Contacts of the helix formed by residues 194 - 213 (chain A) in PDB entry 3UJG
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 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLU* 4.7 1.4 - - - +
193A TYR* 1.3 81.2 - - - +
195A GLY* 1.3 73.2 + - - +
196A LYS* 3.1 23.1 + - - +
197A VAL* 3.8 30.9 - - + +
198A ALA* 3.3 15.4 + - - +
262A PRO* 6.1 2.8 - - + +
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Residues in contact with GLY 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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137A CYS* 4.3 7.2 - - - -
138A HIS* 3.9 30.1 - - - +
193A TYR* 3.6 6.3 + - - -
194A ASP* 1.3 74.1 + - - +
196A LYS* 1.3 64.6 + - - +
197A VAL 3.2 0.2 - - - -
198A ALA* 3.2 6.7 + - - +
199A ASP* 3.1 25.8 + - - +
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Residues in contact with LYS 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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132A HIS* 3.2 78.4 + - + +
135A GLN* 5.7 4.2 - - - +
137A CYS* 4.1 16.0 - - + -
194A ASP* 3.1 15.6 + - - +
195A GLY* 1.3 75.8 - - - +
197A VAL* 1.3 62.9 + - + +
199A ASP* 3.2 10.4 - - - +
200A VAL* 3.4 9.9 + - - +
268A ILE* 5.3 0.2 - - - +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU* 4.6 0.4 - - - +
194A ASP* 3.6 32.3 + - + +
195A GLY 3.2 0.4 - - - -
196A LYS* 1.3 77.9 - - + +
198A ALA* 1.3 64.1 + - - +
199A ASP 3.1 1.3 - - - -
200A VAL* 3.1 23.7 + - + +
262A PRO* 3.8 29.8 - - + +
265A ARG* 3.1 31.2 + - + +
266A ILE 5.7 1.1 - - - +
267A SER* 6.3 4.3 - - - -
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Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A HIS* 3.9 24.2 - - + +
182A TYR 5.2 0.3 - - - +
184A ALA* 4.1 12.2 - - + +
186A GLU* 3.5 18.6 + - - +
187A VAL* 4.4 5.6 - - + -
193A TYR* 4.7 2.7 - - + -
194A ASP 3.3 10.8 + - - +
195A GLY* 3.2 9.3 + - - +
197A VAL* 1.3 78.2 - - - +
199A ASP* 1.3 64.4 + - - +
201A TRP* 3.1 20.6 + - - +
202A SER* 3.4 7.8 + - - -
265A ARG* 4.1 2.0 - - - +
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Residues in contact with ASP 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.6 2.7 - - + -
132A HIS* 3.0 28.8 - - + +
137A CYS* 3.4 2.9 - - - +
138A HIS* 2.8 41.7 + - - +
141A LEU* 3.9 3.9 - - - +
143A LEU* 3.8 21.2 + - + +
195A GLY 3.1 12.6 + - - -
196A LYS 3.2 12.6 - - - +
198A ALA* 1.3 75.6 - - - +
200A VAL* 1.3 63.5 + - - +
202A SER* 3.3 11.5 + - - -
203A CYS* 3.1 27.2 + - - -
268A ILE* 6.0 0.2 - - - -
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LYS 3.4 9.4 + - - +
197A VAL* 3.1 19.8 + - + +
199A ASP* 1.3 76.1 - - - +
201A TRP* 1.3 63.8 + - - +
203A CYS* 3.1 11.6 + - - +
204A GLY 3.0 17.2 + - - -
257A ILE* 3.4 20.3 - - + +
265A ARG* 4.0 8.5 - - + -
266A ILE 3.5 27.1 - - - +
267A SER* 4.6 1.8 - - - -
268A ILE* 4.0 32.3 - - + +
271A ILE* 4.2 15.0 - - + -
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Residues in contact with TRP 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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181A ALA 2.9 20.5 + - - -
182A TYR 3.5 18.4 - - - -
183A ILE 3.5 5.7 + - - -
184A ALA* 3.6 15.5 - - + -
185A PRO* 3.5 37.7 - - + -
197A VAL 3.7 1.4 + - - -
198A ALA 3.1 10.8 + - - +
200A VAL* 1.3 78.9 - - - +
