + +
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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