Contacts of the helix formed by residues 59 - 69 (chain B) in PDB entry 5L08
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 LEU 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B PHE* 4.1 30.7 - - + +
6B ASN* 6.4 1.3 - - + +
7B LEU* 4.6 14.4 - - + -
54B LEU* 3.5 24.2 - - + -
55B GLU 3.1 21.8 - - - +
56B GLU* 4.8 7.6 - - - +
57B SER 4.1 0.8 - - - -
58B ASN* 1.3 71.6 - - - +
60B SER* 1.3 57.7 + - - +
61B PHE 3.2 3.1 - - - -
62B LEU* 3.3 7.1 + - + +
63B LYS* 2.9 26.3 + - - +
79B LEU* 3.7 29.9 - - + +
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Residues in contact with SER 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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58B ASN* 2.6 24.5 + - - -
59B LEU* 1.3 78.7 - - - +
61B PHE* 1.3 59.2 + - - +
63B LYS* 3.3 27.6 - - - +
64B GLU* 3.1 26.3 + - - +
89B GLU* 5.0 5.4 - - - -
97B GLN* 5.2 9.2 + - - +
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Residues in contact with PHE 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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25B LEU 4.9 5.2 - - - -
26B SER* 5.1 6.3 - - - -
29B TYR* 3.6 34.8 - + + -
48B LEU* 3.7 28.9 - - + -
53B MET* 3.3 44.6 + - + +
54B LEU* 5.4 0.7 - - + -
58B ASN* 4.3 1.0 + - - -
59B LEU 3.2 0.6 - - - -
60B SER* 1.3 79.5 + - - +
62B LEU* 1.3 59.9 + - - +
64B GLU* 3.3 7.3 + - - +
65B LEU* 2.9 58.6 + - + +
97B GLN* 3.6 24.9 - - + -
98B ILE* 3.9 20.9 - - + -
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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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7B LEU* 3.5 31.6 - - + -
10B ILE* 3.8 21.5 - - + -
14B LEU* 5.7 2.5 - - + -
22B LEU* 6.2 2.9 - - + -
45B PHE* 4.0 24.0 - - + -
48B LEU* 6.0 1.1 - - + -
54B LEU* 3.8 19.3 - - + +
59B LEU* 3.3 9.4 + - + +
61B PHE* 1.3 75.0 - - - +
63B LYS* 1.3 67.9 + - - +
65B LEU* 3.0 20.8 + - + +
66B LEU* 2.8 38.6 + - + +
79B LEU* 4.2 17.9 - - + -
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Residues in contact with LYS 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 LEU 2.9 14.0 + - - +
60B SER* 3.3 24.5 - - - +
62B LEU* 1.3 76.8 - - - +
64B GLU* 1.3 64.2 + - - +
66B LEU 3.3 0.7 + - - -
67B PHE* 3.1 43.2 + - + -
75B LEU* 3.3 13.2 - - + +
79B LEU* 3.5 16.9 - - + +
81B THR* 4.0 25.5 + - + +
85B GLU* 4.6 13.1 + - + +
88B ARG* 6.3 0.2 - - - +
89B GLU* 2.9 41.4 + - - +
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Residues in contact with GLU 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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60B SER 3.1 10.0 + - - +
61B PHE* 3.5 8.2 - - - +
63B LYS* 1.3 80.3 - - - +
65B LEU* 1.3 52.0 + - - +
67B PHE* 2.8 15.3 + - + +
68B ARG* 2.7 71.0 + - - +
89B GLU* 6.4 4.0 - - + -
96B ALA* 3.7 5.6 - - - +
97B GLN* 2.8 36.8 + - - +
98B ILE* 2.9 36.2 + - + +
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Residues in contact with LEU 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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22B LEU* 3.7 31.0 - - + +
25B LEU* 3.7 16.8 - - + -
26B SER* 5.7 1.1 - - - -
44B LEU* 5.7 4.0 - - + -
45B PHE* 6.1 0.9 - - + -
48B LEU* 4.5 11.2 - - + -
61B PHE* 2.9 48.0 + - + +
62B LEU* 3.0 24.9 + - + +
64B GLU* 1.3 75.0 - - - +
66B LEU* 1.3 58.4 + - + +
68B ARG* 3.0 8.1 + - - +
69B ILE* 2.9 33.7 + - - +
98B ILE* 3.6 23.3 - - + -
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Residues in contact with LEU 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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10B ILE* 4.9 5.4 - - + -
14B LEU* 4.2 6.1 - - + -
22B LEU* 6.2 0.7 - - + -
62B LEU* 2.8 28.7 + - + +
63B LYS 3.5 0.9 - - - +
65B LEU* 1.3 73.0 - - + +
67B PHE* 1.3 60.1 + - - +
69B ILE* 3.4 14.0 + - + -
70B ASN* 2.9 9.0 + - - -
71B ARG* 2.9 36.8 + - + +
74B LEU* 3.6 45.8 - - + +
75B LEU* 3.5 27.2 - - + +
79B LEU* 3.6 30.3 - - + -
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Residues in contact with PHE 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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63B LYS* 3.1 50.7 + - + -
64B GLU* 2.8 14.5 + - + +
66B LEU* 1.3 79.2 - - - +
68B ARG* 1.3 64.6 + - - +
70B ASN* 3.4 19.7 + - - +
72B LEU* 5.2 5.4 - - + -
75B LEU* 3.4 26.2 - - + -
81B THR* 5.1 0.7 - - + -
82B ARG 3.6 15.3 - - - -
83B LYS* 3.2 35.9 - - + -
85B GLU* 4.4 1.6 - - + -
86B MET* 3.6 51.8 - - + +
89B GLU* 6.1 0.7 - - + -
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Residues in contact with ARG 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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25B LEU* 3.4 23.8 - - + -
64B GLU* 2.7 53.7 + - - +
65B LEU 3.0 6.9 + - - +
67B PHE* 1.3 78.3 + - - +
69B ILE* 1.3 57.0 + - - +
70B ASN* 3.4 2.5 + - - +
86B MET* 4.6 20.7 - - - +
90B LEU* 4.1 25.9 - - - +
96B ALA* 4.2 6.1 - - - +
98B ILE* 3.8 22.8 + - + +
103B VAL* 3.5 44.6 - - - +
106B TYR* 3.0 31.5 - - + -
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Residues in contact with ILE 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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14B LEU* 4.1 15.3 - - + -
18B ASP* 4.0 26.9 - - + +
21B SER* 3.3 26.9 - - - +
22B LEU* 3.8 27.1 - - + -
25B LEU* 3.8 8.7 - - + -
65B LEU 2.9 20.3 + - - +
66B LEU* 3.7 12.6 - - + +
68B ARG* 1.3 79.0 - - - +
70B ASN* 1.3 70.7 + - - +
71B ARG* 3.6 31.1 - - + +
106B TYR* 3.6 13.0 + - + +
34I LYS* 5.3 5.0 - - - -
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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
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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