Contacts of the helix formed by residues 49 - 70 (chain A) in PDB entry 3LB2
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 MET 49 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 3.4 32.1 - - + +
38A TYR* 4.1 12.3 - - + -
41A LYS* 3.7 28.0 - - - +
45A GLU 3.5 17.3 - - - -
46A LEU* 3.0 26.3 + - + +
47A LYS 4.5 3.2 - - - +
48A SER* 1.3 81.6 - - - +
50A ALA* 1.3 68.1 + - - +
51A LYS* 3.2 3.4 - - + +
52A PHE* 3.1 20.1 + - + +
53A GLY 3.6 4.0 + - - -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 4.9 1.0 + - - -
48A SER 3.9 3.6 + - - -
49A MET* 1.3 72.2 - - - +
51A LYS* 1.3 58.5 + - + +
53A GLY* 3.5 1.6 + - - -
54A ASP* 3.1 41.4 + - - +
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 5.8 4.2 - - - +
37A ASN* 4.3 23.5 - - - +
38A TYR* 3.9 1.7 + - - +
49A MET* 3.2 3.7 - - + +
50A ALA* 1.3 78.1 - - + +
52A PHE* 1.3 61.5 + - - +
54A ASP* 3.8 2.2 - - - -
55A HIS* 2.8 68.0 + - + +
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 3.7 37.0 - - + -
21A PHE* 3.6 31.9 - + - -
22A LEU* 4.2 21.1 - - + -
38A TYR* 3.6 34.5 + + + -
46A LEU* 3.1 57.4 - - + +
47A LYS* 4.0 14.1 - - + -
49A MET* 3.1 9.7 + - + +
51A LYS* 1.3 77.9 - - - +
53A GLY* 1.3 65.3 + - - +
56A THR* 3.0 29.7 + - + +
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Residues in contact with GLY 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.4 19.3 + - - -
18A GLN* 3.4 24.7 - - - -
47A LYS 5.7 1.3 + - - -
49A MET 3.6 4.4 + - - -
50A ALA 3.5 4.3 + - - -
52A PHE* 1.3 79.3 - - - +
54A ASP* 1.3 63.1 + - - +
56A THR* 3.3 2.2 - - - +
57A GLU* 3.0 26.7 + - - +
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Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.0 28.3 + - - +
50A ALA* 3.1 29.4 + - - +
51A LYS* 4.2 2.6 - - - +
53A GLY* 1.3 76.8 - - - +
55A HIS* 1.3 69.7 + - + +
57A GLU* 3.8 1.9 - - - +
58A LYS* 3.0 45.2 + - - +
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Residues in contact with HIS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 4.1 1.8 - - - +
51A LYS* 2.8 61.3 + - + +
54A ASP* 1.3 76.8 - - + +
56A THR* 1.3 58.4 + - - +
58A LYS* 3.1 3.2 + - + +
59A VAL* 2.9 33.4 + - - +
139A HEM 2.4 64.7 + - + +
191A BML 3.2 18.4 - - + +
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 4.8 1.1 - - + +
17A ALA* 3.3 23.2 + - + +
18A GLN* 3.4 33.5 + - + +
21A PHE* 3.7 19.8 - - - +
52A PHE* 3.0 27.4 + - + +
53A GLY* 3.3 7.9 - - - +
55A HIS* 1.3 77.1 - - - +
57A GLU* 1.3 66.3 + - + +
59A VAL* 3.4 0.6 + - - -
60A PHE* 3.1 32.2 + - - -
191A BML 3.9 18.3 - - - -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.8 26.7 - - + +
14A ARG* 3.0 47.3 + - + +
17A ALA* 4.2 9.2 - - - -
53A GLY 3.0 18.9 + - - +
54A ASP 3.8 3.6 - - - +
56A THR* 1.3 78.6 - - - +
58A LYS* 1.3 62.4 + - + +
60A PHE* 3.3 1.4 + - - -
61A ASN* 2.8 28.6 + - + +
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASP* 3.0 37.2 + - + +
55A HIS* 3.1 5.0 + - - +
57A GLU* 1.3 76.4 - - + +
59A VAL* 1.3 66.7 + - - +
61A ASN* 3.4 10.1 + - + +
62A LEU* 3.1 17.8 + - - +
139A HEM 3.7 42.8 + - + +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A HIS 2.9 20.3 + - - +
56A THR 3.6 5.8 - - - +
57A GLU 3.3 0.2 - - - -
58A LYS* 1.3 76.1 - - - +
60A PHE* 1.3 72.6 - - + +
62A LEU 3.2 2.8 + - - -
63A MET* 2.9 26.2 + - + +
139A HEM 3.5 66.2 - - + +
191A BML 3.6 41.5 - - + -
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 5.3 4.3 - - + -
13A LEU* 3.9 14.4 - - + -
17A ALA* 3.6 39.5 - - + -
20A ILE* 3.6 47.6 - - + -
21A PHE* 4.3 8.7 - - + -
56A THR* 3.1 21.8 + - - +
57A GLU 4.1 0.7 - - - +
59A VAL* 1.3 91.8 - - + +