202A SER* 1.3 65.6 + - - +
204A GLY* 3.0 5.4 + - - -
205A VAL* 2.9 20.6 + - + +
217A PHE* 3.3 40.8 - + - -
233A ILE* 3.9 13.0 - - + -
236A VAL* 4.1 13.0 - - + -
257A ILE* 4.0 18.8 - - - -
258A PHE* 3.7 32.1 - + - -
259A VAL 4.1 5.8 - - - -
265A ARG* 4.1 15.8 - - - +
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Residues in contact with SER 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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143A LEU* 3.8 23.5 - - - +
182A TYR* 3.4 42.8 + - - +
198A ALA 3.4 8.5 + - - -
199A ASP* 3.3 14.7 + - - -
200A VAL 3.3 0.2 - - - -
201A TRP* 1.3 82.2 - - - +
203A CYS* 1.3 56.8 + - - +
205A VAL* 2.8 19.0 + - - +
206A THR* 2.9 13.0 + - - -
385B TRP* 5.0 4.7 - - - -
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Residues in contact with CYS 203 (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 PHE* 3.8 16.9 - - + -
124A LEU* 3.9 23.8 - - + -
125A ILE* 4.2 15.5 - - + -
128A VAL* 3.8 32.3 - - - -
143A LEU* 4.0 4.7 - - - -
199A ASP 3.1 21.5 + - - -
200A VAL* 3.1 12.4 + - + +
202A SER* 1.3 72.2 - - - +
204A GLY* 1.3 69.0 + - - +
206A THR* 3.1 3.9 + - - +
207A LEU* 2.9 22.5 + - - +
257A ILE* 5.6 1.3 - - + -
268A ILE* 5.0 1.3 - - - -
271A ILE* 5.7 0.2 - - + -
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Residues in contact with GLY 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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200A VAL 3.0 7.3 + - - -
201A TRP 3.0 8.9 + - - -
203A CYS* 1.3 77.5 - - - +
205A VAL* 1.3 61.7 + - - +
207A LEU* 3.1 6.3 + - - +
208A TYR* 2.9 23.6 + - - +
254A ILE* 5.8 3.4 - - - +
257A ILE* 3.7 29.7 - - - +
258A PHE* 3.5 12.6 - - - -
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Residues in contact with VAL 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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181A ALA* 3.2 28.9 - - + +
182A TYR* 3.5 35.9 - - + -
201A TRP* 2.9 26.2 + - + +
202A SER 2.8 9.0 + - - +
204A GLY* 1.3 74.1 - - - +
206A THR* 1.3 61.4 + - - +
208A TYR* 3.1 5.4 + - - +
209A VAL* 2.8 28.2 + - - +
215A TYR* 4.0 16.4 - - + -
216A PRO* 4.0 13.5 - - + -
217A PHE* 4.4 0.4 - - + -
258A PHE* 3.9 15.5 - - + -
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Residues in contact with THR 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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102A LEU* 3.9 26.3 - - + +
124A LEU* 4.0 22.1 - - + +
143A LEU* 4.3 2.8 + - - +
146A THR* 3.9 15.5 + - + +
156A LEU* 5.2 2.2 - - + -
182A TYR* 2.9 29.9 + - - +
202A SER 2.9 7.3 + - - -
203A CYS 3.1 7.2 + - - -
205A VAL* 1.3 78.0 - - - +
207A LEU* 1.3 62.6 + - - +
209A VAL* 3.5 4.4 + - - +
210A MET* 3.3 33.3 + - + +
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Residues in contact with LEU 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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117A ALA* 4.3 4.0 - - + -
121A PHE* 3.8 33.1 - - + -
203A CYS 2.9 12.9 + - - +
204A GLY* 3.1 9.2 + - - +
206A THR* 1.3 73.7 - - - +
208A TYR* 1.3 66.1 + - - +
210A MET* 3.2 16.3 + - + +
211A LEU* 3.1 44.1 + - + +
250A CYS* 5.2 1.8 - - - -
253A LEU* 4.2 15.0 - - + -
254A ILE* 4.3 19.3 - - + -
257A ILE* 4.8 4.9 - - + -
276A TRP* 3.6 36.3 - - + -
