Contacts of the helix formed by residues 105 - 111 (chain B) in PDB entry 2ZTC
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 ASN 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B VAL* 2.8 41.6 + - + +
103B ASP* 3.3 13.5 + - + +
104B GLY* 1.3 73.2 - - - +
106B VAL* 1.3 62.0 + - - +
107B ALA* 3.3 8.3 + - - +
108B ALA* 3.1 33.6 + - - +
109B LEU* 3.7 5.7 - - - +
111B ARG* 5.1 5.5 + - - +
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Residues in contact with VAL 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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104B GLY 2.9 16.8 + - - +
105B ASN* 1.3 69.8 + - - +
107B ALA* 1.3 69.4 + - - +
108B ALA 3.1 1.6 - - - -
109B LEU* 2.9 17.5 + - - +
110B THR* 3.1 17.3 + - - +
117B LYS* 4.8 9.0 - - + +
120B ALA* 3.7 22.0 - - + -
121B GLU* 4.3 26.0 - - + +
124B VAL* 4.5 10.5 - - + -
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Residues in contact with ALA 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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194A LYS* 5.7 2.8 + - - +
105B ASN* 3.3 7.0 + - - +
106B VAL* 1.3 81.7 - - - +
108B ALA* 1.3 62.8 + - - +
110B THR* 3.3 8.0 + - - +
111B ARG* 3.0 40.9 + - - +
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Residues in contact with ALA 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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92B HIS* 3.1 27.7 + - + +
100B VAL* 3.6 20.0 - - + -
105B ASN* 3.1 30.4 + - - +
107B ALA* 1.3 80.0 - - - +
109B LEU* 1.3 57.6 + - - +
111B ARG* 3.1 41.1 - - - +
112B VAL 4.2 0.5 + - - -
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Residues in contact with LEU 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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88B ALA* 6.1 2.2 - - + -
92B HIS* 5.1 4.0 - - + -
97B LEU* 4.0 20.2 - - + -
100B VAL* 3.5 19.7 - - + -
101B LEU* 4.1 13.2 - - + -
105B ASN 3.7 11.7 - - - +
106B VAL* 2.9 7.9 + - - +
108B ALA* 1.3 72.4 - - - +
110B THR* 1.3 61.3 + - - +
111B ARG 3.0 1.8 - - - -
112B VAL* 2.9 30.2 + - + +
115B ILE* 3.6 18.5 - - + +
120B ALA* 3.7 28.3 - - + +
123B MET* 4.6 13.2 - - + -
124B VAL* 3.6 30.3 - - + -
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Residues in contact with THR 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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106B VAL* 3.1 23.0 + - - +
107B ALA* 3.3 9.1 + - - -
109B LEU* 1.3 71.3 - - - +
111B ARG* 1.3 58.1 - - - +
112B VAL 2.9 18.9 + - - +
115B ILE* 3.9 20.0 - - - +
116B GLY* 4.4 0.6 + - - -
117B LYS* 4.2 17.8 - - + +
120B ALA* 4.1 6.1 - - - +
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Residues in contact with ARG 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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160A PHE* 4.3 9.7 - - - -
192A LEU 4.0 17.5 - - - +
193A GLY* 2.8 39.6 + - - -
194A LYS* 2.9 55.8 + - + +
195A ALA 5.2 1.8 - - - -
91B VAL* 5.0 2.3 - - - +
92B HIS* 4.9 1.5 - - - +
105B ASN* 5.1 4.6 + - - +
107B ALA* 3.0 29.3 + - - +
108B ALA* 3.1 37.5 - - - +
109B LEU 3.0 0.2 - - - -
110B THR* 1.3 77.4 - - - +
112B VAL* 1.3 58.0 + - + +
113B PRO* 3.6 8.7 - - - +
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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