Contacts of the helix formed by residues 193 - 214 (chain A) in PDB entry 2XZF
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 ILE 193 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLN 3.5 8.5 + - - +
192A LEU* 1.3 76.1 - - - +
194A GLU* 1.3 65.8 + - - +
195A SER* 3.4 23.3 - - - +
196A SER* 3.0 19.4 + - - +
197A ILE* 3.0 20.8 + - - +
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Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 4.6 2.4 - - - +
146A ARG* 4.0 39.8 + - - +
193A ILE* 1.3 74.1 - - - +
195A SER* 1.3 57.9 + - - +
197A ILE* 3.2 10.7 + - - +
198A HIS* 3.0 27.9 + - + +
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE* 3.4 22.6 - - - +
194A GLU* 1.3 79.0 - - - +
196A SER* 1.3 63.6 + - - +
198A HIS* 3.4 8.3 + - - +
199A LEU* 3.1 23.0 + - - +
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Residues in contact with SER 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA 5.7 1.1 - - - -
183A ILE* 3.9 21.2 - - - +
192A LEU* 4.5 10.3 - - - +
193A ILE* 3.0 30.2 + - - +
195A SER* 1.3 78.1 + - - +
197A ILE* 1.3 61.0 + - - +
199A LEU* 3.3 7.5 + - - +
200A LEU* 2.9 30.7 + - - +
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Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 4.6 7.2 - - + +
145A PHE* 3.8 24.1 - - + -
146A ARG* 4.0 38.4 - - + +
149A LEU* 3.9 26.0 - - + -
150A ARG* 5.5 2.0 - - + +
189A THR 5.2 0.4 - - - +
192A LEU* 3.7 37.2 - - + +
193A ILE 3.0 15.2 + - - +
194A GLU* 3.2 7.6 + - - +
196A SER* 1.3 76.0 - - - +
198A HIS* 1.3 57.5 + - - +
200A LEU* 3.4 7.1 + - - +
201A HIS* 2.8 28.1 + - - +
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Residues in contact with HIS 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 2.7 40.9 + - - +
194A GLU* 3.0 16.3 + - + +
195A SER* 3.6 9.4 - - - +
196A SER 3.2 0.2 - - - -
197A ILE* 1.3 78.0 - - - +
199A LEU* 1.3 64.8 + - + +
201A HIS* 3.3 1.6 + - - +
202A ASP* 3.0 50.8 + - - -
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.3 6.3 - - + +
181A ALA* 3.6 34.3 - - - +
182A LYS* 5.3 8.5 - - + -
195A SER 3.1 16.9 + - - +
196A SER* 3.7 7.0 - - - +
198A HIS* 1.3 79.5 - - + +
200A LEU* 1.3 55.5 + - - +
202A ASP* 3.5 5.5 + - + -
203A SER* 2.6 46.0 + - - +
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Residues in contact with LEU 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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145A PHE* 3.8 21.1 - - + -
149A LEU* 4.7 1.8 - - + -
156A ILE* 3.9 26.5 - - + -
160A LEU* 4.3 3.8 - - + -
177A VAL* 3.4 31.9 - - + -
178A LEU* 4.1 15.0 - - + -
181A ALA* 3.8 12.9 - - + +
183A ILE* 3.9 15.3 - - + -
192A LEU* 4.7 7.2 - - + -
196A SER 2.9 18.4 + - - +
197A ILE* 3.6 4.9 - - - +
199A LEU* 1.3 77.0 - - - +
201A HIS* 1.3 62.5 + - - +
203A SER* 3.2 1.1 + - - -
204A ILE* 2.9 39.7 + - + +
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Residues in contact with HIS 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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137A TYR* 4.3 9.6 - + - -
140A PHE* 2.7 57.1 + + - -
142A GLU* 3.4 39.6 + - + +
145A PHE* 4.1 15.9 - + + -
197A ILE 2.8 21.4 + - - +
198A HIS 3.5 3.6 - - - +
200A LEU* 1.3 75.1 - - - +
202A ASP* 1.3 87.4 + - - +
204A ILE* 3.4 4.0 + - - +
205A ILE* 3.4 38.0 + - + +
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Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 3.7 23.8 + - - +
198A HIS* 3.0 47.4 + - - +
199A LEU* 4.1 7.0 - - + +
201A HIS* 1.3 100.9 + - - +
203A SER* 1.3 57.7 + - - +
205A ILE* 3.3 3.9 + - - +
206A GLU* 2.8 38.2 + - + +
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 4.3 10.5 - - - -
180A LEU* 3.7 30.1 - - - +
181A ALA* 3.9 10.7 - - - +
199A LEU* 2.6 41.7 + - - +
200A LEU 3.2 4.5 + - - -
202A ASP* 1.3 73.5 - - - +
204A ILE* 1.3 60.5 + - - +
206A GLU* 4.4 3.6 - - - +
207A ILE* 2.9 35.9 + - - +
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PRO* 4.2 9.6 - - + -
140A PHE* 3.9 26.5 - - + -
145A PHE* 4.1 5.6 - - + -
160A LEU* 4.0 26.2 - - + -
166A VAL* 4.2 12.8 - - + -
169A LEU* 4.3 8.7 - - + -
177A VAL* 3.6 25.4 - - + -
200A LEU* 2.9 31.0 + - + +
201A HIS 3.6 6.1 - - - +
