Contacts of the helix formed by residues 49 - 67 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G GLY* 1.3 70.5 - - - -
50G THR* 1.3 62.4 + - - -
51G ALA* 2.7 4.9 + - - -
52G ASP* 3.1 7.0 + - - -
53G ALA* 2.5 33.6 + - - +
92G GLU* 2.9 20.9 + - - +
93G ALA* 4.3 0.8 - - - +
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Residues in contact with THR 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444F LEU* 3.7 23.2 - - + +
20G VAL* 3.6 31.0 - - + -
21G SER 5.8 1.1 - - - +
22G LEU* 6.5 0.7 - - + -
27G MET* 6.2 1.6 - - - -
46G PHE* 6.4 0.2 - - - -
48G GLY 3.3 5.5 + - - +
49G GLY* 1.3 69.3 - - - +
51G ALA* 1.3 61.9 + - - +
53G ALA* 3.7 3.8 - - - +
54G PHE* 3.2 26.0 + - - -
109L ILE* 4.1 9.0 - - - +
111L ASP* 2.5 28.8 + - - +
113L VAL* 6.1 3.4 - - + -
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Residues in contact with ALA 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLY 2.7 4.6 + - - -
50G THR* 1.3 75.5 + - - +
52G ASP* 1.3 61.6 + - - +
53G ALA 2.7 3.8 + - - -
54G PHE* 2.6 30.1 + - - +
55G THR* 2.9 18.2 + - + +
83L ARG* 4.8 2.0 - - - +
109L ILE* 4.0 34.5 - - + +
110L GLY 4.1 9.4 - - - +
111L ASP* 3.5 16.4 + - - +
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Residues in contact with ASP 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLY* 3.1 6.5 + - - +
51G ALA* 1.3 84.4 - - - +
53G ALA* 1.3 65.8 + - - +
55G THR* 3.2 11.5 + - - +
56G LEU* 2.8 22.7 + - - +
89G ARG* 4.5 10.3 + - - -
90G LYS 3.7 4.3 - - - +
91G LEU* 3.1 20.2 - - - +
92G GLU* 2.7 47.7 + - + +
93G ALA* 4.0 2.9 - - - +
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Residues in contact with ALA 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G PHE* 3.6 34.8 - - + +
48G GLY 4.7 5.4 - - - +
49G GLY 2.5 27.9 + - - +
50G THR* 3.7 7.6 - - - +
51G ALA 2.7 1.4 + - - -
52G ASP* 1.3 77.1 - - - +
54G PHE* 1.3 65.1 + - + +
56G LEU* 2.9 9.0 + - - +
57G PHE* 2.9 15.6 + - - +
93G ALA* 3.6 17.4 - - + +
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Residues in contact with PHE 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441F ARG 3.9 4.9 - - - -
442F PHE 3.5 23.3 - - - -
443F ILE 3.9 2.7 - - - -
444F LEU* 3.5 35.7 - - + -
35G ARG* 3.9 23.6 - - - -
46G PHE* 3.4 33.4 - + - -
50G THR 3.2 16.8 - - - +
51G ALA 2.6 11.0 + - - +
53G ALA* 1.3 75.7 - - + +
55G THR* 1.3 66.1 + - - +
56G LEU 2.7 0.9 + - - -
57G PHE* 2.9 12.3 + + - -
58G GLU* 2.7 39.1 + - - +
83L ARG* 3.3 32.8 - - - +
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Residues in contact with THR 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ALA* 2.9 23.9 + - + +
52G ASP* 3.2 16.6 - - - +
54G PHE* 1.3 72.0 - - - +
56G LEU* 1.3 57.6 + - - +
58G GLU* 4.0 3.0 - - - +
59G LEU* 3.0 33.1 + - - +
89G ARG* 3.7 17.1 + - - +
91G LEU* 3.1 20.8 - - - +
82L TRP 5.2 0.7 - - - +
83L ARG* 3.6 46.7 + - + +
84L THR 5.2 0.9 + - - -
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Residues in contact with LEU 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G ASP 2.8 14.0 + - - +
53G ALA* 3.3 8.3 - - - +
54G PHE 2.7 3.6 + - - -
55G THR* 1.3 72.2 + - - +
57G PHE* 1.3 57.4 + - - +
59G LEU* 2.8 25.5 + - + +
60G PHE* 3.1 6.8 + - - +
78G LEU* 4.2 19.3 - - + -
82G TRP* 4.5 12.1 - - + -
91G LEU* 3.8 17.0 - - + -
93G ALA* 3.7 30.3 - - + +
94G MET 4.1 0.7 - - - -
95G LEU* 3.4 30.7 - - + -
106G ILE* 4.1 16.6 - - + +
107G THR 4.5 0.7 - - - -
108G GLY* 4.4 11.2 - - - +
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Residues in contact with PHE 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441F ARG* 4.5 24.7 - - + -
35G ARG* 4.3 25.4 - - + -
37G LEU* 3.2 37.1 - - + +
44G ALA* 3.5 29.8 - - + -
46G PHE* 4.0 23.8 - + + -
53G ALA 2.9 8.9 + - - +
54G PHE* 3.5 14.8 - + - +
56G LEU* 1.3 79.5 - - - +
58G GLU* 1.3 76.2 + - + +
60G PHE* 3.5 3.8 + - - +
61G GLU* 3.4 20.4 + - - +
95G LEU* 3.3 23.3 - - + +
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Residues in contact with GLU 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441F ARG* 4.7 3.3 - - + +
442F PHE* 3.9 25.6 - - + -
54G PHE* 2.7 27.1 + - - +
