Contacts of the helix formed by residues 36 - 52 (chain H) in PDB entry 6AHU
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 36 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H LEU* 1.3 78.2 - - - +
37H ALA* 1.3 80.5 + - - +
38H ALA* 3.3 15.4 + - - +
39H GLN* 3.8 24.5 - - + +
40H PHE* 2.8 30.5 + - - +
66H TYR* 3.6 10.5 + - - -
68H GLU* 4.5 12.2 - - - +
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Residues in contact with ALA 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H ASN* 1.3 84.5 + - - +
38H ALA* 1.3 58.6 + - - +
40H PHE* 4.6 1.3 - - - +
41H LYS* 3.6 3.8 + - - +
63H ILE* 3.5 27.6 - - + +
66H TYR* 3.5 34.3 - - + -
68H GLU* 5.6 0.2 + - - -
260L PHE* 3.6 26.1 - - + +
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Residues in contact with ALA 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H ASN* 3.3 13.5 - - - +
37H ALA* 1.3 78.8 - - - +
39H GLN* 1.3 68.4 + - - +
40H PHE 3.4 0.2 - - - -
41H LYS* 3.6 4.9 + - - +
42H GLN* 3.5 17.3 + - - +
259L ASN* 3.8 26.7 - - + +
260L PHE* 3.6 31.7 - - + -
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Residues in contact with GLN 39 (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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34H GLY 5.4 4.0 - - - +
35H LEU* 4.7 6.1 - - + -
36H ASN* 3.3 32.9 + - + +
38H ALA* 1.3 82.3 - - + +
40H PHE* 1.3 62.0 + - - +
41H LYS 3.3 0.4 - - - -
42H GLN* 3.4 11.0 + - - +
43H LEU* 3.2 21.7 + - - +
95H TYR* 3.0 47.9 + - + -
259L ASN* 5.9 0.3 + - - -
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Residues in contact with PHE 40 (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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24H VAL* 3.7 22.4 - - + -
26H LEU* 3.7 36.1 - - + -
35H LEU* 4.6 9.6 - - + +
36H ASN 2.8 18.1 + - - +
37H ALA 4.2 4.5 - - - +
38H ALA 3.4 0.2 - - - -
39H GLN* 1.3 73.4 - - - +
41H LYS* 1.3 64.7 + - - +
43H LEU* 3.4 23.0 + - + +
44H LEU* 3.3 50.6 + - + +
63H ILE* 3.6 18.4 - - + -
66H TYR* 4.1 22.0 - + + +
73H ALA* 4.5 11.2 - - + -
75H LEU* 4.3 13.7 - - + -
102H PHE* 5.0 3.4 - + - -
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Residues in contact with LYS 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ALA 3.6 7.4 + - - +
38H ALA 3.8 7.9 - - - +
39H GLN 3.3 0.4 - - - -
40H PHE* 1.3 79.0 - - - +
42H GLN* 1.3 60.7 + - - +
44H LEU* 3.3 5.1 + - + +
45H ILE* 3.3 43.8 + - + +
61H LEU* 3.7 43.8 + - + +
62H ASP* 5.6 0.7 - - - -
63H ILE* 3.7 24.3 - - + +
259L ASN 3.4 27.9 + - - +
260L PHE* 4.6 3.4 - - - -
261L ILE* 4.1 21.8 + - - +
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Residues in contact with GLN 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ALA 3.5 10.4 + - - +
39H GLN* 3.4 16.5 + - - +
40H PHE 3.3 0.4 - - - -
41H LYS* 1.3 78.3 - - - +
43H LEU* 1.3 61.6 + - - +
45H ILE* 3.5 13.1 + - - +
46H SER* 3.3 32.1 + - - -
95H TYR* 4.6 19.1 - - + -
167I ARG* 4.8 14.7 + - - +
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Residues in contact with LEU 43 (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 LEU* 5.9 5.6 - - + -
28H PHE* 5.6 7.9 - - + -
35H LEU* 5.4 10.5 - - + -
39H GLN 3.2 12.8 + - - +
40H PHE* 3.7 29.8 - - + +
41H LYS 3.3 0.4 - - - -
42H GLN* 1.3 76.9 - - - +
44H LEU* 1.3 62.2 + - + +
46H SER* 4.3 3.6 - - - -
47H ALA* 3.4 23.9 + - - +
89H LEU* 4.5 16.8 - - + -
93H GLY 3.4 25.4 - - - +
94H SER* 4.6 2.0 - - - -
95H TYR* 4.2 31.8 - - + +
100H CYS* 6.4 1.8 - - - -
102H PHE* 6.4 0.9 - - + -
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Residues in contact with LEU 44 (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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40H PHE* 3.3 37.3 + - + +
41H LYS* 3.7 11.4 - - - +
42H GLN 3.2 0.6 - - - -
43H LEU* 1.3 79.6 - - + +
45H ILE* 1.3 63.9 + - - +
