Contacts of the helix formed by residues 39 - 56 (chain C) in PDB entry 1G2X
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 ASP 39 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C TYR* 2.4 32.9 + - - -
37C PRO* 3.4 1.3 - - - +
38C VAL* 1.3 85.7 - - - +
40C LYS* 1.3 59.3 + - - +
41C LEU* 3.9 7.4 - - - +
42C ASP* 2.9 24.1 + - - +
43C ARG* 2.9 41.9 + - - +
105C PRO* 4.4 1.9 - - + +
107C ASN* 2.8 23.8 + - - +
110C ASN* 3.6 5.9 + - - +
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Residues in contact with LYS 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASP* 1.3 74.9 - - - +
41C LEU* 1.3 58.9 + - - +
43C ARG* 2.9 30.6 - - + +
44C CYS* 2.8 33.5 + - - -
100C CYS* 5.3 4.0 - - - +
103C SER* 4.8 7.2 + - - +
104C ALA* 3.7 25.8 - - + +
105C PRO* 4.3 18.5 - - + +
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ARG* 5.0 1.1 - - - +
22C TYR* 3.5 35.0 - - + -
25C TYR* 3.7 31.2 - - + -
29C CYS* 4.7 2.0 - - - -
39C ASP* 3.3 3.2 + - - +
40C LYS* 1.3 78.9 - - - +
42C ASP* 1.3 58.9 + - - +
44C CYS* 2.8 30.1 + - - +
45C CYS* 3.1 6.1 + - - -
101C PHE* 3.4 44.9 - - + +
104C ALA* 3.8 6.3 - - + +
105C PRO 3.8 20.3 + - - +
106C TYR* 3.7 19.7 - - + -
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Residues in contact with ASP 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 3.8 4.4 - - + +
26C GLY* 3.8 6.8 - - - -
27C CYS* 2.8 27.8 + - - +
28C TYR* 2.7 28.1 + - - +
29C CYS* 3.6 11.7 + - - -
37C PRO* 3.3 10.3 - - - +
38C VAL* 3.1 26.5 + - + +
39C ASP* 2.9 23.1 + - - +
41C LEU* 1.3 76.8 - - - +
43C ARG* 1.3 57.8 + - - +
45C CYS* 3.4 1.8 + - - +
46C TYR* 2.9 26.7 + - - +
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Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PRO* 4.7 17.8 - - - +
76B ASN* 3.1 34.5 + - - +
37C PRO* 3.7 16.6 + - + +
38C VAL 4.7 1.8 + - - -
39C ASP* 2.9 32.5 + - - +
40C LYS* 2.9 40.4 - - - +
42C ASP* 1.3 75.1 - - - +
44C CYS* 1.3 63.1 + - - +
46C TYR* 3.0 6.4 + - + +
47C THR* 2.9 28.2 + - - +
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Residues in contact with CYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LYS* 2.8 24.8 + - - -
41C LEU* 2.8 18.3 + - - +
43C ARG* 1.3 76.9 - - - +
45C CYS* 1.3 59.9 + - - +
47C THR* 3.1 7.9 + - - -
48C HIS* 3.0 23.7 + - - +
97C ALA* 5.0 2.8 - - - +
100C CYS* 2.0 64.8 - - + -
101C PHE* 3.3 20.9 - - + -
104C ALA* 4.2 2.7 - - - -
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Residues in contact with CYS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C TYR* 5.0 1.8 - - - -
28C TYR* 3.6 4.0 - - - +
29C CYS* 2.0 65.3 - - - +
41C LEU* 3.1 6.3 + - - -
42C ASP 3.7 4.5 - - - +
44C CYS* 1.3 79.8 - - - +
46C TYR* 1.3 57.4 + - - +
48C HIS* 4.0 4.5 + - - +
49C ASP* 2.9 32.4 + - - +
101C PHE* 3.2 32.5 - - - -
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Residues in contact with TYR 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 4.6 4.9 - - - +
73B THR* 2.9 36.7 + - - -
76B ASN* 3.6 31.2 + - + +
77B ILE 5.2 1.6 - - - -
78B THR* 3.5 22.4 + - - -
28C TYR* 3.5 42.6 - + + +
37C PRO* 3.7 16.4 - - + -
42C ASP 2.9 14.3 + - - +
43C ARG* 3.1 10.5 - - + +
45C CYS* 1.3 77.8 - - - +
47C THR* 1.3 69.0 + - - +
49C ASP* 3.4 4.0 - - - +
50C HIS* 3.2 55.7 + + - -
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Residues in contact with THR 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 6.0 0.7 - - - -
95B ARG* 4.9 13.4 + - - +
43C ARG* 2.9 16.8 + - - +
44C CYS* 3.1 9.5 + - - -
46C TYR* 1.3 80.5 - - - +
48C HIS* 1.3 69.6 + - - +
50C HIS* 2.8 20.0 + - + +
51C CYS* 2.9 16.5 + - + +
96C THR* 4.9 17.5 - - + -
