Contacts of the helix formed by residues 49 - 67 (chain I) in PDB entry 1G3I
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 GLY 49 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I GLY* 1.3 71.0 - - - -
50I THR* 1.3 55.1 + - - -
51I ALA* 2.5 19.8 + - - -
52I ASP* 4.0 6.5 - - - -
53I ALA* 2.6 26.7 + - - +
92I GLU* 3.2 16.0 + - - -
93I ALA* 4.3 2.8 - - - +
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Residues in contact with THR 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B LEU* 3.7 33.7 - - + +
109H ILE* 4.2 8.1 - - - +
111H ASP* 2.6 30.7 + - - +
20I VAL* 3.7 23.3 - - + -
21I SER 5.7 1.6 - - - +
27I MET* 6.2 1.8 - - - -
46I PHE* 6.3 0.2 - - - -
48I GLY 3.5 4.9 + - - +
49I GLY* 1.3 69.2 - - - -
51I ALA* 1.3 54.6 + - - -
53I ALA* 4.2 3.6 - - - -
54I PHE* 3.2 30.0 - - - -
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Residues in contact with ALA 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ARG* 5.3 0.9 - - - +
109H ILE* 3.9 33.9 - - + +
110H GLY 4.2 8.5 - - - +
111H ASP* 3.9 17.9 - - - +
49I GLY 2.5 5.0 + - - -
50I THR* 1.3 74.6 + - - +
52I ASP* 1.3 60.8 - - - +
53I ALA 2.6 4.1 + - - -
54I PHE* 2.6 33.0 + - - +
55I THR* 3.0 16.1 + - + +
89I ARG* 5.9 0.2 - - - +
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Residues in contact with ASP 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H ILE 5.7 0.2 - - - +
49I GLY* 3.2 7.0 + - - +
51I ALA* 1.3 83.2 - - - +
53I ALA* 1.3 64.6 + - - +
55I THR* 3.1 11.1 + - - +
56I LEU* 2.8 23.6 + - - +
89I ARG* 3.6 16.8 + - - -
90I LYS 4.1 2.4 - - - +
91I LEU* 3.1 23.9 - - + +
92I GLU* 2.9 44.8 + - + +
93I ALA* 3.9 2.5 - - - +
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Residues in contact with ALA 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I PHE* 3.6 34.9 - - + +
48I GLY 4.7 5.6 - - - +
49I GLY 2.6 28.1 + - - +
50I THR* 4.1 6.5 - - - +
51I ALA 2.6 1.4 + - - -
52I ASP* 1.3 74.1 - - - +
54I PHE* 1.3 66.3 + - + +
56I LEU* 2.9 2.5 + - - +
57I PHE* 2.8 22.6 + - - +
93I ALA* 3.6 18.5 - - + +
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Residues in contact with PHE 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ARG 4.2 3.6 - - - -
442B PHE* 3.5 27.1 - - - -
443B ILE 3.5 19.7 - - - -
444B LEU* 3.7 21.8 - - + -
83H ARG* 3.0 36.6 - - - +
111H ASP* 6.3 0.4 - - + -
35I ARG* 3.9 10.1 - - - -
46I PHE* 3.3 39.5 - + - -
50I THR 3.2 19.7 - - - +
51I ALA 2.6 11.5 + - - +
53I ALA* 1.3 77.2 - - + +
55I THR* 1.3 54.7 + - - +
56I LEU 3.0 0.3 + - - -
57I PHE* 3.0 11.1 + + - -
58I GLU* 2.5 43.1 + - - +
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Residues in contact with THR 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ARG* 3.2 37.7 - - + +
84H THR 4.7 2.6 + - - -
51I ALA* 3.0 8.7 + - + +
52I ASP* 3.1 28.9 - - - +
54I PHE* 1.3 74.2 - - - +
56I LEU* 1.3 61.4 + - - +
58I GLU* 3.9 3.5 - - - +
59I LEU* 3.0 35.4 + - - +
89I ARG* 3.4 18.4 + - - +
91I LEU* 3.3 23.0 - - - +
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Residues in contact with LEU 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I ASP 2.8 16.1 + - - +
53I ALA* 3.3 8.3 - - - +
55I THR* 1.3 72.9 + - - +
57I PHE* 1.3 66.6 + - - +
59I LEU* 2.8 17.6 + - + +
60I PHE* 3.1 10.2 + - - +
78I LEU* 4.1 12.8 - - + -
82I TRP* 4.0 26.7 - - + -
91I LEU* 4.5 8.1 - - + -
93I ALA* 3.7 31.2 - - + +
94I MET* 4.0 1.1 - - - +
95I LEU* 3.6 29.8 - - + -
106I ILE* 4.0 17.0 - - + +
107I THR 4.3 0.7 - - - -
108I GLY* 4.1 10.8 - - - +
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Residues in contact with PHE 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ARG* 4.4 21.8 - - + -
35I ARG* 4.1 25.1 - - + -
37I LEU* 3.2 33.9 - - + +
44I ALA* 3.5 35.7 - - + -
46I PHE* 3.6 30.5 - + + -
53I ALA 2.8 15.0 + - - +
54I PHE* 3.4 10.8 - + + +
56I LEU* 1.3 77.1 - - - +
58I GLU* 1.3 73.7 + - + +
60I PHE* 3.4 4.3 + - - +
61I GLU* 3.3 20.3 + - - +
95I LEU* 3.4 24.3 - - + +
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Residues in contact with GLU 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ARG 4.3 1.6 - - - +
442B PHE* 3.7 28.7 - - + -
