Contacts of the helix formed by residues 175 - 194 (chain A) in PDB entry 1K11
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 ASN 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 6.4 0.2 - - + -
153A SER* 4.1 2.0 - - - +
174A CYS* 1.3 85.4 + - + +
176A SER* 1.3 61.2 + - - +
177A LEU* 3.2 7.5 + - - +
178A GLU* 3.0 52.9 + - - +
179A GLN* 2.9 28.5 + - - +
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Residues in contact with SER 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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143A CYS* 3.0 19.7 - - - +
144A TYR 4.1 9.6 - - - -
153A SER* 3.4 22.7 + - - +
154A LEU 2.8 29.5 + - - -
155A LEU* 3.3 16.1 - - - +
175A ASN* 1.3 75.0 + - - +
177A LEU* 1.3 60.8 + - - +
179A GLN* 3.5 2.2 + - - +
180A ALA* 3.0 25.8 + - - +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A CYS* 4.4 6.3 - - + -
145A ASP* 3.3 44.2 - - + +
175A ASN* 3.2 6.7 + - - +
176A SER* 1.3 81.1 - - - +
178A GLU* 1.3 66.0 + - + +
180A ALA* 3.3 15.5 - - + +
181A GLN* 3.3 30.6 + - + +
788B THR* 4.5 7.9 - - + +
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 3.8 31.6 - - + -
175A ASN* 3.0 38.0 + - - +
177A LEU* 1.3 78.1 - - + +
179A GLN* 1.3 58.7 + - - +
181A GLN* 3.4 6.1 + - - +
182A ALA* 3.1 26.2 + - - +
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Residues in contact with GLN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 3.6 33.5 - - + +
64A ARG 3.6 9.1 + - - -
65A ILE* 3.3 28.0 - - - +
112A MET* 3.1 31.5 - - + +
141A MET* 3.4 5.8 - - - +
155A LEU* 3.5 24.2 - - + +
174A CYS 4.9 1.4 - - - +
175A ASN* 2.9 29.0 + - - +
176A SER* 3.5 4.6 + - - +
177A LEU 3.3 0.2 - - - -
178A GLU* 1.3 74.8 - - - +
180A ALA* 1.3 65.2 + - - +
182A ALA* 4.1 6.7 - - - -
183A ILE* 3.0 30.2 + - + +
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Residues in contact with ALA 180 (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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141A MET* 3.2 17.3 - - + +
143A CYS* 3.4 16.8 - - - -
176A SER 3.0 15.9 + - - +
177A LEU* 3.3 21.1 - - + +
179A GLN* 1.3 75.9 - - - +
181A GLN* 1.3 69.5 + - - +
184A CYS* 2.9 31.7 + - - +
788B THR* 5.8 2.0 - - - -
790B VAL* 5.0 4.9 - - + -
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Residues in contact with GLN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 3.3 18.4 + - - +
178A GLU* 4.0 5.4 - - - +
179A GLN 3.4 0.2 - - - -
180A ALA* 1.3 87.1 - - - +
182A ALA* 1.3 63.0 + - - +
184A CYS* 3.8 10.4 - - - +
185A LYS* 3.1 39.0 + - - +
790B VAL* 6.0 0.9 - - - +
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Residues in contact with ALA 182 (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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61A ALA* 4.6 5.4 - - + -
63A PHE* 3.5 26.0 - - + -
114A VAL* 4.0 15.9 - - + -
178A GLU 3.1 17.5 + - - +
179A GLN* 3.7 5.2 - - - +
181A GLN* 1.3 78.5 - - - +
183A ILE* 1.3 59.3 + - - +
185A LYS* 3.3 6.1 + - - +
186A VAL* 3.1 29.1 + - - +
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Residues in contact with ILE 183 (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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112A MET* 3.8 25.8 - - + -
114A VAL* 3.6 21.1 - - + -
119A ILE* 3.9 24.2 - - + -
138A ILE* 4.9 5.8 - - + -
141A MET* 3.6 33.2 - - + -
155A LEU* 5.2 1.1 - - + -
157A LEU* 4.8 8.3 - - + -
179A GLN 3.0 14.5 + - - +
182A ALA* 1.3 73.0 - - - +
184A CYS* 1.3 59.4 + - - +
186A VAL* 3.6 5.8 - - + +
187A LEU* 2.9 51.3 + - + +
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Residues in contact with CYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A MET* 4.1 0.6 - - - +
180A ALA 2.9 20.3 + - - +
181A GLN* 3.8 13.2 - - - +
183A ILE* 1.3 76.2 - - - +
185A LYS* 1.3 56.8 + - - +
187A LEU* 3.3 3.3 + - - +
188A SER* 2.9 38.9 + - - -
790B VAL* 3.7 34.1 - - + -
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Residues in contact with LYS 185 (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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181A GLN* 3.1 29.4 + - - +
