Contacts of the helix formed by residues 164 - 179 (chain A) in PDB entry 1KSG
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A PHE* 4.2 0.5 - - - -
155A GLN* 3.7 20.9 - - - +
156A GLY 3.1 24.6 - - - +
157A CYS* 3.9 4.0 - - - +
162A GLY 3.4 1.6 + - - -
163A GLU* 1.3 88.7 - - - +
165A LEU* 1.3 61.9 + - - +
167A PRO* 3.3 28.5 - - - +
168A GLY 3.7 7.3 + - - -
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ILE* 4.0 30.5 - - + -
35A LYS* 4.0 23.3 - - + +
36A PHE* 4.1 17.5 - - + -
123A PHE* 3.5 13.2 - - + -
157A CYS* 3.8 27.8 - - + -
158A SER 4.5 0.9 - - - +
159A ALA* 4.2 9.6 - - - -
162A GLY* 3.4 35.6 + - - +
163A GLU 3.3 2.0 - - - +
164A ASP* 1.3 77.5 - - - +
166A LEU* 1.3 66.5 + - + +
168A GLY 3.4 2.1 + - - -
169A ILE* 3.1 26.1 + - - +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 5.1 15.7 - - + -
57A HIS* 4.4 23.8 - - + +
162A GLY 5.5 4.3 - - - +
165A LEU* 1.3 79.5 - - + +
167A PRO* 1.3 65.7 - - + +
169A ILE* 3.2 5.1 + - + +
170A ASP* 2.8 45.3 + - - +
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Residues in contact with PRO 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ARG* 5.3 0.5 + - - -
155A GLN* 3.9 19.9 + - - +
164A ASP* 3.3 32.1 - - - +
166A LEU* 1.3 94.4 - - + +
168A GLY* 1.3 59.4 + - - +
170A ASP* 3.8 7.0 - - + +
171A TRP* 3.1 24.6 + - - +
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Residues in contact with GLY 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 3.6 21.4 - - - +
123A PHE* 3.9 3.4 - - - -
153A ARG* 5.8 0.4 - - - -
155A GLN* 3.8 22.9 - - - +
164A ASP 3.7 3.8 + - - -
165A LEU 3.4 6.3 + - - -
166A LEU 3.2 0.4 - - - -
167A PRO* 1.3 81.7 - - - +
169A ILE* 1.3 61.9 + - - +
171A TRP* 3.4 4.7 + - - +
172A LEU* 3.1 22.2 + - - +
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Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 5.1 4.3 - - + -
36A PHE* 3.4 39.5 - - + -
57A HIS* 4.3 13.7 - - + -
62A LEU* 4.9 7.6 - - + -
64A ILE* 6.2 0.7 - - + -
88A ILE* 4.0 24.7 - - + -
121A LEU* 4.1 9.6 - - + +
123A PHE* 4.2 2.7 - - + -
165A LEU 3.1 14.6 + - - +
166A LEU* 3.2 9.4 + - + +
168A GLY* 1.3 74.6 - - - +
170A ASP* 1.3 58.9 + - - +
172A LEU* 3.2 9.7 + - + +
173A LEU* 2.9 50.3 + - + +
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Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A HIS* 3.4 25.5 + - - -
58A ARG* 3.5 38.6 + - - +
166A LEU* 2.8 30.7 + - - +
167A PRO* 3.8 6.8 - - + +
169A ILE* 1.3 70.0 - - - +
171A TRP* 1.3 65.8 + - - +
173A LEU* 3.3 2.2 + - - -
174A ASP* 3.0 28.5 + - - +
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Residues in contact with TRP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A THR* 3.5 31.2 - - + -
120A LEU 3.7 15.3 - - - -
121A LEU* 4.3 7.9 - - + -
151A HIS* 4.2 2.2 - - + -
152A TRP* 3.6 18.8 - - - -
153A ARG* 3.5 57.1 - - + +
167A PRO 3.1 15.0 + - - +
168A GLY* 3.7 6.1 - - - +
169A ILE 3.4 0.2 - - - -
170A ASP* 1.3 77.5 - - - +
172A LEU* 1.3 86.6 + - + +
174A ASP* 3.1 12.5 + - + +
175A ASP* 3.0 37.6 + - + +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.1 20.0 - - + -
86A GLY* 4.4 2.9 - - - -
87A LEU 4.8 0.7 - - - +
88A ILE* 3.8 34.3 - - + -
119A THR* 3.6 41.1 - - + +
121A LEU* 4.2 20.2 - - + +
168A GLY 3.1 10.3 + - - +
169A ILE* 3.3 13.0 - - + +
171A TRP* 1.3 90.2 - - + +
173A LEU* 1.3 64.0 + - + +
175A ASP* 3.4 1.0 + - - +
176A ILE* 3.1 40.7 + - + +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.7 26.9 - - + -
19A LEU* 4.4 12.8 - - + -
57A HIS* 3.9 28.9 - - + +
58A ARG* 4.0 19.5 - - + -
60A PHE* 3.9 17.8 - - + -
62A LEU* 3.8 20.2 - - + -
169A ILE* 2.9 40.2 + - + +
170A ASP 3.3 3.6 + - - +
172A LEU* 1.3 74.0 - - + +
174A ASP* 1.3 59.4 + - - +
176A ILE* 4.1 7.5 - - + +
177A SER* 3.0 26.2 + - - -
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Residues in contact with ASP 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 2.5 40.4 + - - -
170A ASP* 3.0 14.9 + - - +
171A TRP* 3.1 13.9 + - + +
173A LEU* 1.3 76.0 - - - +
175A ASP* 1.3 66.2 + - - +
177A SER* 3.0 23.3 + - - -
178A SER* 3.3 9.1 + - - -
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Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A THR* 2.9 39.8 + - + +
151A HIS* 2.8 43.2 + - - +
171A TRP* 3.0 27.9 + - + +
172A LEU 4.0 0.2 - - - +
174A ASP* 1.3 76.6 - - - +
176A ILE* 1.3 64.7 + - - +
178A SER* 3.1 23.9 + - - -
179A ARG* 3.7 4.9 + - - +
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ARG* 3.5 29.5 + - - +
17A LEU* 4.0 25.8 - - + -
19A LEU* 3.9 21.1 - - + -
60A PHE* 5.6 0.7 - - + -
85A ASP* 3.5 33.2 - - + +
86A GLY* 4.0 4.0 - - - -
119A THR* 3.5 19.5 - - - +
172A LEU* 3.1 24.9 + - + +
173A LEU* 4.1 6.3 - - + +
175A ASP* 1.3 76.5 - - - +
177A SER* 1.3 61.6 + - - +
179A ARG* 3.1 15.4 + - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ARG* 4.2 8.5 + - - +
60A PHE* 3.0 30.4 - - - -
173A LEU 3.0 8.4 + - - -
174A ASP* 3.0 18.6 + - - -
176A ILE* 1.3 80.1 - - - +
178A SER* 1.3 60.5 + - - +
179A ARG* 3.2 13.9 + - - +
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A HIS* 6.4 1.6 - - - -
174A ASP 3.3 8.9 + - - -
175A ASP* 3.1 15.5 + - - -
177A SER* 1.3 75.6 - - - +
179A ARG* 1.3 72.5 + - - +
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Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ARG* 3.5 53.1 - - - +
117A GLY 5.5 2.4 - - - +
175A ASP 3.7 3.9 + - - +
176A ILE* 3.1 13.1 + - - +
177A SER 3.3 15.1 + - - +
178A SER* 1.3 85.4 - - - +
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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