Contacts of the helix formed by residues 182 - 199 (chain A) in PDB entry 1KXJ
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A TRP* 3.5 11.1 - - - -
137A TYR* 3.1 19.7 - - - +
138A TYR 2.8 26.3 + - - -
178A HIS 2.9 19.2 + - - -
179A PRO* 3.2 11.6 + - - -
180A GLU 2.9 2.6 + - - -
181A LYS* 1.3 75.8 - - - +
183A SER* 1.3 71.6 + - - +
185A ILE* 3.5 11.1 - - - +
186A GLY* 3.3 16.2 + - - -
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TRP* 3.8 14.1 - - - -
179A PRO 4.5 1.6 + - - +
181A LYS* 3.3 5.9 + - - +
182A SER* 1.3 80.9 - - - +
184A LYS* 1.3 73.8 + - - +
185A ILE 4.9 0.2 - - - -
186A GLY* 3.1 3.3 + - - -
187A ARG* 3.1 25.7 + - - +
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Residues in contact with LYS 184 (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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183A SER* 1.3 79.7 + - - +
185A ILE* 1.3 69.3 + - - +
187A ARG* 2.9 30.8 + - + +
188A LYS* 3.0 44.0 + - + +
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Residues in contact with ILE 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PRO* 3.5 22.9 - - + +
134A ASN 3.4 10.5 - - - +
135A GLY* 3.3 34.5 - - - +
136A TYR 3.2 24.5 - - - +
137A TYR* 3.6 21.9 + - + +
182A SER 3.5 9.2 + - - +
184A LYS* 1.3 79.5 - - - +
186A GLY* 1.3 53.8 + - - +
188A LYS* 3.2 8.8 + - + +
189A LEU* 2.8 32.4 + - - +
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Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 4.4 2.9 - - - -
179A PRO* 3.4 26.5 - - - +
182A SER* 3.3 9.7 + - - -
183A SER 3.1 5.9 + - - -
184A LYS 3.0 1.0 - - - -
185A ILE* 1.3 80.9 - - - +
187A ARG* 1.3 65.2 + - - +
189A LEU* 3.7 7.2 - - - +
190A LEU* 3.1 29.6 + - - +
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Residues in contact with ARG 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY* 5.9 2.7 - - - +
22A ARG* 3.4 46.2 - - + +
23A ALA* 4.1 7.0 - - + +
183A SER 3.1 16.7 + - - +
184A LYS* 2.9 20.9 + - + +
186A GLY* 1.3 75.4 - - - +
188A LYS* 1.3 66.0 + - + +
190A LEU* 3.3 8.8 + - - +
191A GLU* 3.1 36.6 + - - +
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Residues in contact with LYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PRO* 4.0 18.3 - - + +
184A LYS* 3.0 44.8 + - + +
185A ILE* 3.4 13.7 - - + +
187A ARG* 1.3 79.9 - - - +
189A LEU* 1.3 60.3 + - - +
191A GLU* 3.3 29.8 + - - +
192A LYS* 3.2 23.4 + - - +
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Residues in contact with LEU 189 (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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128A PHE* 3.5 32.5 - - + -
132A PHE* 3.9 9.2 - - + -
133A PRO* 4.2 8.7 - - - +
137A TYR* 3.6 16.4 - - + +
175A PHE* 3.5 36.1 - - + -
177A PHE* 3.8 9.2 - - + -
179A PRO* 4.0 26.7 - - + -
185A ILE 2.8 19.0 + - - +
186A GLY* 3.3 5.3 + - - +
188A LYS* 1.3 73.7 - - - +
190A LEU* 1.3 68.3 + - + +
192A LYS* 3.1 13.9 + - - +
193A VAL* 3.2 16.7 + - + +
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Residues in contact with LEU 190 (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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16A LEU* 4.5 7.2 - - + -
19A GLY* 4.1 27.8 - - - +
20A VAL* 4.0 22.2 - - + +
23A ALA* 4.1 12.3 - - + -
47A PHE* 4.2 22.1 - - + -
179A PRO* 3.6 40.6 - - + -
180A GLU* 4.4 3.8 - - - +
186A GLY 3.1 15.6 + - - +
187A ARG* 3.8 7.0 - - - +
189A LEU* 1.3 81.8 - - + +
191A GLU* 1.3 61.9 + - - +
193A VAL* 3.3 8.8 + - + +
194A ILE* 3.1 25.7 + - + +
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Residues in contact with GLU 191 (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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23A ALA* 3.8 27.2 - - + +
26A ASN* 3.0 26.0 + - + +
27A PHE* 3.6 16.1 - - + -
187A ARG* 3.1 27.2 + - - +
188A LYS* 3.3 38.6 - - - +
