Contacts of the helix formed by residues 84 - 104 (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 84 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LYS* 2.7 22.3 + - - -
81C ARG* 3.4 24.0 + - - +
82C THR 3.5 1.6 - - - +
83C ALA* 1.3 75.0 - - - +
85C ALA* 1.3 51.4 + - - +
86C CYS* 3.2 11.1 + - - +
87C ALA* 2.6 41.3 + - + +
88C LYS* 2.8 34.3 + - - +
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Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 4.4 11.1 - - + +
82C THR 5.0 1.3 - - - -
83C ALA 3.2 7.5 + - - +
84C ASP* 1.3 72.4 - - - +
86C CYS* 1.3 57.2 + - - +
88C LYS* 3.6 11.4 - - + +
89C PHE* 2.8 31.4 + - - +
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Residues in contact with CYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 3.9 16.2 - - + +
59C PRO 4.6 4.7 - - - +
60C GLY 4.2 1.3 - - - +
61C CYS* 2.0 57.1 - - + -
66C LYS* 3.2 34.1 - - - -
84C ASP* 3.2 7.4 + - - +
85C ALA* 1.3 74.7 - - - +
87C ALA* 1.3 66.1 + - - +
89C PHE* 3.4 1.6 + - - +
90C LEU* 2.9 27.9 + - - +
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Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LYS* 4.0 13.5 - - - +
68C TYR* 3.7 18.1 - - + +
81C ARG* 3.4 28.0 - - + +
84C ASP* 2.6 34.0 + - - +
86C CYS* 1.3 73.6 - - - +
88C LYS* 1.3 63.7 + - - +
90C LEU* 3.9 1.7 - - - +
91C CYS* 2.9 27.5 + - - +
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN* 6.1 1.3 - - - -
89A PHE* 4.7 20.6 - - - -
79C CYS* 5.2 4.6 - - + +
81C ARG* 3.5 28.4 - - - +
82C THR* 3.9 25.6 + - - +
84C ASP 2.8 16.8 + - - +
85C ALA* 3.6 9.6 - - + +
87C ALA* 1.3 78.5 - - - +
89C PHE* 1.3 62.7 + - - +
91C CYS* 3.9 3.5 - - - +
92C ASP* 3.1 25.3 + - + +
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 5.2 7.4 - - + -
88B LYS* 5.1 16.4 - - - -
51C CYS* 3.2 38.8 - - - -
54C GLN* 3.8 23.3 - - + -
55C ALA* 3.6 19.5 - - + -
58C ILE* 3.6 25.4 - - + -
61C CYS* 5.5 0.7 - - - -
85C ALA 2.8 21.8 + - - +
86C CYS 3.7 2.2 - - - +
88C LYS* 1.3 73.7 - - - +
90C LEU* 1.3 61.1 + - - +
92C ASP* 3.3 9.4 + - + +
93C CYS* 3.1 39.6 + - - -
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Residues in contact with LEU 90 (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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1C ASN 4.3 9.9 - - - +
52C TYR* 3.5 35.7 - - + -
55C ALA* 4.2 12.3 - - + -
61C CYS* 4.5 6.7 - - - -
62C ASN 3.7 1.3 - - - +
63C PRO* 3.4 34.3 - - + +
66C LYS* 3.3 35.4 - - + -
68C TYR* 4.1 7.0 - - + -
86C CYS 2.9 14.7 + - - +
87C ALA* 3.9 3.1 - - - +
89C PHE* 1.3 77.6 - - + +
91C CYS* 1.3 64.3 + - - +
93C CYS* 3.2 8.1 + - - +
94C ASP* 3.2 26.6 + - - +
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Residues in contact with CYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C MET* 3.4 18.6 - - - +
68C TYR* 3.5 31.5 - - + -
69C SER 4.1 2.0 - - - +
70C TYR* 3.8 4.0 - - - -
79C CYS* 2.0 60.9 - - + -
81C ARG* 5.9 1.3 - - + -
87C ALA 2.9 18.4 + - - +
88C LYS* 3.9 3.1 - - - +
90C LEU* 1.3 76.2 - - - +
92C ASP* 1.3 58.5 + - - +
94C ASP* 3.4 2.4 + - - +
95C ARG 2.8 25.3 + - - -
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Residues in contact with ASP 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C CYS* 5.0 4.7 - - - -
79C CYS* 3.8 8.2 - - + -
88C LYS* 3.1 19.3 + - + +
89C PHE* 3.4 8.2 - - - +
90C LEU 3.2 0.2 - - - -
91C CYS* 1.3 74.0 - - - +
93C CYS* 1.3 64.1 + - - +
95C ARG* 3.8 8.9 + - - +
96C THR* 2.7 43.4 + - - -
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Residues in contact with CYS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C HIS* 3.5 15.5 - - + +
51C CYS* 2.0 59.5 - - + -
52C TYR* 4.2 4.9 - - + -
89C PHE* 3.1 41.2 + - - -
90C LEU* 3.4 12.6 - - - +
92C ASP* 1.3 77.3 + - - +
94C ASP* 1.3 64.2 + - - +
96C THR* 3.3 6.6 - - - +
97C ALA 3.0 23.2 + - - -
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Residues in contact with ASP 94 (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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1C ASN 3.8 5.0 + - - +
5C PHE* 3.2 33.2 - - + +
8C MET* 3.6 7.8 - - - +
48C HIS* 2.6 30.0 + - - -
52C TYR* 2.8 24.0 + - - -
68C TYR* 2.9 31.0 + - - +
