Contacts of the helix formed by residues 49 - 67 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K ILE* 6.4 0.2 - - - -
48L GLY* 1.3 70.3 - - - -
50L THR* 1.3 68.4 + - - -
51L ALA 2.7 5.0 + - - -
52L ASP* 3.1 7.8 + - - -
53L ALA* 2.6 24.5 + - - +
92L GLU* 3.2 17.0 + - - +
93L ALA* 4.2 1.2 - - - +
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Residues in contact with THR 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444E LEU* 3.6 32.0 - - + +
109K ILE* 4.2 8.0 - - - +
111K ASP* 2.8 28.6 + - - +
113K VAL* 6.2 0.7 - - + -
20L VAL* 3.7 24.0 - - + -
21L SER 5.7 1.8 - - - +
27L MET* 6.2 0.9 - - - -
48L GLY 3.4 5.7 + - - +
49L GLY* 1.3 68.0 - - - +
51L ALA* 1.3 58.0 + - - +
53L ALA* 3.6 4.1 - - - +
54L PHE* 3.0 31.4 + - - -
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Residues in contact with ALA 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K ARG* 4.7 1.8 - - + +
109K ILE* 4.1 25.5 - - + +
110K GLY 3.9 19.5 - - - +
111K ASP* 3.8 13.9 + - + +
49L GLY 2.7 4.6 + - - -
50L THR* 1.3 73.3 + - - +
52L ASP* 1.3 60.0 + - - +
53L ALA 2.6 3.4 + - - -
54L PHE* 2.5 34.9 + - - +
55L THR* 2.9 16.0 + - + -
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Residues in contact with ASP 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L GLY* 3.1 8.4 + - - +
51L ALA* 1.3 82.8 - - - +
53L ALA* 1.3 53.4 + - - +
55L THR* 3.0 13.4 + - - +
56L LEU* 2.7 36.7 + - - +
89L ARG* 4.7 4.5 + - - -
90L LYS 4.4 1.9 - - - +
91L LEU* 3.2 20.2 - - + +
92L GLU* 2.7 48.5 + - + +
93L ALA* 4.0 2.4 - - - +
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Residues in contact with ALA 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L PHE* 3.6 33.2 - - + +
48L GLY 4.6 5.6 - - - +
49L GLY 2.6 24.8 + - - +
50L THR* 3.6 8.7 - - - +
51L ALA 2.6 3.4 + - - -
52L ASP* 1.3 74.2 - - - +
54L PHE* 1.3 66.9 + - + +
56L LEU* 3.3 1.9 - - - +
57L PHE* 2.9 23.4 + - - +
93L ALA* 3.7 18.0 - - + +
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Residues in contact with PHE 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441E ARG 3.7 16.6 - - - -
442E PHE 3.6 25.4 - - - -
443E ILE 3.7 15.9 - - - -
444E LEU* 3.8 24.7 - - + -
83K ARG* 3.1 35.9 - - - +
111K ASP* 6.2 1.6 - - + -
35L ARG* 3.9 11.0 - - - -
46L PHE* 3.5 34.3 - + - -
50L THR 3.0 17.5 - - - +
51L ALA* 2.5 11.7 + - - +
53L ALA* 1.3 76.1 - - - +
55L THR* 1.3 54.4 + - - +
57L PHE* 3.5 10.3 - + - +
58L GLU* 2.6 41.0 + - - +
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Residues in contact with THR 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K ARG* 3.1 38.4 + - + +
84K THR 5.2 0.5 + - - -
51L ALA* 2.9 8.9 + - + +
52L ASP* 3.0 30.1 - - - +
54L PHE* 1.3 71.7 - - - +
56L LEU* 1.3 65.1 + - - +
58L GLU* 3.4 3.4 + - - +
59L LEU* 3.0 29.6 + - - +
89L ARG* 3.3 26.9 + - - +
91L LEU* 3.3 16.3 - - - +
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Residues in contact with LEU 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L ASP 2.7 21.8 + - - +
53L ALA* 3.3 4.7 - - - +
55L THR* 1.3 72.4 + - - +
57L PHE* 1.3 57.6 + - - +
59L LEU* 2.6 27.4 + - + +
60L PHE 3.1 5.4 + - - -
78L LEU* 4.1 21.5 - - + -
82L TRP* 4.7 7.2 - - + -
91L LEU* 4.2 14.8 - - + -
93L ALA* 3.5 31.4 - - + +
94L MET 3.9 0.7 - - - +
95L LEU* 3.5 32.3 - - + -
106L ILE* 3.8 17.5 - - + +
107L THR 4.4 0.7 - - - -
108L GLY* 4.3 14.4 - - - +
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Residues in contact with PHE 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441E ARG* 4.6 25.1 - - - -
35L ARG* 4.2 26.0 - - + -
36L ARG 5.0 0.4 - - - -
37L LEU* 3.1 34.7 - - + +
44L ALA* 3.6 32.5 - - + -
46L PHE* 3.8 28.9 - + + -
53L ALA 2.9 12.7 + - - +
54L PHE* 3.5 9.6 - + + +
56L LEU* 1.3 79.9 - - - +
58L GLU* 1.3 73.5 + - + +
60L PHE* 3.3 11.4 + - - +
61L GLU* 3.3 13.6 + - - +
95L LEU* 3.4 23.9 - - + +
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Residues in contact with GLU 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441E ARG 4.4 1.2 - - - +
442E PHE* 3.7 26.7 - - + -
80K LYS* 5.8 1.9 - - - -
83K ARG* 2.6 51.5 + - - +
