Contacts of the helix formed by residues 194 - 211 (chain A) in PDB entry 2XIK
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 PHE 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A HIS* 3.3 72.3 - + + +
135A ARG* 3.5 36.1 - - + -
136A LYS 3.5 7.0 - - - -
137A ILE* 3.8 9.2 - - + -
165A LEU* 3.6 23.3 - - + -
193A ASP* 1.4 84.6 - - + +
195A LYS* 1.3 59.6 + - + +
196A ALA 3.1 0.2 - - - -
197A ASP* 3.0 27.5 + - - +
198A ILE* 3.6 3.9 + - + +
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Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLU* 4.7 0.9 - - - +
193A ASP* 3.1 22.2 + - - +
194A PHE* 1.3 78.7 - - + +
196A ALA* 1.3 59.8 + - - +
198A ILE* 3.2 11.1 + - + +
199A TRP 3.2 13.0 + - - -
255A PRO* 3.0 47.8 + - + +
256A ARG* 3.6 13.7 + - - +
258A ARG* 2.8 50.5 + - + +
259A PRO 4.3 13.2 - - - +
260A THR* 4.4 15.5 - - - -
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 4.8 5.6 - - + -
139A ARG* 5.8 3.1 - - + -
183A ALA* 3.9 14.2 - - + +
185A GLU* 3.9 6.6 + - - +
186A VAL* 3.7 28.7 - - + -
192A TYR* 4.0 11.7 - - + -
193A ASP 3.1 15.1 + - - +
195A LYS* 1.3 76.5 - - - +
197A ASP* 1.4 61.6 + - - +
199A TRP* 3.4 5.0 + - - +
200A SER* 3.1 25.2 + - - -
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Residues in contact with ASP 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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128A LEU* 3.8 18.4 - - + +
132A HIS* 2.9 28.1 + - + +
137A ILE* 3.4 11.0 - - - +
138A HIS* 2.9 25.4 + - - +
139A ARG* 2.9 29.6 + - - -
141A ILE* 3.8 8.1 - - + +
194A PHE 3.0 10.8 + - - +
196A ALA* 1.4 74.0 - - - +
198A ILE* 1.4 56.9 + - - +
200A SER* 3.3 7.2 + - - -
201A LEU* 2.8 34.8 + - - +
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Residues in contact with ILE 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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128A LEU* 5.0 7.2 - - + -
132A HIS* 4.3 15.0 - - + +
194A PHE 3.9 11.7 - - - +
195A LYS* 3.2 18.3 + - + +
197A ASP* 1.4 71.9 - - - +
199A TRP* 1.3 65.8 + - - +
201A LEU* 3.3 8.6 + - + +
202A GLY 3.1 16.8 + - - -
250A CYS* 3.5 15.8 - - - +
258A ARG* 3.9 17.5 - - + -
259A PRO* 3.4 29.8 - - + +
260A THR* 4.0 2.0 - - - -
261A ALA* 3.7 26.9 - - + +
264A LEU* 3.9 20.6 - - + -
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Residues in contact with TRP 199 (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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180A PHE 5.3 0.4 + - - -
181A TRP 3.6 7.0 - - - -
182A MET 3.3 12.7 + - - -
183A ALA* 3.4 22.7 - - + -
184A PRO* 3.6 26.0 - - + -
195A LYS 3.2 3.8 + - - -
196A ALA 3.6 7.9 - - - +
197A ASP 3.3 0.2 - - - -
198A ILE* 1.3 78.5 - - - +
200A SER* 1.4 59.3 + - - +
202A GLY 3.0 16.5 + - - -
203A ILE* 3.1 24.9 + - + +
227A ILE* 4.3 16.5 - - + +
232A PRO* 3.7 23.6 - - + -
233A PRO* 3.9 17.5 - - + -
250A CYS 3.7 10.9 + - - -
251A LEU* 3.2 40.2 - - + +
252A ASN 3.6 29.2 - - - -
253A LYS* 4.0 10.5 - - + -
258A ARG* 3.6 17.5 - - - +
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Residues in contact with SER 200 (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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139A ARG* 5.4 5.4 + - - -
140A ASP* 5.9 0.2 - - - -
141A ILE* 3.7 29.8 + - - +
181A TRP* 2.6 28.7 + - - +
182A MET* 4.6 1.0 - - - -
183A ALA 4.6 2.3 + - - -
196A ALA 3.1 12.8 + - - -
197A ASP* 3.3 11.0 + - - -
199A TRP* 1.4 77.3 - - - +
201A LEU* 1.3 56.4 + - - +
203A ILE* 3.3 5.0 + - - +
204A THR* 2.9 31.6 + - - -
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Residues in contact with LEU 201 (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* 3.8 25.1 - - + +
124A ILE* 3.8 31.2 - - + -
125A LEU* 3.6 30.3 - - + -
128A LEU* 4.3 8.7 - - + -
141A ILE* 4.1 8.7 - - + +
197A ASP 2.8 16.8 + - - +
198A ILE* 3.4 11.4 - - + +
200A SER* 1.3 70.5 - - - +
202A GLY* 1.3 52.8 + - - +
204A THR* 3.2 4.9 + - - -
205A ALA* 2.8 33.3 + - - +
246A PHE* 4.0 13.9 - - + -
250A CYS* 4.1 4.9 - - - -
264A LEU* 3.9 16.8 - - + -
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Residues in contact with GLY 202 (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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198A ILE 3.1 7.3 + - - -
199A TRP 3.0 9.1 + - - -
201A LEU* 1.3 75.2 - - - +
203A ILE* 1.3 60.6 + - - +
205A ALA* 3.4 8.4 + - - +
206A ILE* 3.3 25.8 + - - +
247A VAL* 4.3 4.6 - - - +