47H ALA* 3.6 3.2 + - - +
48H VAL* 3.3 29.1 + - - +
61H LEU* 3.8 27.7 - - + +
63H ILE* 4.5 2.9 - - + -
75H LEU* 3.7 39.9 - - + -
85H LEU* 4.8 5.2 - - + -
89H LEU* 3.8 34.3 - - + -
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Residues in contact with ILE 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H LYS* 3.3 42.5 + - + +
42H GLN* 3.5 13.9 + - - +
43H LEU 3.4 0.2 - - - -
44H LEU* 1.3 80.6 - - + +
46H SER* 1.3 58.1 + - - +
48H VAL 3.6 0.2 + - - -
49H LYS* 3.1 26.2 + - - +
57H ALA* 3.7 34.6 - - + +
58H ALA* 6.3 0.4 - - - -
61H LEU* 5.7 2.2 - - + -
167I ARG* 3.5 43.1 - - - +
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Residues in contact with SER 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H GLN* 3.3 23.7 + - - +
43H LEU* 4.6 3.8 - - - -
45H ILE* 1.3 78.9 - - - +
47H ALA* 1.3 59.0 + - - +
49H LYS* 3.7 12.7 + - - +
50H ASP* 3.0 33.1 + - - +
167I ARG* 5.9 0.7 - - - +
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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 LEU 3.4 18.9 + - - +
44H LEU 4.0 3.1 - - - +
45H ILE 3.2 1.0 - - - -
46H SER* 1.3 76.2 - - - +
48H VAL* 1.3 63.7 + - + +
50H ASP* 3.4 12.5 + - - +
51H LEU* 3.6 14.6 + - - +
88H SER* 3.6 21.2 - - - +
89H LEU* 3.8 25.6 - - + -
93H GLY* 4.5 17.9 + - - +
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Residues in contact with VAL 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LEU 3.3 18.0 + - - +
45H ILE 4.2 2.7 - - - +
47H ALA* 1.3 75.2 - - + +
49H LYS* 1.3 53.6 + - - +
52H PHE* 2.7 21.2 + - + -
53H GLY 2.6 28.5 + - - -
56H ASP* 3.3 43.1 - - + +
57H ALA* 4.3 4.0 - - - +
59H LEU* 5.4 2.7 - - + -
61H LEU* 5.6 6.1 - - + -
84H LYS* 4.5 7.9 - - + +
85H LEU* 4.3 20.0 - - + -
88H SER* 3.4 22.9 - - - +
89H LEU* 5.9 0.7 - - + -
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Residues in contact with LYS 49 (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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38E ALA 5.4 1.2 - - - +
39E ARG 5.4 4.9 - - - +
41E HIS 4.5 1.0 - - - +
42E GLY* 3.8 6.6 - - - -
45H ILE 3.1 18.0 + - - +
46H SER* 3.8 12.1 - - - +
48H VAL* 1.3 77.8 - - - +
50H ASP* 1.3 63.6 + - - +
53H GLY* 3.4 23.5 + - - +
54H GLU* 4.3 30.9 - - + +
57H ALA* 4.4 2.4 - - + +
167I ARG* 3.5 30.4 - - - +
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Residues in contact with ASP 50 (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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42E GLY* 4.0 0.6 - - - -
43E THR* 3.1 31.8 + - - +
46H SER* 3.0 23.1 + - - +
47H ALA* 3.4 10.6 + - - +
48H VAL 3.2 1.0 - - - -
49H LYS* 1.3 83.2 - - - +
51H LEU* 1.3 60.1 + - - +
93H GLY* 5.8 3.8 - - - -
163J SER* 6.4 1.6 - - - -
166J ARG* 3.6 24.6 + - - +
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Residues in contact with LEU 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E GLY* 3.3 6.5 + - - -
43E THR* 3.9 10.3 - - - +
44E PHE* 3.2 33.8 + - + +
47H ALA* 3.6 13.0 + - - +
48H VAL 3.3 1.4 + - - -
50H ASP* 1.3 80.4 - - - +
52H PHE* 1.3 65.8 + - + +
87H SER* 3.3 38.6 - - - +
88H SER* 3.7 24.5 - - - +
91H LEU* 3.8 20.6 - - + -
166J ARG* 3.4 32.1 - - - +
209J LEU* 5.0 6.5 - - + -
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Residues in contact with PHE 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E VAL 4.4 0.2 - - - +
41E HIS* 3.6 22.7 + - - -
42E GLY 3.4 6.5 - - - +
44E PHE* 4.5 23.1 - + + -
48H VAL* 2.7 14.9 + - + +
51H LEU* 1.3 79.7 - - + +
53H GLY* 1.3 58.0 + - - +
55H VAL* 5.1 0.7 + - - +
56H ASP* 3.4 36.6 + - + +
83H VAL* 5.0 2.0 - - + -
84H LYS* 3.5 51.1 - - + -
87H SER* 3.7 20.4 - - - -
88H SER* 3.2 20.4 - - - -
209J LEU* 3.9 21.1 - - + -
7L LEU* 4.9 14.6 - - + -
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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