Contacts of the helix formed by residues 160 - 172 (chain A) in PDB entry 1KPI
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 GLU 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ASP 5.6 0.7 - - - +
157A ALA 4.1 6.2 - - - +
158A GLY* 3.4 20.1 - - - +
159A PHE* 1.3 85.9 + - - +
161A ARG* 1.3 66.5 + - + +
162A TYR 3.2 0.2 - - - -
163A ASP* 3.1 22.5 + - - +
164A THR* 4.0 3.6 + - - -
229A TYR* 4.1 14.3 + - - -
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Residues in contact with ARG 161 (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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13A LEU* 3.8 23.1 - - + +
14A LYS 2.8 39.0 + - - +
131A TRP* 3.3 21.8 - - + -
132A GLU* 2.7 29.2 + - - +
150A PHE 3.2 32.0 + - - +
151A ALA* 3.8 13.5 - - - -
152A ASP 3.3 10.9 + - - -
153A GLY* 3.4 3.4 - - - -
156A ASP* 3.0 38.1 + - - +
158A GLY 3.0 17.0 + - - +
159A PHE 2.7 5.0 + - - +
160A GLU* 1.3 75.1 - - + +
162A TYR* 1.3 64.4 + - - +
163A ASP 3.1 0.7 + - - -
164A THR* 3.1 15.6 + - - +
165A PHE 3.1 8.8 + - - -
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Residues in contact with TYR 162 (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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147A PHE* 3.4 42.8 + + - -
150A PHE* 4.2 8.5 - - + -
151A ALA* 3.7 31.6 - - + +
159A PHE* 2.7 50.9 + + - +
161A ARG* 1.3 73.2 - - - +
163A ASP* 1.3 62.1 + - - +
165A PHE* 3.2 8.0 + - + +
166A PHE* 3.0 36.2 + + + -
219A ARG 4.0 4.5 + - - -
221A PRO* 3.4 28.7 - - + +
225A GLN* 4.7 8.5 - - + -
226A VAL* 5.3 0.9 - - + -
229A TYR* 3.6 32.8 - + + -
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Residues in contact with ASP 163 (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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160A GLU 3.1 13.8 + - - +
161A ARG 3.0 0.2 - - - -
162A TYR* 1.3 81.2 - - - +
164A THR* 1.3 62.5 + - - +
166A PHE* 3.7 1.4 + - - +
167A LYS* 3.3 29.2 + - - +
228A TYR* 4.7 4.5 - - - -
229A TYR* 3.2 29.5 - - + -
232A ASN* 3.1 38.0 + - - +
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Residues in contact with THR 164 (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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13A LEU* 3.8 29.7 - - + +
131A TRP* 4.4 6.5 - - + -
132A GLU* 6.3 0.7 - - - -
160A GLU 4.6 3.6 + - - -
161A ARG* 3.1 9.1 + - - -
163A ASP* 1.3 77.8 - - - +
165A PHE* 1.3 57.8 + - - +
167A LYS* 3.8 6.6 - - + +
168A LYS* 2.8 43.7 + - + +
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Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 4.0 8.7 - - + -
131A TRP* 3.4 34.4 - + + -
143A SER* 5.6 1.8 - - - -
147A PHE* 3.8 13.5 - + - -
150A PHE* 3.6 32.1 - + + -
161A ARG 3.1 5.3 + - - +
162A TYR* 3.3 11.7 - - + +
164A THR* 1.3 80.9 - - - +
166A PHE* 1.3 104.2 + + - +
169A PHE* 3.0 58.1 + + - -
179A MET* 3.9 25.8 - - + -
181A LEU* 4.7 5.8 - - + -
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE* 3.8 16.8 - + - -
162A TYR* 3.0 33.0 + + + +
163A ASP 4.5 0.7 - - - +
165A PHE* 1.3 102.7 - + - +
167A LYS* 1.3 59.6 + - - +
169A PHE* 5.3 1.3 - - - -
170A TYR* 3.1 12.6 + - - +
179A MET* 4.4 3.6 - - - -
181A LEU* 3.5 23.3 - - + -
226A VAL* 4.3 8.1 - - + -
229A TYR* 3.7 19.1 - - + +
230A SER* 3.5 37.2 - - - -
233A ALA* 3.3 5.0 - - + +
235A TRP* 2.8 36.7 + + + +
300A LEU* 3.6 25.8 - - + -
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Residues in contact with LYS 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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163A ASP* 3.3 22.7 + - - +
164A THR* 3.8 6.3 - - + +
165A PHE 3.2 0.4 - - - -
166A PHE* 1.3 77.1 - - - +
168A LYS* 1.3 68.0 + - - +
170A TYR* 3.0 13.7 + - - +
171A ASN* 3.0 36.6 + - - +
232A ASN* 5.6 0.7 - - - +
233A ALA* 3.8 13.4 - - + +
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Residues in contact with LYS 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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12A GLN* 5.2 4.4 - - - +
131A TRP* 3.0 37.2 - - + +
132A GLU 3.6 17.2 + - - +
133A GLU 4.5 1.2 - - - -
134A PHE 2.6 29.8 + - - -
135A ASP* 4.7 7.1 + - - +
164A THR* 2.8 26.1 + - + +
165A PHE 3.6 4.3 - - - +
167A LYS* 1.3 79.3 - - - +
169A PHE* 1.3 70.0 + - + +
171A ASN* 3.3 7.6 + - - +
172A LEU* 3.1 39.8 + - + +
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Residues in contact with PHE 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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77A LEU* 3.9 21.1 - - + -
79A ILE* 3.8 6.7 - - + -
101A LEU* 5.3 0.2 - - + -
131A TRP* 3.6 41.5 - + + -
134A PHE* 4.0 17.9 - + + -
138A VAL* 5.7 0.4 - - + -
141A ILE* 3.5 26.6 - - + +
165A PHE* 3.0 59.7 + + - +
166A PHE* 5.0 0.9 - - - +
168A LYS* 1.3 80.8 - - + +
170A TYR* 1.3 60.4 + - - +
171A ASN 3.3 0.2 - - - -
172A LEU* 3.7 17.9 - - + +
173A THR* 2.8 28.4 + - - +
179A MET* 3.8 10.3 - - + -
235A TRP* 3.6 7.0 - - + -
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Residues in contact with TYR 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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166A PHE 3.1 19.0 + - - +
167A LYS* 3.0 9.3 + - - +
169A PHE* 1.3 78.4 - - - +
171A ASN* 1.3 71.9 + - - +
173A THR* 3.3 3.5 + - - +
233A ALA 3.6 20.4 - - - +
234A GLY* 3.4 30.9 + - - -
235A TRP* 3.5 30.7 - + - -
302A LYS* 2.7 68.2 + - + +
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Residues in contact with ASN 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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167A LYS* 3.0 38.8 + - - +
168A LYS* 3.7 8.2 - - - +
170A TYR* 1.3 88.6 - - - +
172A LEU* 1.3 61.4 + - + +
173A THR 3.3 7.2 + - - +
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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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134A PHE* 3.8 35.7 - - + +
135A ASP* 3.9 14.1 - - - +
136A GLU 3.2 36.6 - - - +
137A PRO* 3.4 10.3 - - + +
138A VAL* 2.9 30.2 + - + +
168A LYS* 3.1 25.3 + - + +
169A PHE* 3.7 20.8 + - + -
170A TYR 3.3 0.6 - - - -
171A ASN* 1.3 82.2 - - + +
173A THR* 1.3 60.4 + - - +
174A PRO* 4.6 0.2 - - - +
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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