Contacts of the helix formed by residues 51 - 70 (chain B) 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 LYS 51 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS* 3.2 35.6 + - - +
37B ASN* 4.9 3.6 - - - +
38B TYR* 3.6 31.1 + - - +
49B MET* 4.4 13.5 - - + -
50B ALA* 1.3 75.1 - - + +
52B PHE* 1.3 65.6 + - - +
53B GLY 3.4 1.3 - - - -
54B ASP* 2.7 16.2 - - - +
55B HIS* 2.8 57.4 + - + +
139B HEM 4.4 10.7 + - - +
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLN* 3.5 36.3 - - + -
21B PHE* 3.6 36.1 - + - -
22B LEU* 3.7 28.0 - - + -
25B LEU* 4.5 1.8 - - + -
38B TYR* 3.7 34.3 + + + +
46B LEU* 3.1 50.0 - - + +
47B LYS* 4.1 4.3 - - + -
49B MET* 3.8 10.1 + - + +
50B ALA 3.7 1.0 - - - -
51B LYS* 1.3 80.3 - - - +
53B GLY* 1.3 65.0 + - - +
55B HIS* 4.0 0.9 - - - +
56B THR* 3.0 31.9 + - + +
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Residues in contact with GLY 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 3.5 17.9 + - - +
18B GLN* 3.5 26.1 - - - +
47B LYS 5.3 2.2 + - - -
49B MET 4.8 2.6 + - - -
50B ALA 5.3 0.6 + - - -
52B PHE* 1.3 80.3 - - - +
54B ASP* 1.3 57.4 + - - +
56B THR* 2.8 20.0 + - - -
57B GLU* 2.9 19.2 + - - +
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Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 3.3 26.5 - - - +
50B ALA 3.0 10.9 + - - +
51B LYS* 2.7 28.4 - - - +
53B GLY* 1.3 75.4 - - - +
55B HIS* 1.3 95.3 + - - +
57B GLU* 3.4 2.6 + - - +
58B LYS* 3.1 40.2 + - - +
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Residues in contact with HIS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B TYR* 4.6 3.1 - - - +
51B LYS* 2.8 42.3 + - + +
52B PHE 4.0 1.8 - - - +
54B ASP* 1.3 103.9 + - - +
56B THR* 1.3 62.5 + - - +
58B LYS* 3.1 5.5 + - + +
59B VAL* 3.0 26.0 + - - +
88B GLN* 5.2 3.8 - - - -
139B HEM 2.5 64.3 + - + +
192B BML 3.2 16.8 - - - +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 4.7 0.5 + - - -
17B ALA* 4.0 17.4 - - - +
18B GLN* 3.4 17.8 - - + +
21B PHE* 3.4 38.1 - - + -
38B TYR* 5.5 0.2 - - - +
52B PHE* 3.0 37.6 + - + +
53B GLY 2.8 17.5 + - - -
55B HIS* 1.3 75.0 - - - +
57B GLU* 1.3 61.8 + - - +
59B VAL* 3.3 1.5 + - - +
60B PHE* 3.0 30.2 + - - +
192B BML 3.8 14.1 - - + +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.4 29.2 - - + +
14B ARG* 2.9 41.3 + - - +
17B ALA* 4.4 1.8 - - - -
53B GLY 2.9 17.6 + - - +
54B ASP 3.7 5.2 - - - +
56B THR* 1.3 78.4 + - - +
58B LYS* 1.3 61.1 + - + +
60B PHE 3.2 0.5 + - - -
61B ASN 2.7 26.9 + - - -
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ASP* 3.1 29.8 + - - +
55B HIS* 3.1 7.9 + - - +
57B GLU* 1.3 78.0 - - + +
59B VAL* 1.3 62.0 + - - +
61B ASN 3.5 0.2 + - - -
62B LEU* 3.2 17.7 + - - +
139B HEM 3.2 50.1 + - + +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B HIS 3.0 18.3 + - - +
56B THR 3.5 6.7 - - - +
58B LYS* 1.3 76.7 - - - +
60B PHE* 1.3 71.2 + - + +
62B LEU 3.2 2.4 + - - -
63B MET* 2.8 25.6 + - + +
139B HEM 3.5 60.3 - - + +
192B BML 3.5 49.4 - - + -
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 5.1 5.8 - - + -
13B LEU* 4.0 14.8 - - + -
17B ALA* 3.6 35.2 - - + -
20B ILE* 3.7 47.8 - - + -
21B PHE* 4.5 11.4 - - + -
56B THR* 3.0 23.0 + - - +
57B GLU 4.2 0.9 - - - +
59B VAL* 1.3 90.8 - - + +
61B ASN 1.3 55.2 + - - +
63B MET* 3.8 34.3 - - + +
64B MET* 2.9 45.7 + - + +
100B LEU* 4.8 6.1 - - + -
104B LEU* 4.5 2.5 - - + -
192B BML 4.9 7.4 - + + -
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Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 4.9 1.0 - - - -