54L PHE* 2.6 27.9 + - - +
55L THR* 3.7 5.2 - - - +
57L PHE* 1.3 85.6 - - + +
59L LEU* 1.3 64.8 + - + +
61L GLU* 3.6 12.6 + - - +
62L ARG* 3.6 20.3 + - - +
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Residues in contact with LEU 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K ARG 4.5 12.8 - - - +
84K THR 5.5 2.9 - - - +
85K ASP* 5.0 20.4 - - - +
55L THR* 3.0 27.7 + - - +
56L LEU* 2.6 16.7 + - - +
58L GLU* 1.3 73.2 - - + +
60L PHE* 1.3 64.2 + - - +
61L GLU 3.1 2.4 + - - -
62L ARG* 3.2 20.6 + - + +
63L LYS* 3.2 15.2 + - - +
78L LEU* 4.3 21.8 - - + -
82L TRP* 4.7 1.8 - - + -
88L LEU* 3.8 31.2 - - + -
91L LEU* 4.4 15.9 - - + -
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Residues in contact with PHE 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L LEU* 3.8 18.8 - - + -
42L VAL* 5.4 1.3 - - + -
44L ALA* 5.4 0.2 - - + -
56L LEU 3.1 2.8 + - - +
57L PHE 3.3 7.4 + - - +
59L LEU* 1.3 79.8 - - - +
61L GLU* 1.3 56.6 + - - +
63L LYS* 3.3 5.3 - - - +
64L LEU* 2.9 48.7 + - + +
71L LEU* 3.6 26.9 - - + -
74L SER* 4.0 7.4 - - - -
75L ALA* 3.8 24.2 - - + -
78L LEU* 3.7 19.2 - - + +
95L LEU* 4.0 15.5 - - + -
97L VAL* 3.3 29.2 - - + -
106L ILE* 3.5 27.4 - - + -
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Residues in contact with GLU 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E ARG* 3.0 40.5 + - - -
442E PHE* 6.1 0.7 - - - -
37L LEU* 3.5 21.7 - - + +
38L TYR* 4.1 9.2 + - - +
57L PHE* 3.3 10.6 + - + +
58L GLU* 3.8 15.7 - - - +
59L LEU 3.1 0.6 - - - -
60L PHE* 1.3 77.7 - - - +
62L ARG* 1.3 68.8 + - - +
64L LEU* 2.7 12.5 + - + +
65L GLU* 2.6 41.3 + - + +
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Residues in contact with ARG 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F LYS* 3.9 49.0 + - - +
313F VAL* 4.6 21.2 - - + +
85K ASP* 4.7 17.3 + - - -
58L GLU 3.6 12.4 + - - +
59L LEU* 3.2 15.8 + - + +
61L GLU* 1.3 79.8 - - - +
63L LYS* 1.3 56.0 + - + +
65L GLU* 2.9 9.3 + - - +
66L MET* 2.7 50.0 + - - +
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Residues in contact with LYS 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L LEU 3.2 10.4 + - - +
60L PHE* 3.3 12.8 - - - +
61L GLU 3.0 0.2 - - - -
62L ARG* 1.3 84.4 - - + +
64L LEU* 1.3 64.3 + - - +
66L MET* 3.0 27.7 + - - +
67L HIS* 3.0 26.8 + - + +
74L SER* 3.5 32.7 + - - +
77L GLU* 3.8 39.0 + - + -
78L LEU* 4.0 11.7 - - + +
81L ASP* 3.2 24.7 + - - -
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Residues in contact with LEU 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L LEU* 4.0 11.9 - - + -
38L TYR* 4.2 13.6 - - + -
42L VAL* 3.5 33.9 - - + -
60L PHE* 2.9 44.9 + - + +
61L GLU* 2.7 14.7 + - + +
63L LYS* 1.3 71.4 - - - +
65L GLU* 1.3 61.8 + - - +
67L HIS 3.2 4.5 + - - -
69L GLY* 3.0 48.8 + - - +
71L LEU* 4.1 13.2 - - - +
74L SER* 3.3 21.3 + - - +
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Residues in contact with GLU 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312F GLN* 3.9 43.6 - - - +
313F VAL* 5.4 3.4 - - + -
38L TYR* 3.3 33.0 - - - -
39L ASN* 5.3 1.7 + - - -
61L GLU* 2.6 38.4 + - + +
62L ARG* 3.1 13.2 - - - +
64L LEU* 1.3 75.5 - - + +
66L MET* 1.3 60.1 + - + +
67L HIS 3.5 0.3 + - - -
68L GLN* 4.4 4.3 + - - -
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Residues in contact with MET 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F LYS* 6.3 0.7 - - - -
312F GLN* 4.1 24.0 + - - +
313F VAL* 4.9 17.5 - - + -
62L ARG* 2.7 33.9 + - - +
63L LYS* 3.0 19.7 + - - +
65L GLU* 1.3 75.8 - - - +
67L HIS* 1.3 83.9 + - + +
68L GLN* 3.9 1.8 + - - +
77L GLU* 6.0 0.4 - - - +
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Residues in contact with HIS 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L LYS* 3.0 27.0 + - + +
64L LEU 3.2 1.2 + - - -
66L MET* 1.3 106.6 + - + +
68L GLN* 1.3 75.6 + - - +
69L GLY 2.6 7.1 + - - -
70L HIS* 2.9 19.3 + - + +
73L LYS* 3.5 37.1 + - + -
74L SER* 4.0 11.1 + - - +
77L GLU* 3.9 30.9 + - + +
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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