Contacts of the helix formed by residues 49 - 67 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K GLY* 1.3 70.1 - - - -
50K THR* 1.3 69.7 + - - -
51K ALA 2.5 6.1 + - - -
52K ASP* 3.0 7.8 + - - -
53K ALA* 2.7 22.8 + - - +
92K GLU* 3.2 17.6 + - - +
93K ALA* 4.3 2.0 - - - +
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Residues in contact with THR 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D LEU* 3.9 25.4 - - + -
109J ILE* 4.1 8.3 - - - +
111J ASP* 2.5 31.9 + - - +
113J VAL* 6.1 1.1 - - + -
20K VAL* 3.8 28.9 - - + -
21K SER 5.8 1.6 - - - +
27K MET* 6.2 1.3 - - - -
48K GLY 3.4 6.5 + - - +
49K GLY* 1.3 72.5 - - - +
51K ALA* 1.3 62.3 + - - +
53K ALA* 3.5 4.2 - - - +
54K PHE* 3.1 26.2 + - - -
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Residues in contact with ALA 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J ARG* 5.0 1.8 - - + +
109J ILE* 4.2 26.9 - - + +
110J GLY 4.1 17.3 - - - +
111J ASP* 3.9 12.8 + - - +
49K GLY 2.5 4.6 + - - -
50K THR* 1.3 73.8 + - - +
52K ASP* 1.3 63.7 + - - +
53K ALA 2.9 0.9 - - - -
54K PHE* 2.5 33.4 + - - +
55K THR* 2.9 17.3 + - + +
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Residues in contact with ASP 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49K GLY* 3.0 8.6 + - - +
51K ALA* 1.3 80.8 - - - +
53K ALA* 1.3 67.7 + - - +
55K THR* 3.2 13.0 + - - +
56K LEU* 2.7 23.7 + - - +
89K ARG* 4.7 5.2 + - - -
90K LYS 4.1 2.4 - - - +
91K LEU* 3.3 23.1 - - + +
92K GLU* 2.8 50.0 + - + +
93K ALA* 4.1 1.8 - - - -
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Residues in contact with ALA 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46K PHE* 3.7 34.4 - - + +
48K GLY 4.6 7.6 - - - +
49K GLY 2.7 23.5 + - - +
50K THR* 3.5 7.4 - - - +
51K ALA 2.6 3.8 + - - -
52K ASP* 1.3 75.5 - - - +
54K PHE* 1.3 64.2 + - + +
56K LEU* 2.9 2.8 + - - +
57K PHE* 2.9 21.9 + - - +
93K ALA* 3.7 18.2 - - + +
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Residues in contact with PHE 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D ARG 3.1 27.1 - - - -
442D PHE 3.4 17.5 - - - -
443D ILE* 3.6 8.1 - - - -
444D LEU* 3.5 34.1 - - + -
83J ARG* 3.6 36.3 - - - +
111J ASP* 6.5 0.2 - - + -
35K ARG* 4.1 4.0 - - - -
46K PHE* 3.5 36.3 - + - -
50K THR 3.1 14.4 - - - +
51K ALA 2.5 10.9 + - - +
53K ALA* 1.3 76.4 - - - +
55K THR* 1.3 56.9 + - - +
56K LEU 2.9 0.5 + - - -
57K PHE* 3.0 11.6 + + - -
58K GLU* 2.6 41.8 + - - +
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Residues in contact with THR 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J TRP 5.4 0.7 - - - +
83J ARG* 3.3 51.2 + - + +
51K ALA* 2.9 22.0 + - + +
52K ASP* 3.2 17.2 + - - +
54K PHE* 1.3 72.6 - - - +
56K LEU* 1.3 59.0 + - - +
58K GLU* 3.9 3.4 - - - +
59K LEU* 2.9 34.7 + - - +
89K ARG* 4.6 4.5 + - - +
91K LEU* 3.2 26.0 - - + +
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Residues in contact with LEU 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52K ASP 2.7 15.6 + - - +
53K ALA* 3.4 8.3 - - - +
55K THR* 1.3 70.9 + - - +
57K PHE* 1.3 67.8 + - - +
59K LEU* 3.0 4.6 + - - +
60K PHE* 3.0 17.3 + - - +
78K LEU* 3.9 22.0 - - + -
82K TRP* 4.4 11.2 - - + -
91K LEU* 4.0 18.4 - - + -
93K ALA* 3.7 32.1 - - + +
94K MET* 3.9 4.5 - - - -
95K LEU* 3.5 30.3 - - + -
106K ILE* 4.1 13.5 - - + +
107K THR 4.3 0.9 - - - -
108K GLY* 4.1 7.6 - - - +
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Residues in contact with PHE 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D ARG* 4.6 27.1 - - - -
35K ARG* 4.2 27.4 - - + -
37K LEU* 3.2 34.6 - - + +
44K ALA* 3.6 31.6 - - + -
46K PHE* 3.8 26.5 - + + -
53K ALA 2.9 12.1 + - - +
54K PHE* 3.4 15.0 - + - +
56K LEU* 1.3 78.9 - - - +
58K GLU* 1.3 74.7 + - + +
60K PHE* 3.2 4.2 + - - +
61K GLU* 3.2 20.3 + - + +
95K LEU* 3.5 22.1 - - + +
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Residues in contact with GLU 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D ARG* 4.9 0.8 - - - +
442D PHE* 3.8 26.5 - - + -
80J LYS* 5.7 3.8 - - - +
83J ARG* 2.5 51.8 + - + +
54K PHE* 2.6 26.0 + - - +
