Contacts of the helix formed by residues 104 - 112 (chain C) in PDB entry 1Z10
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 GLN 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C GLU* 1.3 73.5 - - - +
105C ALA* 1.3 55.0 + - - +
106C THR* 2.9 25.1 + - - -
107C PHE* 3.0 32.3 + - + +
108C ASP* 2.7 35.9 + - - +
118C PHE* 3.9 26.0 - - + -
212C THR* 4.0 10.9 - - - +
217C GLY 5.4 0.4 + - - -
218C GLN* 4.5 2.4 + - - -
221C GLU* 3.1 29.9 + - - +
370C LEU* 5.9 2.9 - - + -
371C ALA 6.2 1.1 - - - +
480C PHE* 3.9 38.1 - - + +
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ARG* 4.8 0.4 - - - +
103C GLU* 3.9 17.0 - - - +
104C GLN* 1.3 72.2 - - - +
106C THR* 1.3 60.4 + - - +
108C ASP* 3.3 9.0 + - - +
109C TRP* 3.2 18.4 + - - +
220C TYR* 3.6 25.0 + - + +
221C GLU* 2.9 26.3 + - - +
224C SER* 3.8 20.6 - - - +
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Residues in contact with THR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLN* 2.9 11.1 + - - -
105C ALA* 1.3 75.7 - - - +
107C PHE* 1.3 66.4 + - + +
109C TRP* 3.2 19.4 + - - +
208C ILE* 4.7 6.7 - - + -
211C PHE* 3.3 32.0 - - + -
212C THR* 3.6 23.5 - - + +
217C GLY 4.5 2.1 + - - -
220C TYR* 3.4 17.8 - - - -
221C GLU* 3.2 7.7 + - - -
237C ALA* 4.6 7.9 - - + -
238C PHE* 4.8 6.2 - - + -
241C LEU* 3.3 20.6 - - + +
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Residues in contact with PHE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLN* 3.0 37.7 + - + +
106C THR* 1.3 77.3 - - - +
108C ASP* 1.3 60.6 + - - +
110C VAL* 3.1 12.1 + - - +
111C PHE* 3.1 33.5 + + + -
118C PHE* 3.6 31.0 - + + -
208C ILE* 3.5 29.8 - - + -
209C PHE* 4.2 10.8 - + - -
212C THR* 4.2 7.2 - - + -
241C LEU* 4.3 12.8 - - + -
300C ILE* 4.9 7.9 - - + -
480C PHE* 3.6 36.1 - + - -
501C COU 3.7 25.4 - + - -
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Residues in contact with ASP 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C GLU* 5.4 6.5 - - + -
104C GLN 2.7 24.8 + - - +
105C ALA* 3.6 11.4 - - - +
106C THR 3.2 0.2 - - - -
107C PHE* 1.3 73.3 - - - +
109C TRP* 1.3 65.1 + - - +
111C PHE* 4.9 2.7 - - - -
112C LYS* 3.0 43.1 + - - +
113C GLY* 3.9 6.4 + - - -
118C PHE* 5.5 8.7 - - + +
228C LYS* 5.7 2.6 + - - -
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Residues in contact with TRP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ALA 3.2 10.2 + - - +
106C THR 3.2 14.6 - - - +
107C PHE 3.1 0.2 - - - -
108C ASP* 1.3 78.6 - - - +
110C VAL* 1.3 72.4 + - + +
112C LYS* 3.7 21.2 + - - +
220C TYR* 4.1 6.7 - - - +
228C LYS* 4.6 18.2 + - + +
235C GLN* 5.8 0.4 - - - -
238C PHE* 3.5 81.7 - + + -
241C LEU* 4.5 2.9 - - + -
242C GLN* 3.8 28.3 - - + -
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C THR 4.3 0.2 + - - -
107C PHE 3.1 12.2 + - - +
109C TRP* 1.3 89.0 - - + +
111C PHE* 1.3 91.9 + - + +
112C LYS* 3.4 13.7 + - - +
241C LEU* 3.8 38.6 - - + +
242C GLN* 5.0 0.9 - - - +
245C GLU* 3.3 42.1 - - + +
289C LYS* 4.4 0.9 + - - -
293C MET* 3.3 20.1 - - + +
296C LEU* 4.6 4.7 - - + -
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Residues in contact with PHE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C PHE* 3.1 36.7 + + - +
108C ASP* 4.9 1.1 - - - -
110C VAL* 1.3 87.7 - - + +
112C LYS* 1.3 69.8 + - - +
113C GLY 4.3 3.4 - - - +
114C TYR* 2.8 33.5 + - - +
118C PHE* 3.5 30.7 - + + -
241C LEU* 5.1 0.2 - - + -
289C LYS* 4.8 0.2 - - - -
293C MET* 3.6 32.8 - - + +
296C LEU* 3.5 35.9 - - + -
297C ASN* 3.1 26.2 - - - -
300C ILE* 4.4 6.7 - - + -
501C COU 3.7 16.6 - - - -
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Residues in contact with LYS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ASP* 3.0 29.3 + - - +
109C TRP* 3.7 17.4 + - - +
110C VAL* 3.8 11.2 + - - +
111C PHE* 1.3 76.6 - - - +
113C GLY* 1.3 59.1 - - - +
114C TYR* 3.4 20.4 - - + -
123C ARG* 5.0 0.7 + - - -
245C GLU* 5.6 3.2 + - - -
289C LYS* 4.6 16.4 - - - +
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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