Contacts of the helix formed by residues 189 - 213 (chain A) in PDB entry 4KZJ
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 GLU 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 5.3 1.5 - - + +
100A SER* 3.9 17.0 + - - +
103A ASP* 2.8 15.9 + - - +
188A GLN* 1.3 87.4 - - + +
190A PRO* 1.3 66.9 - - - +
191A ARG 3.2 2.9 - - - -
192A ARG* 2.5 64.8 + - + +
193A VAL* 3.3 12.0 + - + +
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Residues in contact with PRO 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASP* 4.7 9.3 - - - +
184A ARG 5.7 0.9 - - - +
187A LEU* 3.5 34.9 - - + +
188A GLN 3.3 10.1 - - - +
189A GLU* 1.3 89.3 - - - +
191A ARG* 1.4 63.4 + - + +
193A VAL* 3.2 2.9 + - - +
194A GLU* 2.9 37.3 + - - +
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU 3.0 1.6 + - - -
190A PRO* 1.4 82.2 - - + +
192A ARG* 1.3 62.6 + - + +
194A GLU* 3.7 17.7 + - - +
195A GLU* 2.8 28.9 + - - +
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY 5.0 1.6 + - - -
98A GLU* 2.8 44.5 + - - +
99A LEU* 3.7 23.9 - - + +
100A SER 4.1 0.8 - - - +
189A GLU* 2.5 61.4 + - + +
191A ARG* 1.3 76.8 - - + +
193A VAL* 1.3 67.5 + - - +
195A GLU* 3.3 8.3 + - - +
196A LEU* 3.0 23.4 + - - +
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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
----------------------------------------------------------
99A LEU* 4.3 16.2 - - + -
103A ASP* 4.6 3.8 - - + +
107A LEU* 4.2 15.9 - - + -
181A ILE* 3.6 14.5 - - + +
182A THR* 3.5 42.0 - - - +
183A ASP* 5.1 0.4 - - - -
187A LEU* 3.9 28.5 - - + -
189A GLU 3.7 12.3 - - - +
190A PRO 3.2 6.8 + - - +
192A ARG* 1.3 77.8 - - - +
194A GLU* 1.3 52.7 + - + +
196A LEU* 3.2 2.8 + - - -
197A GLN* 2.8 33.1 + - - +
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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
----------------------------------------------------------
183A ASP* 2.5 39.1 - - - +
190A PRO* 2.9 25.6 + - - +
191A ARG* 3.7 21.4 + - - +
193A VAL* 1.3 77.0 - - + +
195A GLU* 1.3 55.5 + - - +
197A GLN* 3.3 12.9 + - + +
198A ASN* 2.8 39.4 + - - +
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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
----------------------------------------------------------
191A ARG 2.8 21.6 + - - +
192A ARG* 3.5 9.0 - - - +
193A VAL 3.2 0.2 - - - -
194A GLU* 1.3 74.1 - - - +
196A LEU* 1.3 57.5 + - - +
198A ASN* 3.3 18.4 + - - +
199A ARG* 3.0 65.9 + - - +
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 6.0 2.9 - - + -
93A ILE* 4.8 1.3 - - + -
94A PRO 3.4 20.9 - - - +
95A GLY* 4.0 25.1 - - - +
96A PHE* 4.0 6.5 - - + +
99A LEU* 4.4 10.5 - - + -
181A ILE* 3.9 26.9 - - + -
192A ARG 3.0 16.5 + - - +
193A VAL 3.7 3.6 - - - +
195A GLU* 1.3 74.3 - - - +
197A GLN* 1.3 66.1 + - - +
199A ARG* 3.3 30.6 + - + +
200A ILE* 3.0 44.4 + - + +
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Residues in contact with GLN 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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178A LEU* 3.7 18.4 - - + +
181A ILE* 3.2 28.0 + - - +
182A THR* 3.7 25.6 + - - +
183A ASP* 4.5 8.7 + - - +
193A VAL 2.8 15.1 + - - +
194A GLU* 3.4 16.0 - - - +
196A LEU* 1.3 76.3 - - - +
198A ASN* 1.3 70.1 + - - +
200A ILE* 3.2 2.1 + - - -
201A ALA* 2.9 29.2 + - - +
301A GOL 4.0 8.7 + - - -
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Residues in contact with ASN 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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194A GLU* 2.8 25.8 + - - +
195A GLU* 3.4 23.0 + - - +
197A GLN* 1.3 79.2 - - - +
199A ARG* 1.3 62.9 + - - +
201A ALA* 3.3 7.0 + - - +
202A SER* 3.0 28.0 + - - +
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.8 18.4 - - + +
94A PRO 5.2 2.6 + - - -
95A GLY* 5.2 6.1 - - - -
195A GLU* 3.0 49.4 + - - +
196A LEU* 3.3 33.5 + - + +
198A ASN* 1.3 77.3 - - + +
200A ILE* 1.3 60.9 + - - +
202A SER* 3.6 6.4 + - - -
203A CYS* 3.2 21.8 + - - +
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Residues in contact with ILE 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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33A LEU* 4.4 10.5 - - + -
37A LEU* 4.1 22.0 - - + -
93A ILE* 4.3 8.1 - - + -
174A CYS* 3.5 29.1 - - + +
177A ALA* 4.0 20.6 - - + +
178A LEU* 3.8 12.3 - - + -
181A ILE* 4.1 17.7 - - + -
196A LEU* 3.0 44.2 + - + +
