Contacts of the helix formed by residues 124 - 132 (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 ILE 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C TYR* 3.1 44.3 + - + +
115C LEU* 4.8 6.7 - - + -
123C SER* 1.3 73.2 - - - +
125C SER* 1.3 61.8 + - - +
126C ALA 3.1 0.7 - - - -
127C LEU* 3.0 39.3 + - + +
128C ASN* 3.8 2.8 + - - +
182C ASP* 5.5 0.2 - - - -
183C HIS* 6.0 7.4 - - + +
186C ILE* 4.0 19.5 - - + -
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Residues in contact with SER 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.7 28.3 - - - +
114C TYR 3.9 0.4 + - - -
115C LEU* 2.5 51.6 + - - +
123C SER* 3.0 12.7 - - - -
124C ILE* 1.3 79.6 - - - +
126C ALA* 1.3 61.3 + - - +
128C ASN* 3.2 17.2 + - - +
129C LEU* 3.4 12.4 + - - +
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Residues in contact with ALA 126 (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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123C SER* 3.3 14.0 + - - +
124C ILE 3.1 0.6 - - - -
125C SER* 1.3 79.3 - - - +
127C LEU* 1.3 61.8 + - - +
129C LEU* 3.3 16.7 + - + +
130C MET* 3.2 19.8 + - - +
175C VAL* 4.4 4.0 - - - +
178C LYS* 3.7 34.1 - - + +
179C GLY* 3.9 17.1 - - - +
182C ASP* 4.1 4.3 - - - +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C SER 5.1 0.4 - - - +
124C ILE* 3.0 32.0 + - + +
126C ALA* 1.3 79.6 - - + +
128C ASN* 1.3 55.8 + - - +
130C MET* 3.1 19.0 + - + +
131C ASN* 2.8 47.6 + - - +
179C GLY* 3.0 41.3 - - - +
180C MET* 5.5 0.7 - - - -
183C HIS* 3.7 36.8 - - + +
366C FER 5.2 3.1 - - - +
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Residues in contact with ASN 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PRO* 3.7 15.8 + - - +
36C LEU* 3.5 24.9 - - + +
37C LYS* 3.2 29.2 - - - +
40C LEU* 4.0 14.0 - - + +
115C LEU* 6.2 0.7 - - + -
124C ILE 3.8 1.9 + - - +
125C SER* 3.2 14.6 + - - +
127C LEU* 1.3 80.5 - - - +
129C LEU* 1.3 61.3 + - - +
131C ASN* 4.9 0.4 - - - -
132C GLN* 2.9 47.3 + - - +
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Residues in contact with LEU 129 (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* 4.1 28.2 - - + -
40C LEU* 4.1 23.3 - - + +
41C GLU* 4.1 20.2 - - + +
125C SER 3.4 13.0 + - - +
126C ALA* 3.3 17.0 + - + +
127C LEU 3.2 0.2 - - - -
128C ASN* 1.3 78.3 - - - +
130C MET* 1.3 60.9 + - - +
132C GLN 4.1 0.3 - - - -
133C ASP* 3.3 23.6 + - - +
175C VAL* 3.7 15.1 - - + +
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Residues in contact with MET 130 (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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126C ALA 3.2 9.0 + - - +
127C LEU* 3.1 30.0 + - + +
129C LEU* 1.3 76.1 - - - +
131C ASN* 1.3 70.7 + - - +
132C GLN 3.1 1.1 - - - -
133C ASP* 2.9 22.0 + - - +
136C LEU* 3.5 24.2 - - + +
172C PHE* 4.8 4.4 - - + -
175C VAL* 3.6 16.6 - - + +
176C PHE* 3.2 50.0 - - + +
179C GLY* 4.8 1.1 - - - -
180C MET* 4.0 13.5 - - - -
366C FER 3.3 35.2 - - + +
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Residues in contact with ASN 131 (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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127C LEU* 2.8 35.1 + - - +
130C MET* 1.3 75.6 - - - +
132C GLN* 1.3 75.7 + - - +
133C ASP 3.3 0.7 + - - -
136C LEU* 4.0 19.2 - - - +
137C MET* 3.7 15.8 + - - +
140C TRP* 5.2 2.3 + - - -
319C ILE* 3.5 29.1 - - + +
323C HIS* 5.7 0.8 + - - -
366C FER 2.8 31.4 + - - +
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Residues in contact with GLN 132 (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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33C PRO* 3.9 26.1 - - + +
34C MET* 3.8 28.1 - - - +
37C LYS* 2.7 38.1 + - + +
128C ASN* 2.9 50.6 + - - +
129C LEU 4.1 0.2 - - - -
131C ASN* 1.3 88.4 - - - +
133C ASP* 1.3 60.1 + - - +
134C LYS 3.5 0.2 + - - -
137C MET* 3.5 19.7 - - + +
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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