Contacts of the helix formed by residues 70 - 80 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D GLY* 4.2 1.3 - - - -
26D VAL* 3.8 17.5 - - + -
27D ASN* 3.8 24.9 - - + +
68D GLY 4.7 1.1 - - - +
69D ALA* 1.3 75.8 - - - +
71D HIS* 1.3 65.3 + - - +
72D LYS* 3.7 8.9 + - - +
73D GLN* 3.1 39.9 + - - +
74D ALA* 3.0 20.7 + - - +
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Residues in contact with HIS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D VAL* 2.9 36.2 + - + +
23D THR* 4.0 2.4 - - - -
24D GLY 3.2 36.2 + - - +
27D ASN* 3.4 20.0 + - - +
28D THR* 4.8 3.6 - - + -
35D ILE* 5.7 1.3 - - + -
70D THR* 1.3 72.3 - - - +
72D LYS* 1.3 69.3 + - + +
74D ALA* 3.1 6.3 + - + +
75D VAL* 3.0 41.3 + - + +
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Residues in contact with LYS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASN* 5.1 5.6 - - - +
70D THR* 3.3 8.4 + - - +
71D HIS* 1.3 83.9 - - + +
73D GLN* 1.3 59.0 + - + +
75D VAL* 3.5 4.9 + - - +
76D GLU* 3.0 36.0 + - - +
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Residues in contact with GLN 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D GLY 3.9 5.0 - - - +
69D ALA* 3.4 14.2 - - + +
70D THR* 3.1 41.7 + - - +
72D LYS* 1.3 76.4 - - + +
74D ALA* 1.3 55.6 + - - +
76D GLU* 3.2 6.1 + - - +
77D THR* 2.7 41.4 + - - +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D VAL* 4.9 4.7 - - + -
35D ILE* 3.6 44.6 - - + -
66D LEU* 4.8 8.2 - - + +
69D ALA* 4.2 8.0 - - + +
70D THR 3.0 8.0 + - - +
71D HIS* 3.1 8.5 + - + +
73D GLN* 1.3 75.7 - - - +
75D VAL* 1.3 62.9 + - - +
77D THR* 3.3 8.0 + - - -
78D LEU* 3.0 31.0 + - + +
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Residues in contact with VAL 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D VAL* 3.8 16.2 - - + -
71D HIS* 3.0 40.1 + - + +
72D LYS* 3.7 8.7 - - - +
74D ALA* 1.3 75.9 - - - +
76D GLU* 1.3 63.0 + - - +
78D LEU* 3.3 10.5 + - - +
79D ARG* 3.0 65.4 + - + +
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Residues in contact with GLU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LYS* 3.0 25.3 + - - +
73D GLN* 3.2 7.8 + - - +
75D VAL* 1.3 80.8 - - - +
77D THR* 1.3 60.1 + - - +
79D ARG* 3.2 26.7 + - - +
80D ASN* 2.9 34.4 + - + +
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Residues in contact with THR 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D VAL* 3.9 20.0 - - + +
64D VAL* 5.9 2.9 - - + +
66D LEU* 3.8 28.1 - - + +
73D GLN* 2.7 24.6 + - - +
74D ALA 3.5 5.2 - - - -
76D GLU* 1.3 73.7 - - - +
78D LEU* 1.3 62.6 + - - +
80D ASN* 3.5 10.3 + - - +
81D THR* 3.4 17.0 - - - +
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 4.0 20.1 - - + +
20D ILE* 4.7 13.2 - - + -
22D VAL* 4.0 31.4 - - + -
35D ILE* 5.4 2.5 - - + -
58D VAL* 5.0 5.6 - - + -
61D VAL* 3.7 28.0 - - + -
66D LEU* 5.5 2.9 - - + -
74D ALA* 3.0 26.4 + - + +
75D VAL* 3.6 8.5 - - - +
76D GLU 3.3 0.2 - - - -
77D THR* 1.3 76.3 - - - +
79D ARG* 1.3 56.5 + - + +
81D THR* 2.7 30.0 + - - +
87D LEU* 3.9 16.8 - - + -
97D IOD 4.0 9.4 - - - +
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Residues in contact with ARG 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LYS* 3.9 5.1 + - - +
75D VAL* 3.0 42.5 + - - +
76D GLU* 3.2 25.0 + - - +
78D LEU* 1.3 74.9 - - + +
80D ASN* 1.3 50.6 + - - +
81D THR* 2.8 25.0 + - - +
97D IOD 4.4 16.6 - - + -
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Residues in contact with ASN 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B SER* 3.8 12.4 + - - +
49B ASP 4.7 4.2 - - - +
50B GLY* 6.3 0.6 - - - -
62D ASN* 5.4 0.2 + - - -
76D GLU* 2.9 18.3 + - + +
77D THR* 3.5 6.5 + - - +
78D LEU 3.4 0.6 - - - -
79D ARG* 1.3 72.1 - - - +
81D THR* 1.3 63.3 + - - +
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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