55K THR* 3.9 4.5 - - - +
57K PHE* 1.3 85.2 - - + +
59K LEU* 1.3 63.6 + - + +
61K GLU* 3.4 13.0 + - - +
62K ARG* 3.3 19.6 + - - +
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Residues in contact with LEU 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J ARG* 4.5 10.3 - - + +
85J ASP* 4.0 19.1 - - - +
55K THR* 2.9 29.2 + - - +
56K LEU* 3.0 9.9 + - - +
58K GLU* 1.3 74.6 - - + +
60K PHE* 1.3 68.5 + - - +
61K GLU 3.0 3.1 + - - -
62K ARG* 3.1 16.8 + - - +
63K LYS* 3.2 14.6 + - - +
78K LEU* 4.3 18.2 - - + -
81K ASP* 5.9 0.7 - - - +
82K TRP* 4.5 9.6 - - + -
88K LEU* 4.1 35.7 - - + -
91K LEU* 4.7 5.8 - - + -
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Residues in contact with PHE 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K LEU* 3.9 13.9 - - + -
42K VAL* 5.4 1.3 - - + -
56K LEU 3.0 11.7 + - - +
57K PHE 3.5 7.9 - - - +
59K LEU* 1.3 76.8 - - - +
61K GLU* 1.3 57.0 + - - +
63K LYS* 3.3 5.4 - - - +
64K LEU* 3.0 53.1 + - + +
71K LEU* 3.5 27.4 - - + -
74K SER* 4.2 5.4 - - - -
75K ALA* 3.7 29.2 - - + -
78K LEU* 3.7 16.3 - - + +
95K LEU* 4.0 9.0 - - + -
97K VAL* 3.4 27.1 - - + -
106K ILE* 3.4 27.6 - - + -
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Residues in contact with GLU 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441D ARG* 2.5 47.9 + - - -
37K LEU* 3.4 26.6 - - + +
38K TYR* 4.0 13.0 + - - +
57K PHE* 3.2 10.9 + - + +
58K GLU* 3.6 15.9 - - - +
59K LEU 3.0 0.8 - - - -
60K PHE* 1.3 75.1 - - - +
62K ARG* 1.3 53.2 + - - +
63K LYS 2.6 6.3 + - - -
64K LEU* 2.6 32.6 + - + +
65K GLU* 2.6 34.9 + - + +
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Residues in contact with ARG 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E VAL* 5.0 13.6 - - + +
58K GLU 3.3 8.6 + - - +
59K LEU* 3.1 11.9 + - - +
61K GLU* 1.3 80.2 - - - +
63K LYS* 1.3 59.2 + - + +
65K GLU* 3.8 9.2 - - - +
66K MET* 3.2 34.9 + - - +
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Residues in contact with LYS 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K LEU 3.2 12.1 + - - +
60K PHE* 3.3 13.5 - - - +
61K GLU 2.6 5.1 + - - -
62K ARG* 1.3 76.0 - - + +
64K LEU* 1.3 65.5 + - - +
65K GLU 3.1 1.1 - - - -
66K MET* 3.0 25.3 + - + +
67K HIS* 3.0 27.3 + - + +
74K SER* 3.2 31.8 + - - +
77K GLU* 3.6 38.7 + - + -
78K LEU* 4.0 13.2 - - + +
81K ASP* 3.2 26.2 + - - -
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Residues in contact with LEU 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K LEU* 4.0 12.1 - - + -
38K TYR* 4.2 12.6 - - + -
42K VAL* 3.5 34.3 - - + -
60K PHE* 3.0 44.1 + - + +
61K GLU* 2.6 14.6 + - + +
63K LYS* 1.3 72.4 - - - +
65K GLU* 1.3 62.1 + - + +
67K HIS 3.2 4.2 + - - -
69K GLY* 3.0 56.0 + - - +
71K LEU* 4.1 12.3 - - - +
74K SER* 3.3 17.5 - - - +
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Residues in contact with GLU 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441D ARG* 5.5 1.6 + - - -
312E GLN* 3.7 45.5 - - - +
313E VAL* 5.3 3.4 - - + -
38K TYR* 3.3 33.3 - - - -
39K ASN* 5.2 1.4 + - - -
61K GLU* 2.6 43.3 + - + +
62K ARG* 3.8 9.2 - - - +
64K LEU* 1.3 75.0 - - + +
66K MET* 1.3 60.1 + - - +
67K HIS 3.6 0.2 + - - -
68K GLN* 4.5 3.6 + - - -
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Residues in contact with MET 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E LYS* 6.3 0.9 - - - -
312E GLN* 3.9 24.6 + - - +
313E VAL* 5.0 14.6 - - + -
389E GLU* 5.5 3.1 - - - +
62K ARG* 3.2 22.9 + - - +
63K LYS* 3.0 23.1 + - - +
65K GLU* 1.3 79.8 - - - +
67K HIS* 1.3 81.7 + - + +
68K GLN* 3.8 2.3 + - - +
77K GLU* 5.9 0.9 - - - +
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Residues in contact with HIS 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389E GLU* 6.1 0.9 - - - -
63K LYS* 3.0 23.9 + - + +
64K LEU 3.2 1.2 + - - -
66K MET* 1.3 105.3 + - + +
68K GLN* 1.3 74.7 + - - +
69K GLY 2.7 7.2 + - - -
70K HIS* 2.9 19.8 + - + +
73K LYS* 3.6 34.7 + - + -
74K SER* 3.9 15.0 + - - +
77K GLU* 4.0 31.8 + - + +
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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