80H LYS* 5.6 3.6 - - - +
83H ARG* 2.7 57.9 + - - +
54I PHE* 2.5 24.0 + - - +
55I THR* 3.9 4.9 - - - +
57I PHE* 1.3 87.2 - - + +
59I LEU* 1.3 62.5 + - + +
61I GLU* 3.5 12.7 + - - +
62I ARG* 3.4 17.3 + - - +
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Residues in contact with LEU 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ARG 4.7 11.7 - - - +
84H THR* 4.9 14.4 - - + -
85H ASP* 5.5 5.6 - - - +
55I THR* 3.0 29.3 + - - +
56I LEU* 2.8 15.3 + - - +
58I GLU* 1.3 71.2 - - + +
60I PHE* 1.3 64.3 + - - +
61I GLU 3.0 2.4 + - - -
62I ARG* 3.1 9.3 + - - +
63I LYS* 3.0 23.0 + - - +
78I LEU* 4.2 19.3 - - + -
81I ASP* 6.2 0.2 - - - +
82I TRP* 4.7 7.2 - - + -
88I LEU* 3.8 35.7 - - + -
91I LEU* 4.9 4.7 - - + -
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Residues in contact with PHE 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I LEU* 3.9 17.9 - - + -
42I VAL* 5.5 1.1 - - + -
56I LEU 3.1 6.4 + - - +
57I PHE 3.7 7.2 - - - +
59I LEU* 1.3 80.0 - - - +
61I GLU* 1.3 56.3 + - - +
63I LYS* 3.3 4.8 - - - +
64I LEU* 2.9 48.2 + - + +
71I LEU* 3.6 27.4 - - + -
74I SER* 4.2 6.1 - - - -
75I ALA* 3.8 25.1 - - + -
78I LEU* 3.6 21.9 - - + +
95I LEU* 4.0 11.4 - - + -
97I VAL* 3.3 29.2 - - + -
106I ILE* 3.3 29.8 - - + -
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Residues in contact with GLU 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ARG* 4.2 23.2 + - - +
442B PHE* 5.8 4.0 - - - -
37I LEU* 3.5 32.5 - - + +
38I TYR 4.1 12.1 + - - +
57I PHE* 3.3 12.1 + - + +
58I GLU* 3.6 17.0 - - - +
59I LEU 3.0 0.6 - - - -
60I PHE* 1.3 75.8 - - - +
62I ARG* 1.3 71.2 + - - +
63I LYS 2.8 1.3 - - - -
64I LEU* 2.8 11.7 + - + +
65I GLU* 2.7 42.6 + - + +
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Residues in contact with ARG 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C VAL* 5.3 12.9 - - + +
58I GLU 3.4 8.8 + - - +
59I LEU* 3.1 12.2 + - - +
61I GLU* 1.3 78.1 - - - +
63I LYS* 1.3 67.1 + - + +
65I GLU* 3.4 9.7 + - - +
66I MET* 2.9 32.1 + - - +
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Residues in contact with LYS 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I LEU 3.0 13.1 + - - +
60I PHE* 3.3 13.0 - - - +
61I GLU 2.8 1.0 + - - -
62I ARG* 1.3 77.1 - - + +
64I LEU* 1.3 67.3 + - - +
66I MET* 2.7 29.0 + - - +
67I HIS* 3.0 23.6 + - + +
74I SER* 3.4 31.1 + - - +
77I GLU* 3.9 38.9 + - + -
78I LEU* 3.9 14.4 - - + +
81I ASP* 3.2 24.5 + - - -
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Residues in contact with LEU 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I LEU* 3.9 11.4 - - + -
38I TYR* 4.3 14.4 - - + +
42I VAL* 3.6 30.3 - - + -
60I PHE* 2.9 45.6 + - + +
61I GLU* 2.8 11.2 + - + +
63I LYS* 1.3 72.6 - - - +
65I GLU* 1.3 64.2 + - + +
67I HIS 3.1 2.9 + - - -
68I GLN 3.7 0.2 + - - -
69I GLY* 3.1 48.3 + - - +
71I LEU* 4.1 14.8 - - + -
74I SER* 3.2 22.6 + - - +
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Residues in contact with GLU 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLN* 3.9 45.0 - - + +
313C VAL* 5.4 4.3 - - + -
38I TYR* 3.4 33.6 - - - -
39I ASN* 5.3 0.7 + - - -
61I GLU* 2.7 42.0 + - + +
62I ARG* 3.5 9.2 - - - +
64I LEU* 1.3 75.6 - - + +
66I MET* 1.3 60.4 + - + +
67I HIS 3.5 0.5 + - - -
68I GLN* 4.2 4.9 + - - -
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Residues in contact with MET 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C LYS* 6.4 0.2 - - - -
312C GLN* 3.9 23.7 + - - +
313C VAL* 5.1 15.7 - - + -
389C GLU* 5.6 1.4 - - - +
62I ARG* 2.9 21.1 + - - +
63I LYS* 2.7 31.4 + - - +
65I GLU* 1.3 73.0 - - - +
67I HIS* 1.3 80.4 + - + +
68I GLN* 3.8 2.6 + - - +
77I GLU* 5.9 0.7 - - - +
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Residues in contact with HIS 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I LYS* 3.0 20.9 + - + +
64I LEU 3.1 1.0 + - - -
66I MET* 1.3 106.9 - - + +
68I GLN* 1.3 64.3 + - - +
69I GLY 2.6 17.9 + - - -
70I HIS* 2.9 19.2 + - + +
73I LYS* 3.4 38.0 + - + -
74I SER* 3.9 16.0 + - - +
77I GLU* 3.8 30.8 + - + +
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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