250A CYS* 3.5 24.4 - - - +
251A LEU* 3.9 12.6 - - - +
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Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PHE 3.4 25.6 - - - +
181A TRP* 3.4 24.7 - - + +
199A TRP* 3.1 34.6 + - + +
200A SER 3.3 7.2 + - - +
201A LEU 3.3 0.2 - - - -
202A GLY* 1.3 75.9 - - - +
204A THR* 1.3 57.0 + - - +
206A ILE* 3.2 6.0 + - - +
207A GLU* 2.9 25.6 + - - +
213A PRO* 3.8 7.6 - - + -
214A PRO* 3.7 24.7 - - + +
233A PRO* 3.8 28.7 - - + -
251A LEU* 3.9 13.9 - - + -
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Residues in contact with THR 204 (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* 5.1 1.6 - - + -
124A ILE* 4.6 16.8 - - + -
141A ILE* 3.5 8.0 + - + +
142A LYS* 3.4 23.8 + - - +
143A ALA* 3.8 24.2 - - - +
146A VAL* 5.0 0.4 - - + -
181A TRP* 3.6 1.4 - - - -
200A SER 2.9 14.5 + - - -
201A LEU* 3.5 12.6 - - + -
203A ILE* 1.3 73.6 - - - +
205A ALA* 1.4 53.1 + - - +
207A GLU* 3.2 12.4 + - - +
208A LEU* 2.8 48.8 + - + +
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Residues in contact with ALA 205 (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* 3.9 31.8 - - + +
201A LEU 2.8 16.3 + - - +
202A GLY* 3.5 11.4 - - - +
203A ILE 3.3 0.2 - - - -
204A THR* 1.4 72.7 - - - +
206A ILE* 1.4 60.5 + - - +
208A LEU* 3.4 5.0 + - - +
209A ALA 3.2 16.1 + - - -
243A PHE* 3.5 18.1 - - + -
246A PHE* 4.3 6.7 - - + -
247A VAL* 3.8 19.1 - - + -
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Residues in contact with ILE 206 (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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202A GLY 3.3 6.8 + - - +
203A ILE* 3.2 8.3 + - - +
205A ALA* 1.4 72.1 - - - +
207A GLU* 1.4 55.7 + - - +
209A ALA* 3.1 7.0 + - - -
210A LYS* 2.8 51.1 + - + +
212A GLU 4.3 2.0 - - - +
214A PRO* 3.8 39.0 - - + -
233A PRO* 4.0 3.1 - - + -
234A THR 4.0 17.0 - - - +
235A LEU* 4.4 14.8 - - + -
247A VAL* 3.8 19.1 - - + -
251A LEU* 3.7 28.9 - - + -
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Residues in contact with GLU 207 (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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104A LEU* 3.6 17.3 - - - +
107A LEU* 3.9 5.6 - - + +
142A LYS* 4.9 0.2 - - - +
143A ALA* 3.0 40.3 + - + +
144A ALA* 4.7 1.2 + - - +
181A TRP* 2.8 41.7 + - - +
203A ILE 2.9 13.1 + - - +
204A THR* 3.2 10.1 + - - +
206A ILE* 1.4 76.5 - - - +
208A LEU* 1.4 55.8 + - - +
211A GLY* 2.7 36.8 + - - +
212A GLU* 3.6 16.4 - - - +
213A PRO* 4.1 17.4 - - + +
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Residues in contact with LEU 208 (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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103A ALA* 4.1 25.8 - - + +
107A LEU* 3.4 32.2 - - + +
112A LEU* 4.0 23.6 + - + +
117A ILE* 3.7 33.2 - - + +
120A ILE* 4.0 22.7 - - + -
121A LEU* 3.9 28.9 - - + -
124A ILE* 4.8 0.4 - - + -
143A ALA* 4.4 7.0 - - + -
204A THR* 2.8 30.0 + - + +
205A ALA* 3.7 5.2 - - - +
207A GLU* 1.4 72.8 - - - +
209A ALA* 1.3 59.0 + - - +
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Residues in contact with ALA 209 (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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107A LEU* 5.7 0.2 - - - -
111A PRO* 5.2 9.9 - - - +
112A LEU 5.6 1.6 + - - +
117A ILE* 3.8 8.7 - - + +
205A ALA 3.2 4.9 + - - +
206A ILE 3.1 7.9 + - - +
208A LEU* 1.3 79.2 - - - +
210A LYS* 1.3 59.1 + - + +
235A LEU* 3.8 17.5 - - + -
239A HIS* 3.8 21.7 - - + +
243A PHE* 3.6 32.8 - - + -
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Residues in contact with LYS 210 (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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206A ILE* 2.8 35.7 + - + +
209A ALA* 1.3 74.9 - - + +
211A GLY* 1.3 56.7 + - - +
212A GLU* 3.2 26.0 + - + +
235A LEU* 4.3 7.0 - - - -
236A GLU* 2.7 37.4 + - - +
237A GLY* 4.3 4.4 - - - -
238A GLN 5.2 0.4 - - - +
239A HIS* 3.3 21.5 + - - +
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Residues in contact with GLY 211 (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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104A LEU* 4.4 18.4 - - - +
107A LEU* 4.1 24.0 - - - +
207A GLU* 2.7 26.2 + - - +
209A ALA 3.8 0.6 - - - -
210A LYS* 1.3 70.9 - - - +
212A GLU* 1.3 57.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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