197A GLN* 3.2 3.6 + - - +
199A ARG* 1.3 72.6 - - - +
201A ALA* 1.3 60.7 + - - +
203A CYS* 3.2 7.4 + - - +
204A LEU* 2.9 26.9 + - - +
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 4.1 19.3 - - + +
197A GLN* 2.9 20.7 + - - +
198A ASN* 3.6 7.9 - - - +
200A ILE* 1.3 76.7 - - - +
202A SER* 1.3 56.4 + - - +
204A LEU* 3.2 4.9 + - - +
205A LYS* 2.9 29.7 + - - +
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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
----------------------------------------------------------
198A ASN* 3.0 17.0 + - - +
199A ARG* 3.7 7.4 - - - -
201A ALA* 1.3 72.7 - - - +
203A CYS* 1.3 65.2 + - - +
205A LYS* 3.8 8.3 - - - +
206A GLU* 3.0 26.5 + - - +
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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
----------------------------------------------------------
31A ALA* 4.0 8.1 - - + -
33A LEU* 4.0 17.5 - - + -
34A LEU* 3.5 51.8 - - - +
37A LEU* 4.4 1.8 - - - -
174A CYS* 4.0 7.2 - - - -
199A ARG 3.2 12.6 + - - +
200A ILE* 3.2 8.9 + - - +
202A SER* 1.3 75.5 - - - +
204A LEU* 1.3 66.6 + - - +
206A GLU* 3.5 13.3 + - - +
207A HIS* 3.0 23.4 + - - +
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Residues in contact with LEU 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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171A ALA* 3.8 31.2 - - + +
174A CYS* 3.8 19.3 - - + -
175A LEU* 3.7 30.3 - - + -
178A LEU* 4.1 13.9 - - + -
200A ILE 2.9 13.1 + - - +
201A ALA* 3.6 8.3 - - - +
203A CYS* 1.3 77.2 - - - +
205A LYS* 1.3 57.2 + - - +
207A HIS* 3.0 7.0 + - + +
208A VAL* 2.8 48.2 + - + +
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Residues in contact with LYS 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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201A ALA 2.9 16.8 + - - +
202A SER* 3.8 9.0 - - - +
204A LEU* 1.3 77.7 - - - +
206A GLU* 1.3 58.8 + - - +
208A VAL* 3.0 14.9 - - + +
209A ALA* 3.0 30.2 + - + +
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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
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31A ALA* 4.2 29.9 + - - +
34A LEU* 6.5 0.7 - - + -
202A SER 3.0 21.0 + - - +
203A CYS* 3.9 10.4 - - - +
205A LYS* 1.3 77.7 - - - +
207A HIS* 1.3 60.2 + - - +
209A ALA* 3.5 6.8 + - - +
210A ALA* 2.9 29.5 + - + +
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Residues in contact with HIS 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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34A LEU* 3.9 24.9 - - + +
168A ASP* 3.1 32.0 + - - -
170A PRO* 3.4 30.9 - - + +
171A ALA* 4.0 19.3 - - + -
203A CYS 3.0 15.5 + - - +
204A LEU* 3.0 8.5 + - + +
206A GLU* 1.3 76.5 - - + +
208A VAL* 1.3 74.4 + - + +
210A ALA* 3.7 7.5 - - - +
211A VAL* 3.1 40.2 + - + +
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA* 5.2 4.5 - - + -
204A LEU* 2.8 41.4 + - + +
205A LYS* 3.0 28.7 - - + +
207A HIS* 1.3 78.1 - - + +
209A ALA* 1.3 59.8 + - + +
211A VAL* 3.1 9.9 + - - +
212A ALA* 2.9 28.5 + - - +
221A LEU* 6.2 5.4 - - + -
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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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205A LYS* 3.0 19.1 + - + +
206A GLU* 3.9 7.4 - - - +
208A VAL* 1.3 79.7 - - + +
210A ALA* 1.3 57.1 + - - +
212A ALA* 3.2 6.6 + - - +
213A GLY* 2.8 32.7 + - - +
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Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU* 2.9 22.3 + - + +
207A HIS* 3.7 9.9 - - - +
208A VAL 3.2 0.2 - - - -
209A ALA* 1.3 71.4 - - - +
211A VAL* 1.3 66.0 + - + +
213A GLY* 3.2 14.1 + - - +
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 4.0 12.3 - - - +
207A HIS* 3.1 39.1 + - + +
208A VAL* 3.5 10.1 - - - +
210A ALA* 1.3 77.2 - - + +
212A ALA* 1.3 61.2 + - + +
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL 2.9 15.8 + - - +
209A ALA* 3.8 7.9 - - - +
211A VAL* 1.3 79.1 - - + +
213A GLY* 1.3 65.0 + - - +
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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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209A ALA* 2.8 20.3 + - - +
210A ALA* 3.2 10.5 + - - -
211A VAL 3.7 0.2 + - - -
212A ALA* 1.3 82.4 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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