90C LEU* 3.2 11.9 + - - +
91C CYS 3.8 0.7 - - - +
93C CYS* 1.3 75.1 - - - +
95C ARG* 1.3 59.7 + - - +
98C ALA* 2.9 31.7 + - - +
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Residues in contact with ARG 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 4.9 13.7 + - - +
8C MET* 3.4 10.0 - - - -
77C ILE* 2.7 45.6 + - + +
78C THR* 4.7 0.8 - - - +
79C CYS* 4.0 20.2 - - - +
91C CYS 2.8 21.0 + - - +
92C ASP* 3.8 10.6 + - - +
94C ASP* 1.3 73.0 - - - +
96C THR* 1.3 66.5 + - - +
98C ALA* 3.7 2.0 - - - +
99C ILE* 2.9 57.5 + - + +
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Residues in contact with THR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 4.9 18.2 - - + -
48C HIS* 6.2 1.1 - - - +
92C ASP* 2.7 37.7 + - - -
93C CYS* 3.3 7.0 - - - +
95C ARG* 1.3 81.4 + - - +
97C ALA* 1.3 59.5 + - - +
99C ILE* 3.8 5.4 - - - +
100C CYS* 2.8 37.1 + - + +
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Residues in contact with ALA 97 (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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5C PHE* 3.5 29.6 - - + -
44C CYS 5.0 2.7 - - - +
48C HIS* 3.6 29.2 - - + -
93C CYS 3.0 6.8 + - - +
95C ARG 3.3 0.2 - - - -
96C THR* 1.3 77.4 - - - +
98C ALA* 1.3 54.2 + - - +
100C CYS* 3.0 6.3 + - - -
101C PHE* 2.6 51.6 + - + -
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Residues in contact with ALA 98 (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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5C PHE* 4.0 1.0 - - + -
8C MET* 3.5 37.0 - - + +
9C ILE* 3.9 15.2 - - + +
12C ALA* 4.0 4.3 - - + +
13C GLY 5.1 0.5 + - - -
77C ILE* 3.8 10.3 - - + -
94C ASP 2.9 21.3 + - - +
95C ARG 3.7 2.9 - - - +
97C ALA* 1.3 72.7 - - - +
99C ILE* 1.3 63.6 + - - +
101C PHE* 3.3 8.3 + - - +
102C ALA* 3.1 21.7 + - - +
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Residues in contact with ILE 99 (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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12C ALA* 4.3 16.4 - - + -
77C ILE* 4.9 5.8 - - + +
95C ARG* 2.9 64.9 + - + +
96C THR* 3.8 5.4 - - - +
98C ALA* 1.3 70.6 - - - +
100C CYS* 1.3 66.6 + - - +
102C ALA* 3.1 5.2 + - - +
103C SER* 3.1 30.4 + - - +
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Residues in contact with CYS 100 (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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40C LYS* 5.3 5.4 - - - -
44C CYS* 2.0 51.7 - - + -
47C THR* 6.4 0.2 - - - -
96C THR* 2.8 27.2 + - + +
97C ALA* 3.4 6.1 - - - +
99C ILE* 1.3 73.6 - - - +
101C PHE* 1.3 62.3 + - - +
103C SER* 3.4 4.6 + - - +
104C ALA* 3.0 27.5 + - - +
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Residues in contact with PHE 101 (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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5C PHE* 3.9 21.5 - + - -
9C ILE* 4.3 19.1 - - + -
17C ARG* 3.2 23.6 + - - -
22C TYR* 3.4 43.1 + + + +
41C LEU* 3.4 17.0 - - + +
44C CYS* 3.3 30.5 - - + -
45C CYS* 3.2 37.0 - - - -
48C HIS* 5.4 1.6 - - + -
97C ALA* 2.6 34.0 + - + +
98C ALA* 3.4 5.8 - - - +
100C CYS* 1.3 74.9 - - - +
102C ALA* 1.3 58.6 + - - +
104C ALA 3.6 5.2 + - - +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 3.4 27.8 - - + +
13C GLY* 3.8 13.7 - - - -
17C ARG* 4.6 4.4 + - - +
22C TYR* 5.1 1.3 - - - -
98C ALA 3.1 12.4 + - - +
99C ILE* 3.1 8.9 + - + +
101C PHE* 1.3 77.8 - - - +
103C SER* 1.3 63.4 + - - +
104C ALA 3.5 4.7 + - - +
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Residues in contact with SER 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LYS* 4.8 7.4 + - - -
99C ILE* 3.1 23.5 + - - +
100C CYS* 4.2 3.8 - - - -
102C ALA* 1.3 77.1 - - - +
104C ALA* 1.3 63.1 + - - +
105C PRO* 3.9 4.0 - - - +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ARG* 3.3 19.9 + - - -
40C LYS* 3.7 20.1 - - + +
41C LEU* 3.8 29.4 - - + +
44C CYS* 4.2 1.1 - - - -
100C CYS 3.0 18.1 + - - +
101C PHE 3.6 3.9 - - - +
102C ALA 3.3 3.5 - - - +
103C SER* 1.3 79.6 - - - +
105C PRO* 1.3 73.0 - - + +
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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