202A ASP 3.3 0.2 - - - -
203A SER* 1.3 77.3 - - - +
205A ILE* 1.3 62.6 + - - +
207A ILE* 4.2 0.5 - - - +
208A LEU* 3.2 42.1 + - + +
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PRO* 3.7 29.6 - - - +
136A THR* 3.8 16.2 - - - +
137A TYR* 3.6 47.6 - - + +
140A PHE* 3.9 9.2 - - + -
201A HIS* 3.4 41.0 + - + +
202A ASP 3.3 6.5 + - - +
204A ILE* 1.3 76.2 - - - +
206A GLU* 1.3 59.4 + - - +
209A GLN* 2.9 47.2 + - + +
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 2.8 33.3 + - - +
180A LEU* 5.3 6.3 - - + -
202A ASP* 2.8 28.6 + - + +
203A SER* 4.0 5.2 - - - +
205A ILE* 1.3 73.7 - - - +
207A ILE* 1.3 55.1 + - - +
209A GLN* 3.4 6.5 + - - +
210A LYS* 2.9 30.8 + - - +
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TYR* 3.9 28.5 - - + -
176A GLU* 4.6 20.0 - - + +
177A VAL* 3.9 25.8 - - + -
180A LEU* 3.6 26.9 - - + -
203A SER 2.9 22.4 + - - +
206A GLU* 1.3 71.8 - - - +
208A LEU* 1.3 60.1 + - + +
210A LYS* 3.3 11.9 + - + +
211A ALA* 2.9 27.9 + - - +
231A MET* 4.2 16.7 - - + +
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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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3A LEU* 5.0 5.8 - - + -
4A PRO* 3.6 28.6 - - + +
135A PRO* 3.6 33.0 - - + -
166A VAL* 5.8 0.2 - - + -
167A ALA 4.5 5.4 - - - +
168A GLY* 4.6 8.5 - - - +
169A LEU* 3.9 21.8 - - + -
173A TYR* 3.8 30.7 - - + -
204A ILE* 3.2 18.1 + - + +
207A ILE* 1.3 78.9 - - + +
209A GLN* 1.3 70.7 + - - +
211A ALA* 3.3 1.7 + - - +
212A ILE* 2.9 33.2 + - - +
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Residues in contact with GLN 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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135A PRO* 2.7 32.9 + - - +
136A THR* 4.9 9.2 - - - +
205A ILE* 2.9 40.5 + - + +
206A GLU* 4.0 7.6 - - - +
208A LEU* 1.3 85.8 - - - +
210A LYS* 1.3 62.7 + - - +
212A ILE* 3.3 20.1 + - - +
213A LYS* 3.0 23.6 + - - +
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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 GLU 2.9 18.1 + - - +
207A ILE* 3.6 12.4 - - + +
209A GLN* 1.3 77.4 - - - +
211A ALA* 1.3 65.1 + - - +
213A LYS* 3.1 8.7 + - + +
214A LEU* 2.9 31.3 + - + +
231A MET* 4.1 14.9 - - + +
234A GLU* 3.2 48.5 + - - +
236A GLN* 6.1 0.4 - - - +
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Residues in contact with ALA 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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4A PRO* 3.5 28.9 - - + -
173A TYR* 3.6 21.1 - - + +
207A ILE 2.9 16.6 + - - +
208A LEU* 3.7 0.4 - - - +
210A LYS* 1.3 77.2 - - - +
212A ILE* 1.3 61.7 + - - +
214A LEU* 3.3 1.7 + - - +
215A GLY 3.1 4.3 + - - -
216A GLY 2.8 26.9 + - - -
231A MET* 3.7 20.4 - - + -
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Residues in contact with ILE 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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3A LEU* 3.7 22.7 - - + -
4A PRO* 3.8 24.2 - - + -
7A GLU* 4.0 17.3 - - + -
8A THR* 4.5 3.5 + - - +
11A ARG* 3.4 42.2 + - - +
54A ARG* 5.2 3.1 - - - +
208A LEU 2.9 21.8 + - - +
209A GLN* 3.6 26.0 - - - +
211A ALA* 1.3 76.4 - - - +
213A LYS* 1.3 65.2 + - - +
215A GLY* 3.0 14.7 + - - -
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Residues in contact with LYS 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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11A ARG* 5.5 3.4 - - - +
209A GLN 3.0 13.9 + - - +
210A LYS* 3.1 11.6 + - - +
212A ILE* 1.3 79.4 - - - +
214A LEU* 1.3 69.5 + - + +
215A GLY* 3.4 0.9 + - - -
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Residues in contact with LEU 214 (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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210A LYS* 2.9 27.6 + - + +
211A ALA 3.3 3.3 + - - +
212A ILE 3.2 0.2 - - - -
213A LYS* 1.3 86.9 - - + +
215A GLY* 1.3 57.5 + - - +
216A GLY 3.4 0.9 - - - -
228A THR 4.8 0.3 - - - +
229A GLY* 3.6 1.2 - - - -
230A LYS* 2.9 46.2 + - + +
231A MET* 3.9 26.2 - - - +
234A GLU* 3.6 33.7 - - + +
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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