Contacts of the helix formed by residues 54 - 70 (chain U) in PDB entry 3H1J
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 CYS 54 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Q PRO* 3.5 6.5 - - + +
139Q ALA* 2.6 46.3 + - - +
37U LEU* 3.8 9.8 - - + +
40U CYS* 2.0 47.6 - - + -
41U ASP* 3.3 5.4 - - - +
44U VAL* 3.4 7.4 - - - -
53U GLN* 1.3 73.0 - - - +
55U THR* 1.3 65.9 + - - +
57U GLU* 2.9 11.7 - - - +
58U LEU* 3.0 24.1 + - - +
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Residues in contact with THR 55 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1Q GLY 5.8 1.1 - - - +
3Q LEU* 3.4 21.5 - - + -
138Q PRO* 3.6 10.2 - - - +
141Q VAL* 3.4 24.6 - - - +
149Q TYR* 4.6 5.5 + - - +
156Q GLN* 5.1 6.5 - - + +
53U GLN* 3.5 13.6 + - - +
54U CYS* 1.3 75.3 - - - +
56U GLU* 1.3 65.3 + - - +
58U LEU* 2.9 5.9 + - - +
59U PHE* 2.8 58.3 + - + +
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Residues in contact with GLU 56 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Q LEU* 4.0 15.2 - - + +
70T LYS 4.8 0.7 - - - +
71T ARG* 3.1 40.3 + - - +
72T LYS* 2.8 55.8 + - + +
36U ARG* 4.6 6.0 + - - +
53U GLN 5.2 0.2 + - - -
54U CYS* 4.4 0.2 - - - +
55U THR* 1.3 79.9 - - - +
57U GLU* 1.3 67.7 + - - +
59U PHE* 3.2 6.1 + - - +
60U ASP* 2.9 43.0 + - - +
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Residues in contact with GLU 57 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72T LYS* 2.4 41.4 + - - -
33U ALA 4.8 0.9 - - - +
36U ARG* 3.5 37.1 + - - +
37U LEU* 3.4 25.9 - - + +
40U CYS* 3.7 18.1 - - + +
43U ARG* 4.6 1.4 + - - -
54U CYS* 2.9 26.9 - - - -
56U GLU* 1.3 73.4 + - - +
58U LEU* 1.3 61.1 + - - +
60U ASP* 3.3 8.4 + - - +
61U PHE* 2.8 30.5 + - - +
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Residues in contact with LEU 58 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135Q CYS* 4.6 5.2 - - - -
136Q ASP 4.1 6.7 - - - +
138Q PRO* 3.4 39.7 - - + -
149Q TYR* 3.9 19.3 - - + +
37U LEU* 3.5 22.1 - - + +
54U CYS 3.0 13.6 + - - +
55U THR 2.9 9.3 + - - +
57U GLU* 1.3 75.6 - - - +
59U PHE* 1.3 55.4 - - + +
61U PHE* 3.3 5.0 + - + +
62U LEU* 2.7 69.3 + - + +
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Residues in contact with PHE 59 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Q LEU* 3.8 28.0 - - + -
4Q GLU* 4.0 5.6 - - - -
5Q LEU* 3.9 33.0 - - + +
149Q TYR* 3.9 8.3 - - - -
151Q PRO* 3.4 38.1 - - + -
156Q GLN* 3.7 23.1 - - + -
55U THR* 2.8 38.1 + - + -
56U GLU* 3.4 8.7 - - - +
58U LEU* 1.3 76.2 - - + +
60U ASP* 1.3 59.5 + - - +
61U PHE 3.0 1.3 - - - -
62U LEU* 4.2 4.0 - - + -
63U HIS* 2.6 39.3 + - - +
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Residues in contact with ASP 60 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71T ARG* 2.6 46.9 + - - -
33U ALA* 4.3 7.2 - - + +
36U ARG* 3.6 20.5 + - - +
56U GLU* 2.9 31.1 + - - +
57U GLU 3.7 3.8 - - - +
59U PHE* 1.3 72.2 - - - +
61U PHE* 1.3 62.7 + - - +
63U HIS* 3.8 6.3 - - - +
64U ALA* 3.2 23.6 + - - +
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Residues in contact with PHE 61 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U GLU* 3.1 34.8 - - + -
30U CYS* 3.8 24.9 - - + -
33U ALA* 3.7 13.9 - - + +
34U ARG* 3.5 57.0 - - + -
37U LEU* 4.4 16.4 - - + -
57U GLU 2.8 17.9 + - - +
58U LEU* 3.4 9.6 - - + +
60U ASP* 1.3 75.5 - - - +
62U LEU* 1.3 64.9 + - + +
64U ALA* 3.1 4.0 + - - +
65U ARG* 2.8 55.4 + - + +
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Residues in contact with LEU 62 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q LEU* 3.9 15.3 - - + -
133Q GLY 6.1 0.2 - - - +
135Q CYS* 4.9 7.2 - - + -
