Contacts of the helix formed by residues 121 - 136 (chain X) in PDB entry 1KKC
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 SER 121 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115X ILE* 4.4 0.2 - - - +
116X GLU* 3.8 12.5 + - - +
119X TRP* 3.1 7.0 + - - +
120X GLY* 1.3 79.3 - - - +
122X PHE* 1.3 64.5 + - - +
123X ASP* 3.4 8.0 + - - +
124X LYS* 3.0 33.7 + - - +
125X PHE* 3.1 21.5 + - - +
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Residues in contact with PHE 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X GLY 5.7 1.8 - - - -
105X ILE* 3.6 44.6 - - + -
112X LYS* 4.0 22.4 - - + -
115X ILE* 4.3 15.3 - - + -
116X GLU* 4.2 8.5 + - + +
121X SER* 1.3 72.8 - - - +
123X ASP* 1.3 64.4 + - - +
125X PHE* 3.2 15.1 + + - +
126X LYS* 3.0 65.9 + - + +
196X TRP* 4.9 0.9 - + + -
201X TRP* 3.6 37.7 - + - -
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Residues in contact with ASP 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X SER* 3.2 7.4 + - - +
122X PHE* 1.3 83.8 - - - +
124X LYS* 1.3 65.7 + - + +
126X LYS* 3.2 32.1 + - - +
127X ASP* 3.1 29.0 + - - +
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Residues in contact with LYS 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119X TRP* 3.4 31.4 - - + +
120X GLY* 4.9 3.3 - - - -
121X SER* 3.0 24.7 + - - +
123X ASP* 1.3 77.0 - - + +
125X PHE* 1.3 63.2 + - - +
127X ASP* 3.4 11.6 + - - +
128X ALA* 3.1 22.7 + - - +
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Residues in contact with PHE 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115X ILE* 3.3 27.1 - - + -
119X TRP* 3.6 38.7 - + + +
121X SER 3.1 8.2 + - - +
122X PHE* 3.2 20.2 - + - +
123X ASP 3.1 0.2 - - - -
124X LYS* 1.3 77.4 - - - +
126X LYS* 1.3 60.9 + - + +
128X ALA* 3.2 2.9 + - - +
129X PHE* 2.9 44.8 + + - +
144X LEU* 3.9 25.6 - - + -
155X ILE* 3.8 20.0 - - + -
171X PHE* 3.8 19.3 - + - -
196X TRP* 3.7 24.9 - + - -
201X TRP* 4.2 7.4 - + - -
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Residues in contact with LYS 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122X PHE* 3.0 51.6 + - + +
123X ASP* 3.2 35.7 + - - +
125X PHE* 1.3 78.4 - - + +
127X ASP* 1.3 58.1 + - - +
129X PHE* 3.2 2.1 + - - +
130X ASN* 2.9 38.7 + - - +
196X TRP* 3.7 57.9 - - + +
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Residues in contact with ASP 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123X ASP* 3.1 20.3 + - - +
124X LYS* 3.8 10.4 - - - +
125X PHE 3.3 0.2 - - - -
126X LYS* 1.3 75.8 - - - +
128X ALA* 1.3 62.5 + - - +
130X ASN* 3.4 14.8 + - - +
131X THR* 3.0 27.2 + - - -
193X LYS* 6.1 0.7 - - - -
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Residues in contact with ALA 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119X TRP* 4.1 23.1 - - + +
124X LYS 3.1 14.1 + - - +
125X PHE 3.6 6.7 - - - +
127X ASP* 1.3 77.1 - - - +
129X PHE* 1.3 62.2 + - - +
131X THR* 3.4 7.6 + - - -
132X THR* 3.1 26.1 + - - -
155X ILE* 4.2 6.3 - - + -
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Residues in contact with PHE 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125X PHE* 2.9 31.4 + + + +
126X LYS 3.5 4.3 - - - +