190A LEU* 1.3 74.7 - - - +
192A LYS* 1.3 59.6 + - - +
194A ILE* 3.2 4.7 + - - +
195A GLU* 2.8 34.0 + - - +
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Residues in contact with LYS 192 (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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131A THR* 3.7 39.3 + - + +
132A PHE* 3.6 17.3 - - + -
133A PRO* 4.9 7.9 - - + -
188A LYS 3.2 8.3 + - - +
189A LEU* 3.1 10.8 + - - +
191A GLU* 1.3 76.7 - - + +
193A VAL* 1.3 59.9 + - - +
195A GLU* 3.3 40.6 + - - +
196A CYS* 2.9 37.9 + - - -
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.0 27.6 - - + -
47A PHE* 4.1 13.2 - - + -
79A TYR* 5.5 3.7 - - + -
81A VAL* 4.1 12.3 - - + -
132A PHE* 4.0 17.5 - - + -
173A LEU* 4.6 7.9 - - + -
175A PHE* 4.0 21.3 - - + -
189A LEU* 3.2 20.8 + - + +
190A LEU* 3.5 12.1 - - + +
191A GLU 3.2 0.2 - - - -
192A LYS* 1.3 73.8 - - - +
194A ILE* 1.3 69.0 + - - +
196A CYS* 3.1 13.3 + - - +
197A SER* 3.2 12.1 + - - -
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Residues in contact with ILE 194 (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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1A MET* 4.5 10.5 - - + -
3A ILE* 3.5 32.5 - - + -
20A VAL* 4.9 8.3 - - + +
23A ALA* 5.2 1.8 - - + -
24A SER* 4.2 22.0 - - - +
27A PHE* 3.6 35.4 - - + -
30A VAL* 4.7 1.8 - - + -
45A LEU* 3.9 7.9 - - + -
47A PHE* 5.7 1.6 - - + -
190A LEU 3.1 16.5 + - - +
191A GLU* 3.5 5.6 - - - +
193A VAL* 1.3 74.5 - - - +
195A GLU* 1.3 55.8 + - - +
197A SER* 2.7 36.3 + - - -
198A LEU* 2.9 18.1 + - + -
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Residues in contact with GLU 195 (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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27A PHE* 4.0 22.9 - - + -
191A GLU* 2.8 26.7 + - - +
192A LYS* 3.3 39.5 + - - +
194A ILE* 1.3 73.4 - - - +
196A CYS* 1.3 59.4 + - - +
198A LEU* 3.6 18.8 + - + +
199A SER* 3.7 8.0 + - - -
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Residues in contact with CYS 196 (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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79A TYR* 3.2 36.4 + - + +
131A THR* 4.2 23.3 - - - -
132A PHE* 4.3 10.8 - - - -
173A LEU* 5.6 1.6 - - + -
192A LYS* 2.9 30.1 + - - +
193A VAL* 3.5 6.5 - - - +
194A ILE 3.0 0.2 - - - -
195A GLU* 1.3 74.1 - - - +
197A SER* 1.3 59.5 + - - +
198A LEU 3.1 5.2 - - - -
199A SER* 3.2 23.3 + - - +
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Residues in contact with SER 197 (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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1A MET* 2.9 25.7 - - - +
44A ASP* 4.1 15.4 - - - +
45A LEU* 3.5 33.2 - - - +
79A TYR* 3.6 23.9 - - - -
193A VAL 3.2 5.0 + - - -
194A ILE 2.7 21.6 + - - -
196A CYS* 1.3 72.7 - - - +
198A LEU* 1.3 59.5 + - - +
199A SER 3.5 5.1 + - - +
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Residues in contact with LEU 198 (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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-1A GLY 5.9 1.8 - - - +
1A MET* 3.4 34.5 - - + -
27A PHE* 3.4 44.6 - - + -
28A GLU 5.4 5.4 - - - +
30A VAL* 5.9 0.4 - - + -
194A ILE* 2.9 12.8 + - + +
195A GLU* 3.7 11.9 - - + +
196A CYS 3.1 0.6 - - - -
197A SER* 1.3 80.0 - - - +
199A SER* 1.3 66.5 + - - +
200A ARG* 3.1 7.4 + - - +
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Residues in contact with SER 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 4.7 2.9 + - - -
171A ARG* 4.9 12.6 + - - -
195A GLU 3.7 7.0 + - - -
196A CYS* 3.2 17.8 + - - +
197A SER 3.5 4.9 - - - +
198A LEU* 1.3 77.2 - - - +
200A ARG* 1.3 61.2 + - - +
201A ARG* 3.3 18.8 + - - +
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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