Contacts of the helix formed by residues 100 - 105 (chain B) in PDB entry 1U3W
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 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B CYS* 3.3 7.5 - - - -
99B LYS* 1.3 81.5 - - - +
101B ARG* 1.3 66.6 + - - +
102B ILE* 3.1 8.5 + - - -
103B CYS* 3.1 14.9 + - - -
104B LYS* 3.0 22.5 + - - -
112B LEU* 3.5 39.9 - - + -
113B LYS* 5.3 4.5 - - - +
375B ZN 2.3 34.5 - - - -
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Residues in contact with ARG 101 (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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194A THR* 4.3 2.8 + - - -
258A THR 3.0 9.0 + - - -
259A ASP* 3.0 49.1 + - - +
261A GLY 2.9 29.5 + - - -
262A VAL 4.0 0.6 - - - -
263A ASP* 2.9 36.0 + - - +
283A HIS* 3.4 18.3 - - - +
286A CYS* 3.7 16.0 - - - -
100B CYS* 1.3 74.3 - - - +
102B ILE* 1.3 69.5 + - + +
104B LYS* 3.3 18.1 + - - +
105B ASN* 3.1 24.5 + - + +
112B LEU* 4.8 9.0 - - + +
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Residues in contact with ILE 102 (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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283A HIS* 3.4 38.8 - - + +
285A ALA* 3.6 8.5 - - + -
286A CYS* 3.8 22.0 - - + -
100B CYS* 3.1 7.6 - - - -
101B ARG* 1.3 80.8 - - + +
103B CYS* 1.3 66.7 + - - +
105B ASN* 3.3 4.0 + - + +
108B SER* 3.0 30.5 + - - +
109B ASN 3.9 2.9 - - - +
110B TYR* 3.4 48.0 - - - +
111B CYS 4.1 0.4 - - - +
112B LEU* 4.0 12.1 - - + -
323B LYS* 3.2 10.0 + - - -
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Residues in contact with CYS 103 (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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96B GLN* 3.9 18.2 + - + -
97B CYS 3.5 8.1 - - - -
98B GLY* 3.3 36.9 - - - +
100B CYS* 3.1 4.9 + - - +
102B ILE* 1.3 78.1 - - - +
104B LYS* 1.3 59.8 + - - +
109B ASN* 5.7 3.4 - - - +
111B CYS* 3.8 9.9 - - - -
323B LYS* 2.8 25.6 + - - +
375B ZN 2.3 35.0 - - - -
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Residues in contact with LYS 104 (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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98B GLY 4.2 15.0 - - - +
99B LYS* 3.4 19.7 + - - +
100B CYS 3.0 24.6 + - - +
101B ARG* 3.8 14.1 - - - +
103B CYS* 1.3 77.5 - - - +
105B ASN* 1.3 61.2 + - - +
106B PRO* 3.5 9.5 - - - +
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Residues in contact with ASN 105 (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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263A ASP* 4.0 10.9 + - - -
286A CYS* 3.6 30.3 + - + +
101B ARG* 3.1 18.5 + - + +
102B ILE* 3.3 2.7 + - - +
104B LYS* 1.3 76.9 - - - +
106B PRO* 1.3 71.0 - - - +
107B GLU* 3.1 23.3 + - - +
108B SER* 3.2 19.0 + - - +
323B LYS* 2.7 23.4 + - - -
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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