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Residues in contact with TYR 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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204A GLY 2.9 12.6 + - - +
205A VAL 3.1 8.5 + - - +
207A LEU* 1.3 78.3 - - - +
209A VAL* 1.3 56.7 + - - +
211A LEU* 3.2 6.4 + - - -
212A VAL* 2.9 56.4 + - + +
214A ALA 3.3 19.1 - - - -
215A TYR 4.1 1.1 - - - -
216A PRO* 3.4 44.9 + - + +
238A TYR* 4.0 22.2 - + - -
239A ALA 2.8 28.9 + - - -
240A ILE* 4.0 12.8 - - + -
241A PRO* 4.2 2.8 - - - +
254A ILE* 4.8 12.1 - - + +
258A PHE* 4.3 13.5 - + + -
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Residues in contact with VAL 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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102A LEU* 6.3 1.1 - - + -
103A PHE* 3.9 28.3 - - + -
106A ILE* 3.7 15.0 - - + +
182A TYR* 4.5 1.1 - - - +
205A VAL* 2.8 23.1 + - + +
206A THR* 4.0 7.2 - - - +
208A TYR* 1.3 74.9 - - - +
210A MET* 1.3 57.7 + - - +
213A GLY* 2.8 31.3 + - - -
214A ALA 3.8 27.6 - - - +
215A TYR* 3.4 35.0 - - + +
216A PRO* 4.5 0.7 - - + -
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Residues in contact with MET 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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102A LEU* 4.2 14.1 - - + -
106A ILE* 3.7 13.7 - - + -
111A ARG* 3.6 2.3 - - - -
112A PHE* 2.8 58.3 + - + +
117A ALA* 3.8 30.7 - - + +
120A PHE* 3.7 24.0 - - + -
121A PHE* 4.2 14.4 - - + +
124A LEU* 5.7 0.2 - - + -
156A LEU* 5.1 2.2 - - + -
206A THR* 3.3 29.1 + - + +
207A LEU* 3.2 21.7 + - + +
208A TYR 3.2 0.6 - - - -
209A VAL* 1.3 79.5 - - - +
211A LEU* 1.3 59.8 - - - +
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Residues in contact with LEU 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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111A ARG* 3.3 23.8 + - - +
112A PHE 4.1 3.6 - - - +
113A SER 4.4 1.3 - - - +
114A GLU* 3.9 24.9 - - + +
117A ALA* 3.4 27.1 - - + -
207A LEU* 3.1 31.4 + - + +
208A TYR* 3.2 3.3 + - - +
210A MET* 1.3 78.6 - - - +
212A VAL* 1.3 63.6 + - + +
244A VAL* 3.7 11.6 - - + +
246A ILE* 4.2 22.8 - - + +
250A CYS* 3.5 27.4 - - - -
254A ILE* 4.0 13.7 - - + -
276A TRP* 5.0 0.4 - - + -
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Residues in contact with VAL 212 (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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111A ARG* 3.8 15.5 - - - +
208A TYR* 2.9 57.0 + - + +
211A LEU* 1.3 83.3 - - + +
213A GLY* 1.3 61.2 + - - +
214A ALA* 3.9 16.3 - - + +
240A ILE* 4.4 12.3 - - + -
241A PRO* 4.0 32.1 - - + -
243A TYR* 4.3 13.6 + - - +
244A VAL* 4.6 4.9 - - + -
246A ILE* 6.2 0.2 - - + -
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Residues in contact with GLY 213 (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 PHE* 4.6 8.0 - - - -
106A ILE* 3.6 23.3 - - - +
107A CYS* 5.4 4.7 - - - -
111A ARG* 3.7 8.9 - - - +
209A VAL* 2.8 25.0 + - - -
211A LEU 3.7 1.0 - - - -
212A VAL* 1.3 73.5 - - - +
214A ALA* 1.3 60.3 + - - +
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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
------------------------------------------------------------
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