151Q PRO* 3.7 35.2 - - + -
152Q TYR* 5.0 1.3 - - + -
58U LEU* 2.7 57.0 + - + +
59U PHE* 3.6 3.4 - - + +
61U PHE* 1.3 77.4 - - + +
63U HIS* 1.3 59.2 + - - +
65U ARG* 3.0 27.0 + - - +
66U ASP* 2.8 51.0 + - - +
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Residues in contact with HIS 63 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q LEU* 3.8 21.9 - - + +
6Q HIS* 4.7 12.3 + - + +
152Q TYR* 5.4 0.9 - - - -
59U PHE 2.6 22.9 + - - +
60U ASP* 3.8 7.2 - - - +
62U LEU* 1.3 73.1 - - - +
64U ALA* 1.3 60.7 + - - +
66U ASP* 5.3 1.3 - - - -
67U HIS* 3.0 46.6 + + + +
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Residues in contact with ALA 64 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U THR* 6.1 0.2 - - - +
29U LYS* 4.3 29.2 - - + -
30U CYS* 4.2 13.8 - - - +
33U ALA* 5.1 1.8 - - + -
60U ASP 3.2 14.5 + - - +
61U PHE* 3.1 4.8 + - - +
63U HIS* 1.3 80.9 + - - +
65U ARG* 1.3 70.2 + - - +
67U HIS* 3.7 4.7 - - - +
68U CYS* 3.3 17.2 + - - +
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Residues in contact with ARG 65 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Q GLY* 5.9 2.4 - - - -
21U ARG* 3.1 52.2 - - - +
24U CYS* 4.5 2.7 - - + -
25U GLU* 3.6 40.2 + - + -
30U CYS* 3.7 15.4 - - - -
34U ARG* 5.7 0.4 - - - +
61U PHE* 2.8 34.8 + - + +
62U LEU* 3.5 23.5 - - - +
64U ALA* 1.3 72.9 - - - +
66U ASP* 1.3 87.6 + - - +
68U CYS* 2.7 29.7 + - - +
69U VAL* 2.9 16.9 + - + +
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Residues in contact with ASP 66 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q PRO* 4.5 9.9 - - + -
10Q PHE* 6.1 1.1 - - + -
133Q GLY* 6.5 0.4 - - - -
152Q TYR* 3.0 33.1 + - - +
21U ARG* 4.2 6.2 + - - -
62U LEU* 2.8 34.7 + - - +
63U HIS* 4.7 0.7 - - - +
65U ARG* 1.3 104.1 + - - +
67U HIS* 1.3 56.2 + - - +
69U VAL* 3.3 13.9 - - + +
70U ALA* 2.7 36.8 + - - +
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Residues in contact with HIS 67 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q PRO* 4.2 17.0 - - + +
63U HIS* 3.0 39.2 + + + +
64U ALA* 3.7 6.5 - - - +
66U ASP* 1.3 76.5 - - - +
68U CYS* 1.3 66.3 + - - +
70U ALA* 3.5 3.8 + - - +
71U HIS* 3.2 46.8 + + - -
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Residues in contact with CYS 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23U HIS* 4.9 0.7 - - - -
24U CYS* 2.0 48.2 - - + +
27U THR* 4.3 13.9 - - + +
30U CYS* 5.4 1.6 - - - -
64U ALA 3.3 8.9 + - - +
65U ARG* 2.7 13.3 + - - +
67U HIS* 1.3 81.2 + - - +
69U VAL* 1.3 63.8 + - - +
71U HIS* 2.8 23.4 + - - +
72U LYS* 3.4 29.5 - - - +
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Residues in contact with VAL 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q PHE* 5.5 2.5 - - + -
17U LEU* 3.8 30.1 - - + +
20U ILE* 4.3 8.4 - - + +
21U ARG* 3.9 20.9 - - + -
24U CYS* 3.4 13.9 - - - -
65U ARG* 2.9 26.0 + - + +
66U ASP* 3.3 26.5 - - - +
68U CYS* 1.3 76.4 - - - +
70U ALA* 1.3 54.4 + - - +
71U HIS 2.8 11.3 + - - -
72U LYS* 3.2 1.7 + - - +
73U LEU* 2.9 41.4 + - + +
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Residues in contact with ALA 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q PRO* 3.7 17.5 - - + -
9Q ALA 4.3 5.9 - - - +
10Q PHE* 3.6 44.8 - - + +
11Q PRO* 3.9 21.8 - - - +
66U ASP 2.7 18.9 + - - +
67U HIS 3.8 4.3 - - - +
69U VAL* 1.3 71.7 - - - +
71U HIS* 1.3 58.3 + - - +
72U LYS 3.5 0.9 - - - -
73U LEU* 4.6 3.1 - - - -
74U PHE 5.7 0.8 + - - -
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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
------------------------------------------------------------
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