182A ALA* 3.6 5.9 - - - +
184A CYS* 1.3 76.0 - - - +
186A VAL* 1.3 58.6 + - + +
188A SER* 3.3 5.1 + - - -
189A THR* 3.0 46.5 + - + +
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASP* 5.6 6.1 - - - +
114A VAL* 3.9 20.0 - - + +
115A SER 3.2 28.9 - - - +
116A LYS* 3.5 16.8 - - + +
135A LEU* 3.6 20.6 - - + -
182A ALA 3.1 17.4 + - - +
183A ILE* 3.6 7.4 - - + +
184A CYS 3.3 0.2 - - - -
185A LYS* 1.3 77.8 - - + +
187A LEU* 1.3 57.9 + - + +
189A THR* 2.9 19.6 + - - -
190A ALA* 3.0 18.4 + - - +
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Residues in contact with LEU 187 (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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135A LEU* 3.6 33.9 - - + -
138A ILE* 4.6 7.2 - - + -
139A ILE 4.9 0.7 - - - +
141A MET* 5.6 2.0 - - + +
183A ILE* 2.9 36.2 + - + +
184A CYS* 3.3 5.4 + - - +
186A VAL* 1.3 73.4 - - + +
188A SER* 1.3 66.1 + - - +
190A ALA* 3.4 5.7 + - - +
191A PHE* 3.2 24.3 + - - +
790B VAL* 3.7 28.0 - - + +
791B VAL 4.2 0.7 - - - +
792B ASN* 3.5 44.8 - - + +
793B PRO* 4.2 11.8 - - + +
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Residues in contact with SER 188 (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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184A CYS* 2.9 25.0 + - - -
185A LYS* 3.3 6.5 + - - -
187A LEU* 1.3 76.7 - - - +
189A THR* 1.3 59.5 + - - +
191A PHE* 3.1 6.9 + - - +
192A ASP* 2.9 41.0 + - - +
793B PRO* 5.0 5.3 - - - +
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Residues in contact with THR 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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116A LYS* 3.6 25.3 - - - +
185A LYS* 3.0 28.8 + - + +
186A VAL* 2.9 20.4 + - - -
188A SER* 1.3 75.8 - - - +
190A ALA* 1.3 60.0 + - - +
192A ASP* 3.3 11.7 + - - +
193A SER* 2.9 29.8 + - - -
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Residues in contact with ALA 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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116A LYS* 4.0 16.4 - - - +
135A LEU* 3.8 22.0 - - + -
136A TYR* 4.8 19.7 + - + +
186A VAL 3.0 18.4 + - - +
187A LEU* 3.8 4.0 - - - +
188A SER 3.3 0.2 - - - -
189A THR* 1.3 74.9 + - - +
191A PHE* 1.3 62.8 + - - +
193A SER* 3.3 14.3 + - - -
194A VAL* 3.4 12.5 + - - +
792B ASN* 5.8 0.4 - - - +
794B LYS* 4.8 5.9 - - + +
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Residues in contact with PHE 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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187A LEU 3.2 14.8 + - - +
188A SER* 3.1 5.1 + - - +
190A ALA* 1.3 74.0 - - - +
192A ASP* 1.3 69.9 + - - +
194A VAL* 3.1 23.4 - - + +
195A LEU* 3.1 46.4 - - + +
793B PRO* 3.5 50.3 - - + -
794B LYS* 3.7 29.5 - - + +
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Residues in contact with ASP 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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188A SER* 2.9 36.5 + - - +
189A THR* 3.3 11.7 + - - +
191A PHE* 1.3 81.3 - - - +
193A SER* 1.3 61.7 + - - +
195A LEU* 3.3 31.8 + - - +
196A THR* 4.1 7.1 + - - -
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Residues in contact with SER 193 (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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116A LYS* 3.5 19.0 + - - -
189A THR 2.9 16.2 + - - -
190A ALA* 3.6 6.7 - - - -
191A PHE 3.2 0.4 - - - -
192A ASP* 1.3 78.5 - - - +
194A VAL* 1.3 57.9 + - - +
195A LEU 3.4 0.4 - - - -
196A THR* 4.5 8.0 + - - -
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Residues in contact with VAL 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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136A TYR* 5.8 3.6 - - - +
190A ALA 3.4 4.2 + - - +
191A PHE* 3.1 30.1 - - + +
193A SER* 1.3 78.4 - - - +
195A LEU* 1.3 67.2 + - + +
794B LYS* 3.6 41.3 - - + +
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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