61A ASN* 1.3 61.1 + - - +
63A MET* 3.6 34.5 - - + +
64A MET* 2.9 39.9 + - + +
100A LEU* 4.6 9.0 - - + -
104A LEU* 4.4 1.6 - - + -
191A BML 4.9 5.6 - + + -
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Residues in contact with ASN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.9 18.3 - - + +
57A GLU* 2.8 23.4 + - + +
58A LYS* 3.7 10.8 + - + +
60A PHE* 1.3 73.2 - - - +
62A LEU* 1.3 57.2 + - - +
64A MET* 3.2 7.0 + - - +
65A GLU* 2.8 56.9 + - - +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LYS 3.1 15.2 + - - +
59A VAL 3.2 6.7 + - - +
61A ASN* 1.3 72.8 - - - +
63A MET* 1.3 66.0 + - - +
65A GLU* 3.0 29.6 + - + +
66A VAL* 2.9 40.9 + - + +
69A ARG* 4.5 7.2 - - - +
79A ASP* 5.6 0.4 - - - +
82A THR* 4.8 13.2 - - + -
83A LEU* 3.9 25.1 - - + -
86A MET* 4.6 7.6 - - - -
139A HEM 3.9 28.5 - - + -
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Residues in contact with MET 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 2.9 16.3 + - + +
60A PHE* 3.6 33.7 - - + +
61A ASN 3.3 0.2 - - - -
62A LEU* 1.3 76.4 - - - +
64A MET* 1.3 75.9 + - + +
66A VAL* 3.3 5.6 + - - +
67A ALA* 2.8 26.5 + - - +
100A LEU* 4.0 21.3 - - + -
101A PHE* 4.0 23.1 - - + -
104A LEU* 3.7 24.5 - - + -
120A TRP* 4.5 3.4 - - - -
123A PHE* 4.5 13.3 - - + -
139A HEM 3.6 24.3 - - + +
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Residues in contact with MET 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.1 27.6 - - + +
9A ILE* 3.9 41.7 - - + -
10A ARG 5.0 1.6 - - - +
13A LEU* 4.3 7.4 - - + -
60A PHE* 2.9 24.5 + - + +
61A ASN* 3.7 6.5 - - - +
63A MET* 1.3 100.0 - - + +
65A GLU* 1.3 58.9 + - - +
67A ALA* 3.7 2.2 - - - +
68A ASP* 2.8 32.6 + - - +
104A LEU* 5.8 0.7 - - + -
120A TRP* 3.7 32.3 - - + -
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASN* 2.8 43.3 + - - +
62A LEU* 3.0 33.8 + - + +
64A MET* 1.3 75.0 - - - +
66A VAL* 1.3 62.3 + - - +
68A ASP* 3.3 5.7 + - - +
69A ARG* 3.0 56.7 + - - +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 2.9 37.4 + - + +
63A MET* 3.6 6.7 - - + +
65A GLU* 1.3 74.8 - - - +
67A ALA* 1.3 63.5 + - - +
69A ARG* 3.3 2.8 + - - +
70A ALA* 3.1 21.8 + - - +
75A PRO* 4.0 15.1 - - + +
79A ASP* 3.8 43.3 - - + +
83A LEU* 5.0 10.8 - - + -
123A PHE* 3.9 15.9 - - + -
127A LEU* 4.6 12.6 - - + -
139A HEM 5.5 1.6 - - + -
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PHE* 3.5 32.0 - - + -
3A LYS* 4.6 1.7 + - - -
6A ILE* 3.8 12.9 - - + +
63A MET 2.8 17.2 + - - +
64A MET* 3.7 5.8 - - - +
66A VAL* 1.3 77.8 - - - +
68A ASP* 1.3 59.8 + - - +
70A ALA* 3.3 18.9 + - - +
120A TRP* 4.0 14.1 - - + -
123A PHE* 3.7 17.7 - - + -
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LYS* 2.9 46.6 + - - +
6A ILE* 3.7 18.7 - - + +
64A MET 2.8 21.7 + - - +
65A GLU* 3.8 5.6 - - - +
66A VAL 3.3 0.2 - - - -
67A ALA* 1.3 73.8 - - - +
69A ARG* 1.3 61.0 + - + +
70A ALA 3.5 1.9 + - - +
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.5 7.7 - - - +
65A GLU* 3.0 50.6 + - - +
66A VAL* 3.9 7.8 - - - +
67A ALA 3.3 0.2 - - - -
68A ASP* 1.3 74.7 - - + +
70A ALA* 1.3 65.8 + - - +
71A THR* 3.8 3.8 + - - -
76A LEU* 3.9 34.2 - - + +
79A ASP* 2.9 43.8 + - - +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PHE* 5.0 1.1 - - + -
3A LYS* 4.4 7.4 + - - -
66A VAL 3.1 11.5 + - - +
67A ALA 3.3 17.0 + - - +
68A ASP 3.8 6.9 - - - +
69A ARG* 1.3 80.7 - - - +
71A THR* 1.3 60.5 + - - +
72A ASP 4.1 0.7 + - - -
73A CYS* 4.2 10.5 - - - +
74A VAL 3.3 31.2 - - - +
75A PRO* 3.9 7.0 - - + -
123A PHE* 4.3 7.2 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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