Contacts of the helix formed by residues 105 - 111 (chain B) in PDB entry 1LNU
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 CYS 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 5.4 0.2 - - - -
41B CYS* 2.0 49.1 - - + -
43B PHE* 3.1 33.3 - - - -
50B ILE* 3.5 18.2 - - - -
52B TYR* 4.5 0.4 - - + -
100B GLU 3.2 11.0 + - - +
101B LEU* 3.5 9.2 - - - +
102B ASP 3.8 0.4 + - - -
103B THR 3.5 2.0 + - - -
104B VAL* 1.3 82.6 - - - +
106B ARG* 1.3 66.4 + - - +
107B HIS 3.2 2.3 - - - +
108B ASN* 3.9 8.9 - - - +
109B TYR 3.2 10.2 + - - -
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Residues in contact with ARG 106 (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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47B THR* 3.4 30.8 + - - +
50B ILE* 3.9 13.2 - - + +
101B LEU* 3.3 27.4 + - - +
102B ASP* 2.7 37.0 + - - +
105B CYS* 1.3 77.9 - - - +
107B HIS* 1.3 58.5 + - - +
109B TYR* 4.5 2.0 - - - -
110B GLU* 2.8 70.2 + - - +
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Residues in contact with HIS 107 (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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1B PHE* 6.2 0.9 - - + -
2B GLU* 2.6 31.7 + - + +
4B GLN* 3.6 18.4 + - + +
102B ASP 2.9 18.2 + - - +
103B THR* 3.3 14.6 - - - +
106B ARG* 1.3 77.9 - - - +
108B ASN* 1.3 77.1 + - - +
110B GLU* 3.8 5.3 - - - +
111B GLY* 2.8 33.0 + - - -
112B PRO* 4.5 3.7 - - + +
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Residues in contact with ASN 108 (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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9A TYR* 4.1 31.6 - - + +
25A PHE* 4.4 1.2 - - - -
3B ALA* 3.1 16.0 - - + +
4B GLN* 2.7 47.4 + - - +
104B VAL 4.0 16.6 + - - -
105B CYS* 3.7 9.3 + - - +
106B ARG 3.4 0.2 - - - -
107B HIS* 1.3 86.3 - - - +
109B TYR* 1.3 59.7 + - - +
112B PRO* 3.1 10.6 - - + +
113B GLU* 2.7 36.4 + - + +
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Residues in contact with TYR 109 (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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5A HIS* 3.5 26.5 + + + -
27A PHE* 5.2 0.7 - + - -
43B PHE* 3.0 62.5 - + + -
46B GLY* 4.1 29.0 + - - -
47B THR* 4.3 15.3 - - + -
105B CYS 3.2 6.1 + - - +
106B ARG* 3.7 4.5 - - - +
108B ASN* 1.3 77.0 - - - +
110B GLU* 1.3 66.0 + - + +
113B GLU* 3.4 14.8 - - + +
114B THR* 2.8 39.0 + - - -
118B LEU* 3.1 36.7 - - + +
303B NAG 5.4 1.6 + - - -
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Residues in contact with GLU 110 (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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1B PHE* 5.1 0.3 - - - -
47B THR* 3.7 25.9 - - + +
106B ARG* 2.8 50.7 + - + +
107B HIS* 4.2 3.7 + - - +
109B TYR* 1.3 85.7 - - + +
111B GLY* 1.3 59.6 + - - +
114B THR* 3.9 9.7 - - - -
115B HIS* 3.9 13.0 + - - -
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Residues in contact with GLY 111 (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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1B PHE* 3.6 19.6 - - - -
107B HIS* 2.8 18.9 + - - -
109B TYR 3.1 1.4 + - - -
110B GLU* 1.3 73.7 - - - +
112B PRO* 1.3 71.3 - - - +
115B HIS* 2.7 31.2 + - - -
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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
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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