Contacts of the helix formed by residues 133 - 138 (chain C) in PDB entry 1KYZ
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 ASP 133 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LYS* 3.3 8.6 - - - +
129C LEU 3.3 13.2 + - - +
130C MET* 2.9 19.1 + - - +
132C GLN* 1.3 79.5 - - - +
134C LYS* 1.3 73.3 + - - +
135C VAL* 2.7 38.6 + - - +
136C LEU* 3.2 2.6 + - - -
137C MET* 3.1 18.2 + - - +
171C ARG* 2.7 34.5 + - - -
172C PHE* 4.0 16.8 - - + -
175C VAL* 4.6 8.4 - - + +
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Residues in contact with LYS 134 (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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37C LYS* 3.3 24.3 - - - +
41C GLU* 4.4 7.9 + - - -
132C GLN 3.5 1.6 + - - -
133C ASP* 1.3 75.2 + - - +
135C VAL* 1.3 71.7 + - + +
137C MET* 3.8 8.9 - - - +
138C GLU* 3.3 22.3 + - - +
158C TYR* 4.2 0.2 + - - -
171C ARG* 3.3 30.2 - - - +
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ASP* 2.7 20.5 + - - +
134C LYS* 1.3 79.8 - - + +
136C LEU* 1.3 61.9 + - - +
138C GLU* 3.2 8.0 + - - +
139C SER 4.2 1.0 + - - -
154C PHE* 4.1 7.7 - - + -
158C TYR* 2.6 38.9 + - + +
165C TYR* 3.5 38.1 - - + +
169C ASP* 4.7 2.9 - - - +
171C ARG* 4.6 6.3 - - - +
172C PHE* 3.3 34.1 - - + -
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Residues in contact with LEU 136 (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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130C MET* 3.5 38.4 - - + +
131C ASN* 4.0 22.9 - - - +
133C ASP 3.2 4.8 + - - +
135C VAL* 1.3 74.5 - - - +
137C MET* 1.3 61.3 + - - +
138C GLU 3.1 5.9 + - - -
139C SER* 3.3 7.5 + - - -
140C TRP* 3.9 5.6 + - - -
154C PHE* 4.6 11.0 - - + -
172C PHE* 3.3 27.3 - - + -
323C HIS* 3.2 56.3 - - + +
366C FER 3.7 21.8 - - + -
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Residues in contact with MET 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C SER* 6.0 4.5 - - - -
34C MET* 4.3 23.1 - - + -
131C ASN 3.7 14.6 - - - +
132C GLN* 3.5 29.2 - - + +
133C ASP 3.1 20.1 + - - +
134C LYS* 3.8 9.6 - - - +
135C VAL 3.2 0.2 - - - -
136C LEU* 1.3 77.0 - - - +
138C GLU* 1.3 62.0 + - - +
139C SER 3.3 0.2 - - - -
140C TRP* 3.5 37.0 + - + +
141C TYR* 3.3 28.8 - - + +
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Residues in contact with GLU 138 (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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134C LYS 3.3 9.7 + - - +
135C VAL 3.2 14.3 + - - +
136C LEU 3.1 0.4 - - - -
137C MET* 1.3 77.1 - - - +
139C SER* 1.3 65.2 + - - +
141C TYR* 3.1 35.9 + - - +
142C HIS* 3.4 24.7 + - - -
157C ALA* 3.9 11.6 - - + +
158C TYR* 3.4 26.5 - - + +
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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
------------------------------------------------------------
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