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Residues in contact with HIS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LEU* 5.9 0.4 - - + -
5C PHE* 3.6 22.5 - + - -
44C CYS 3.0 13.5 + - - +
45C CYS* 4.0 6.7 + - - +
47C THR* 1.3 80.5 - - - +
49C ASP* 1.3 64.3 + - - +
51C CYS* 3.1 8.7 + - - +
52C TYR* 3.0 57.0 + + - +
93C CYS* 3.5 23.8 - - + +
94C ASP* 2.6 29.5 + - - -
96C THR* 6.4 0.7 - - - -
97C ALA* 3.6 23.3 - - + -
101C PHE* 5.4 1.7 - - + -
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Residues in contact with ASP 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 4.2 25.3 - - + +
30C GLY 5.5 1.6 - - - -
32C GLY* 4.4 18.8 + - - +
33C GLY 4.7 0.5 + - - -
45C CYS 2.9 20.7 + - - +
46C TYR* 3.4 8.5 - - - +
47C THR 3.0 0.2 - - - -
48C HIS* 1.3 80.6 + - - +
50C HIS* 1.3 64.1 + - - +
52C TYR* 3.5 6.4 + - - +
53C ASN* 3.2 19.8 + - - +
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Residues in contact with HIS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 4.4 8.9 - - + +
78B THR* 3.6 32.6 + - + +
80B THR* 5.2 4.3 - - + -
28C TYR* 5.7 1.6 - + - -
46C TYR* 3.2 57.7 + + - -
47C THR* 2.8 14.0 + - - +
49C ASP* 1.3 76.6 - - - +
51C CYS* 1.3 59.2 + - - +
53C ASN* 3.2 17.4 - - + +
54C GLN* 2.7 46.6 + - - +
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Residues in contact with CYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 2.9 16.5 + - + +
48C HIS* 3.2 13.5 - - - +
50C HIS* 1.3 76.7 - - - +
52C TYR* 1.3 59.9 + - - +
54C GLN* 3.3 8.4 + - - +
55C ALA 2.9 22.7 + - - -
89C PHE* 3.2 22.2 - - - -
92C ASP* 5.0 5.4 - - - -
93C CYS* 2.0 54.5 - - + -
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Residues in contact with TYR 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LEU* 4.5 11.0 - - + +
5C PHE* 4.0 8.8 - - - +
48C HIS* 3.0 38.6 + + - +
49C ASP* 3.8 10.5 - - - +
51C CYS* 1.3 73.8 - - - +
53C ASN* 1.3 68.6 + - - +
55C ALA* 2.9 21.5 + - - +
56C ASP* 3.5 9.2 - - - +
63C PRO* 3.4 36.1 + - + +
64C ASN* 3.8 22.4 - - - -
90C LEU* 3.5 20.4 - - + -
93C CYS* 4.2 4.0 - - + -
94C ASP* 2.8 40.0 + - - -
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Residues in contact with ASN 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ASP 3.2 12.2 + - - +
50C HIS* 3.2 24.0 - - + +
52C TYR* 1.3 80.9 - - - +
54C GLN* 1.3 64.9 + - - +
56C ASP* 3.2 23.1 + - - +
57C SER* 4.3 1.6 + - - -
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Residues in contact with GLN 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B THR* 4.1 5.6 - - - +
79B CYS 2.8 28.8 + - - +
80B THR* 4.0 16.8 - - - +
81B ARG 4.7 4.8 + - - -
82B THR* 3.8 17.7 + - - +
50C HIS* 2.7 42.2 + - - +
51C CYS* 3.5 8.8 - - - +
53C ASN* 1.3 75.3 - - - +
55C ALA* 1.3 65.8 + - - +
57C SER* 2.8 26.5 + - - +
58C ILE* 4.1 3.6 + - - +
89C PHE* 3.8 17.8 - - + -
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Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C CYS 2.9 12.6 + - - +
52C TYR* 2.9 19.0 + - - +
54C GLN* 1.3 78.0 - - - +
56C ASP* 1.3 55.0 + - - +
58C ILE* 2.8 30.1 + - - +
61C CYS* 3.4 16.5 - - - +
63C PRO* 4.3 10.8 - - + -
89C PHE* 3.6 22.4 - - + -
90C LEU* 4.2 15.7 - - + -
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Residues in contact with ASP 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C TYR 3.5 11.8 - - - +
53C ASN* 3.2 15.1 + - - +
54C GLN 3.1 0.8 - - - -
55C ALA* 1.3 74.6 - - - +
57C SER* 1.3 59.0 + - - +
58C ILE 2.9 13.6 + - - +
61C CYS 3.8 11.4 - - - +
62C ASN* 5.7 0.2 - - - -
63C PRO* 3.5 19.0 - - - +
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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