55G THR* 4.0 4.3 - - - +
57G PHE* 1.3 85.6 - - + +
59G LEU* 1.3 67.1 + - + +
61G GLU* 3.5 12.9 + - - +
62G ARG* 3.4 18.4 + - - +
80L LYS* 5.6 3.5 - - - +
83L ARG* 2.7 55.3 + - - +
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Residues in contact with LEU 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G THR* 3.0 23.3 - - - +
56G LEU* 2.8 9.7 + - - +
58G GLU* 1.3 77.0 - - + +
60G PHE* 1.3 66.7 + - - +
61G GLU 3.0 3.2 + - - -
62G ARG* 3.3 8.3 + - + +
63G LYS* 3.2 24.6 + - - +
78G LEU* 4.2 22.7 - - + -
82G TRP* 4.8 1.8 - - + -
88G LEU* 3.8 33.4 - - + -
91G LEU* 4.7 9.0 - - + -
83L ARG 4.1 16.2 - - - +
84L THR* 5.1 1.1 - - - -
85L ASP* 4.9 17.7 - - + +
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Residues in contact with PHE 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G LEU* 4.0 14.1 - - + -
42G VAL* 5.5 1.3 - - + -
56G LEU 3.1 7.0 + - - +
57G PHE 3.8 7.0 - - - +
58G GLU 3.4 0.2 - - - -
59G LEU* 1.3 79.2 - - - +
61G GLU* 1.3 57.4 + - - +
63G LYS* 3.5 3.6 - - + +
64G LEU* 3.1 46.8 + - + +
71G LEU* 3.6 26.5 - - + -
74G SER* 4.0 7.2 - - - -
75G ALA* 3.7 25.4 - - + -
78G LEU* 3.5 21.5 - - + +
95G LEU* 4.1 10.8 - - + -
97G VAL* 3.2 32.1 - - + -
106G ILE* 3.5 25.8 - - + -
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Residues in contact with GLU 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441F ARG* 3.5 24.7 + - - +
442F PHE* 6.1 1.9 - - - -
37G LEU* 3.4 31.3 - - + +
38G TYR 4.2 7.9 + - - +
57G PHE* 3.4 11.8 + - - +
58G GLU* 3.6 16.8 - - - +
59G LEU 3.0 0.4 - - - -
60G PHE* 1.3 76.9 - - - +
62G ARG* 1.3 70.5 + - - +
63G LYS 2.8 1.1 - - - -
64G LEU* 2.5 25.5 + - + +
65G GLU* 2.7 32.4 + - + +
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Residues in contact with ARG 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A VAL* 4.9 11.0 - - + +
58G GLU 3.4 9.9 + - - +
59G LEU* 3.3 11.6 + - - +
61G GLU* 1.3 80.7 - - - +
63G LYS* 1.3 58.8 - - + +
65G GLU* 3.3 10.6 + - - +
66G MET* 2.9 40.7 + - - +
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Residues in contact with LYS 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G LEU 3.2 11.7 + - - +
60G PHE* 3.5 12.8 - - - +
61G GLU 2.6 4.0 + - - -
62G ARG* 1.3 76.7 - - + +
64G LEU* 1.3 65.6 + - - +
66G MET* 3.0 19.1 + - + +
67G HIS* 3.0 34.0 + - + +
74G SER* 3.6 29.9 + - - +
77G GLU* 3.8 22.3 + - + -
78G LEU* 3.7 31.6 - - + +
81G ASP* 3.1 28.1 + - - -
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Residues in contact with LEU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G LEU* 4.0 12.1 - - + -
38G TYR* 4.2 13.3 - - + -
42G VAL* 3.5 33.7 - - + -
60G PHE* 3.1 45.4 + - + +
61G GLU* 2.5 15.3 + - + +
63G LYS* 1.3 72.0 - - - +
65G GLU* 1.3 63.2 + - - +
67G HIS 3.0 11.8 + - - -
69G GLY* 3.1 41.6 + - - +
71G LEU* 4.1 11.4 - - + -
74G SER* 3.3 23.1 + - - +
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Residues in contact with GLU 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLN* 3.8 45.4 - - - +
313A VAL* 5.2 3.1 - - + -
38G TYR* 3.3 34.4 - - - -
39G ASN* 5.1 1.4 + - - -
61G GLU* 2.7 40.6 + - + +
62G ARG* 3.3 13.0 - - - +
64G LEU* 1.3 73.8 - - + +
66G MET* 1.3 59.9 + - - +
67G HIS 3.5 0.2 + - - -
68G GLN* 4.3 4.5 + - - -
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Residues in contact with MET 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LYS* 6.1 2.0 - - - -
312A GLN* 3.9 26.6 + - - +
313A VAL* 4.6 18.4 - - + -
62G ARG* 2.9 27.4 + - - +
63G LYS* 3.0 22.8 + - + +
65G GLU* 1.3 78.5 - - - +
67G HIS* 1.3 81.4 + - + +
68G GLN* 3.9 1.5 + - - +
77G GLU* 6.1 0.2 - - - +
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Residues in contact with HIS 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G LYS* 3.0 28.0 + - + +
64G LEU 3.0 5.3 + - - -
66G MET* 1.3 103.9 + - + +
68G GLN* 1.3 74.6 + - - +
69G GLY 2.7 6.8 + - - -
70G HIS* 2.9 20.1 + - + +
73G LYS* 3.6 34.8 + - + -
74G SER* 4.1 11.2 + - - +
77G GLU* 3.8 34.5 + - + +
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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