13B LEU* 4.3 5.7 - - - +
57B GLU 2.7 21.8 + - - -
58B LYS 3.5 1.0 + - - -
60B PHE* 1.3 70.9 + - - +
62B LEU* 1.3 59.4 - - - +
64B MET* 3.4 3.8 - - - -
65B GLU* 3.1 31.1 - - - -
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LYS 3.2 14.0 + - - +
59B VAL 3.7 7.0 - - - +
61B ASN 1.3 73.9 - - - +
63B MET* 1.3 64.9 + - - +
65B GLU* 3.1 18.0 + - - +
66B VAL* 2.9 29.8 + - + +
69B ARG* 4.1 19.1 - - - +
79B ASP* 5.1 1.6 - - - +
82B THR* 5.2 9.2 - - + -
83B LEU* 4.1 22.9 - - + -
86B MET* 4.6 8.1 - - - -
139B HEM 4.0 27.1 - - + -
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Residues in contact with MET 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B VAL* 2.8 17.5 + - + +
60B PHE* 3.3 33.2 + - + +
62B LEU* 1.3 76.3 - - - +
64B MET* 1.3 75.9 + - + +
66B VAL* 3.3 7.0 + - + +
67B ALA* 2.9 26.5 + - - +
100B LEU* 4.0 27.4 - - + -
101B PHE* 4.0 18.4 - - + -
104B LEU* 3.8 24.7 - - + -
120B TRP* 4.7 3.1 - - - -
123B PHE* 4.5 8.0 - - + -
139B HEM 3.7 28.2 - - + +
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Residues in contact with MET 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.0 14.9 - - + +
9B ILE* 3.8 46.7 - - + -
10B ARG* 3.6 32.0 + - + +
13B LEU* 4.3 3.6 - - + -
60B PHE* 2.9 25.3 + - + +
61B ASN 3.9 2.9 - - - -
63B MET* 1.3 99.7 - - + +
65B GLU* 1.3 60.6 + - - +
67B ALA* 3.4 2.4 + - - +
68B ASP* 2.8 30.5 + - - +
104B LEU* 5.9 0.7 - - + -
120B TRP* 3.7 28.9 - - + -
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 3.7 17.3 - - - +
61B ASN 3.1 18.9 - - - -
62B LEU* 3.1 24.0 + - - +
64B MET* 1.3 73.1 - - - +
66B VAL* 1.3 59.8 + - - +
68B ASP* 3.2 2.9 + - - +
69B ARG* 2.9 64.4 + - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 2.9 34.0 + - + +
63B MET* 3.6 9.4 - - + +
65B GLU* 1.3 75.0 - - - +
67B ALA* 1.3 63.4 + - - +
69B ARG* 3.4 3.3 + - - +
70B ALA* 3.2 21.3 + - - +
75B PRO* 3.9 25.1 - - + +
79B ASP* 3.8 38.4 - - + +
83B LEU* 4.8 12.8 - - + -
123B PHE* 3.9 11.2 - - + -
127B LEU* 4.6 11.4 - - + -
139B HEM 5.4 1.6 - - + -
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PHE* 3.6 26.2 - - + -
3B LYS* 4.7 1.7 + - - -
6B ILE* 3.6 20.6 - - + +
63B MET 2.9 17.0 + - - +
64B MET* 3.6 5.8 - - - +
66B VAL* 1.3 77.6 - - - +
68B ASP* 1.3 62.6 + - - +
70B ALA* 3.3 17.5 + - - +
120B TRP* 4.0 10.8 - - + -
123B PHE* 3.7 18.3 - - + -
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LYS* 2.8 48.5 + - - +
6B ILE* 3.6 12.1 - - + +
10B ARG* 2.9 32.0 + - - +
64B MET 2.8 18.4 + - - +
65B GLU* 3.2 4.5 + - - +
67B ALA* 1.3 77.4 - - - +
69B ARG* 1.3 62.2 + - + +
70B ALA 3.5 1.4 + - - +
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 4.1 13.1 - - - +
65B GLU* 2.9 54.5 + - - +
66B VAL 3.8 1.8 - - - +
68B ASP* 1.3 75.1 - - + +
70B ALA* 1.3 65.4 + - - +
71B THR* 4.6 2.9 + - - -
76B LEU* 3.9 39.7 - - + +
79B ASP* 2.9 43.1 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PHE* 4.9 1.6 - - + -
3B LYS* 4.4 8.7 + - - -
66B VAL 3.2 12.3 + - - +
67B ALA* 3.3 19.0 - - - +
68B ASP 3.2 7.9 - - - +
69B ARG* 1.3 82.1 - - - +
71B THR* 1.3 61.1 + - - +
72B ASP 4.4 0.3 + - - -
73B CYS* 4.1 10.1 - - - +
74B VAL 3.2 31.9 - - - +
75B PRO* 3.9 6.1 - - + -
76B LEU* 4.9 0.4 - - - +
123B PHE* 4.4 3.8 - - + -
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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
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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