128X ALA* 1.3 75.1 - - - +
130X ASN* 1.3 66.1 - - - +
132X THR* 3.1 5.7 + - - -
133X LEU* 2.9 56.8 + - + +
142X GLY* 3.7 24.7 - - - -
143X TRP* 3.6 27.8 - - - -
144X LEU* 3.9 4.9 - - + -
155X ILE* 3.9 20.1 - - + +
171X PHE* 3.7 21.1 - + - -
173X VAL* 3.8 14.6 - - + -
196X TRP* 3.6 22.4 - + + -
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Residues in contact with ASN 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X LYS* 2.9 25.8 + - - +
127X ASP* 3.7 15.0 + - - +
129X PHE* 1.3 76.1 - - - +
131X THR* 1.3 56.3 + - - +
133X LEU* 3.2 8.5 + - - +
134X LEU* 2.9 39.7 + - + +
192X ALA* 3.5 22.1 - - + +
193X LYS* 4.1 26.0 - - + +
196X TRP* 2.8 31.5 + - - +
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Residues in contact with THR 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127X ASP 3.0 18.3 + - - -
128X ALA* 3.6 8.4 - - - -
130X ASN* 1.3 77.2 - - - +
132X THR* 1.3 63.3 + - - +
134X LEU* 3.4 8.0 + - - +
135X GLY* 3.0 20.1 + - - -
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Residues in contact with THR 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X ALA 3.1 14.7 + - - -
129X PHE* 3.1 7.8 + - - -
131X THR* 1.3 76.6 - - - +
133X LEU* 1.3 65.6 + - - +
135X GLY* 3.0 12.3 + - - -
136X ILE* 3.3 12.5 + - - +
142X GLY* 5.5 2.7 - - - -
155X ILE* 3.5 31.7 - - + +
156X THR* 4.4 1.6 - - - +
157X THR* 3.2 32.0 - - + +
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Residues in contact with LEU 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129X PHE* 2.9 43.5 + - + +
130X ASN* 3.2 11.0 + - - +
132X THR* 1.3 76.9 - - - +
134X LEU* 1.3 64.4 + - + +
136X ILE* 3.2 23.9 + - + +
142X GLY* 3.5 31.6 - - - -
173X VAL* 3.9 22.7 - - + -
175X MET* 3.4 40.8 - - + +
188X LYS* 5.2 0.5 - - - +
192X ALA* 3.9 23.8 - - + +
195X ILE* 5.6 0.7 - - + -
196X TRP* 5.3 0.9 - - + -
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Residues in contact with LEU 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X ASN* 2.9 25.9 + - + +
131X THR* 3.9 6.7 - - - +
133X LEU* 1.3 78.9 - - + +
135X GLY* 1.3 61.4 + - - +
136X ILE 3.3 0.7 - - - +
175X MET* 4.5 1.8 - - + -
188X LYS* 3.3 50.3 + - + +
189X ALA* 3.7 38.1 - - + +
192X ALA* 4.2 11.4 - - + -
193X LYS* 5.8 2.7 - - - +
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Residues in contact with GLY 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131X THR 3.0 14.5 + - - -
132X THR* 3.0 6.6 + - - -
134X LEU* 1.3 77.6 - - - +
136X ILE* 1.3 64.3 + - - +
137X GLN* 3.3 15.2 + - - +
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Residues in contact with ILE 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132X THR 3.3 8.7 + - - +
133X LEU* 3.2 19.1 + - - +
134X LEU 4.0 5.7 - - - +
135X GLY* 1.3 78.9 - - - +
137X GLN* 1.3 66.4 + - - +
138X GLY 3.7 19.6 + - - +
139X SER 4.7 0.2 - - - +
140X GLY* 4.0 16.2 - - - -
141X TRP 3.3 40.4 - - - +
142X GLY* 3.9 4.5 - - - +
157X THR* 3.8 19.5 - - + -
158X THR 5.3 1.6 - - - +
159X HIS* 5.5 1.6 - - - +
175X MET* 4.0 17.9 - - + -
188X LYS* 4.1 10.6 + - - -
80Y PHE* 5.5 0.3 - - - -
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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