Contacts of the helix formed by residues 70 - 80 (chain B) in PDB entry 3LNX
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 THR 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B GLY* 4.0 1.6 - - - -
26B VAL* 3.8 19.1 - - + +
27B ASN* 3.4 23.3 - - + +
68B GLY 4.7 0.2 - - - +
69B ALA* 1.3 77.3 - - - +
71B HIS* 1.3 66.0 + - - +
72B LYS* 3.6 7.4 + - - +
73B GLN* 2.9 46.1 + - - +
74B ALA* 2.9 21.0 + - - +
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Residues in contact with HIS 71 (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 VAL* 3.1 32.5 + - + +
23B THR* 4.1 2.8 - - - -
24B GLY 3.1 39.6 + - - +
27B ASN* 2.9 24.1 + - - +
28B THR* 4.5 4.3 - - + -
35B ILE* 5.6 0.2 - - + -
70B THR* 1.3 71.8 - - - +
72B LYS* 1.3 65.9 + - - +
74B ALA* 3.1 5.9 + - - +
75B VAL* 3.0 43.7 + - + +
99B IOD 3.9 16.4 - - + +
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Residues in contact with LYS 72 (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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27B ASN* 5.6 0.4 - - - +
70B THR* 3.3 6.5 + - - +
71B HIS* 1.3 79.9 + - - +
73B GLN* 1.3 88.1 + - - +
75B VAL* 3.3 2.4 + - - +
76B GLU* 3.0 50.2 + - + +
99B IOD 4.1 24.0 - - + -
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Residues in contact with GLN 73 (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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68B GLY 3.6 6.6 - - - +
69B ALA* 3.4 12.7 - - + -
70B THR* 2.9 43.7 + - - +
72B LYS* 1.3 97.6 - - - +
74B ALA* 1.3 56.2 + - - +
76B GLU* 3.4 1.9 + - - +
77B THR* 2.8 35.2 + - - +
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Residues in contact with ALA 74 (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 VAL* 5.0 3.8 - - + -
35B ILE* 3.6 46.7 - - + -
66B LEU* 4.7 7.5 - - + +
69B ALA* 4.2 7.5 - - + +
70B THR 2.9 8.0 + - - +
71B HIS* 3.6 7.0 - - - +
73B GLN* 1.3 73.1 - - - +
75B VAL* 1.3 67.1 + - - +
77B THR* 3.2 7.2 + - - -
78B LEU* 2.9 30.7 + - + +
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Residues in contact with VAL 75 (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 VAL* 4.0 16.2 - - + -
71B HIS* 3.0 37.0 + - + +
72B LYS 3.6 7.4 - - - +
74B ALA* 1.3 75.9 - - - +
76B GLU* 1.3 74.6 + - - +
78B LEU* 3.3 10.0 + - + +
79B ARG* 3.1 37.8 + - + +
99B IOD 4.1 15.7 - - + -
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Residues in contact with GLU 76 (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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72B LYS* 3.0 51.1 + - + +
73B GLN 3.8 3.4 - - - +
75B VAL* 1.3 81.1 - - - +
77B THR* 1.3 58.8 + - - +
79B ARG* 3.7 22.5 + - - +
80B ASN* 2.9 56.1 + - - +
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Residues in contact with THR 77 (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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61B VAL* 4.0 20.3 - - + +
64B VAL* 5.8 4.3 - - + +
66B LEU* 3.9 26.3 - - + +
73B GLN* 2.8 21.5 + - - +
74B ALA 3.2 5.4 + - - -
76B GLU* 1.3 76.7 - - - +
78B LEU* 1.3 62.1 + - - +
80B ASN* 3.6 9.2 + - - +
81B THR* 3.4 17.0 - - - +
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Residues in contact with LEU 78 (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 LYS* 4.1 0.3 + - - -
18B LEU* 3.9 21.5 - - + +
20B ILE* 4.3 15.0 - - + +
22B VAL* 4.0 31.0 - - + -
35B ILE* 5.3 3.4 - - + -
58B VAL* 4.9 6.5 - - + -
61B VAL* 3.7 27.8 - - + -
66B LEU* 5.7 1.6 - - + -
74B ALA* 2.9 24.1 + - + +
75B VAL* 3.6 8.1 - - - +
77B THR* 1.3 78.1 - - - +
79B ARG* 1.3 54.1 + - - +
81B THR* 2.8 29.7 + - - +
87B LEU* 3.9 17.3 - - + -
97B IOD 4.1 14.8 - - + +
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Residues in contact with ARG 79 (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 LYS* 3.7 11.5 + - - +
16B ASN* 5.8 2.1 + - - -
75B VAL* 3.1 27.7 + - + +
76B GLU* 3.7 28.3 + - - +
78B LEU* 1.3 76.2 - - - +
80B ASN* 1.3 62.3 + - - +
81B THR 2.9 11.4 + - - +
97B IOD 4.4 16.6 - - + -
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Residues in contact with ASN 80 (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 ASN* 5.4 0.2 + - - -
76B GLU* 2.9 39.9 + - - +
77B THR* 3.6 6.3 + - - +
78B LEU 3.4 0.6 - - - -
79B ARG* 1.3 77.3 - - - +
81B THR* 1.3 64.6 + - - +
48C SER 4.1 7.9 - - - +
49C ASP 4.9 3.1 - - - +
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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