Contacts of the helix formed by residues 185 - 201 (chain E) in PDB entry 5TJ4
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 185 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E GLY 2.6 28.1 + - - +
167E TYR* 3.5 24.1 - - + -
182E GLY* 3.5 15.1 + - - -
183E VAL 3.4 1.0 - - - -
184E ASP* 1.3 82.2 - - - +
186E ALA* 1.3 64.2 + - - +
187E GLY 3.1 6.2 + - - -
188E ALA* 2.8 22.9 + - - +
189E LYS* 3.0 19.8 + - - +
365E GLN* 4.5 0.6 + - - +
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Residues in contact with ALA 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E ASP* 4.8 1.8 - - - +
185E ASN* 1.3 74.5 - - - +
187E GLY* 1.3 53.1 + - - +
189E LYS* 3.1 11.6 + - - +
190E ALA* 2.8 36.6 + - - +
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Residues in contact with GLY 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E ILE 3.5 10.4 - - - +
164E ASP* 3.5 45.4 + - - +
165E GLY* 4.2 2.0 - - - -
185E ASN* 3.1 7.1 + - - -
186E ALA* 1.3 79.0 - - - +
188E ALA* 1.3 56.7 + - - +
190E ALA* 3.6 2.1 + - - +
191E GLY* 3.0 22.7 + - - -
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Residues in contact with ALA 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E ILE* 3.6 29.5 + - + +
166E GLY* 4.0 10.7 - - - +
182E GLY 4.1 0.9 - - - +
183E VAL* 3.2 30.5 - - - +
185E ASN* 2.8 17.3 + - - +
187E GLY* 1.3 72.1 - - - +
189E LYS* 1.3 66.6 + - - +
191E GLY 3.4 0.3 + - - -
192E LEU* 2.9 26.7 + - - +
361E LEU* 3.9 2.9 - - + +
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Residues in contact with LYS 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E ASP* 3.1 39.3 + - - +
185E ASN 3.0 15.6 + - - +
186E ALA* 3.4 11.2 - - - +
188E ALA* 1.3 77.7 - - - +
190E ALA* 1.3 51.3 + - - +
192E LEU* 3.6 0.7 - - - +
193E THR* 2.6 45.3 + - - +
357E VAL* 4.0 0.8 - - + +
358E ASP* 3.6 46.3 + - - +
361E LEU* 3.9 19.3 - - + -
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Residues in contact with ALA 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E ASP* 4.0 8.1 - - - +
186E ALA 2.8 19.3 + - - +
187E GLY 3.6 5.4 - - - +
189E LYS* 1.3 73.7 - - - +
191E GLY* 1.3 60.5 + - - +
193E THR* 3.7 5.7 - - - -
194E PHE* 3.0 25.5 + - - +
250E PHE* 3.6 6.0 - - + -
251E LYS* 3.7 28.9 - - - +
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Residues in contact with GLY 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E LEU* 3.6 33.2 - - - +
161E ILE* 4.2 4.5 - - - -
187E GLY 3.0 15.3 + - - -
188E ALA 3.8 0.9 - - - -
189E LYS 3.3 0.2 - - - -
190E ALA* 1.3 74.4 - - - +
192E LEU* 1.3 63.8 + - - +
194E PHE* 3.4 4.2 + - - +
195E LEU 3.2 15.6 + - - -
250E PHE* 3.7 17.0 - - - -
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Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E ILE* 4.1 25.3 - - + +
188E ALA 2.9 17.2 + - - +
189E LYS 3.9 1.8 - - - +
191E GLY* 1.3 73.1 - - - +
193E THR* 1.3 66.3 + - - +
195E LEU* 3.0 29.5 + - + +
196E VAL* 2.9 36.2 + - + +
346E ALA 4.7 7.9 - - - +
347E VAL* 4.3 17.9 - - + +
350E ALA* 4.1 14.4 - - + -
351E ALA* 6.5 0.2 - - + -
357E VAL* 3.8 15.0 - - + +
360E ALA* 5.4 0.4 - - + -
361E LEU* 3.6 32.3 - - + -
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Residues in contact with THR 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E LYS* 2.6 30.9 + - - +
190E ALA* 3.7 7.0 - - - +
192E LEU* 1.3 71.7 - - - +
194E PHE* 1.3 62.1 - - - +
196E VAL* 3.3 4.5 + - - +
197E ASP* 3.1 38.7 + - - +
357E VAL* 3.4 29.4 - - + +
358E ASP* 4.7 3.3 + - - -
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Residues in contact with PHE 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E TRP* 3.4 50.7 - + + -
130E GLU* 4.1 15.7 - - + -
133E PRO* 4.4 12.8 - - + -
160E LEU* 4.3 12.6 - - + -
190E ALA 3.0 17.9 + - - +
191E GLY 3.5 4.3 - - - +
193E THR* 1.3 74.5 - - - +
195E LEU* 1.3 67.1 + - - +
197E ASP* 3.0 23.9 + - + +
198E LEU* 3.0 41.9 + - + +
250E PHE* 3.6 26.9 - + + -
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Residues in contact with LEU 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E TRP* 5.6 0.4 - - + -
149E PHE* 4.1 19.7 - - + -
151E LEU* 4.4 12.3 - - + -
157E THR* 3.3 31.2 - - + -
160E LEU* 3.9 22.7 - - + -
161E ILE* 6.3 0.2 - - + -
191E GLY 3.2 4.4 + - - +
192E LEU* 3.0 25.2 + - + +
194E PHE* 1.3 78.4 - - - +
196E VAL* 1.3 63.0 + - + +
198E LEU* 3.3 18.8 + - + +
199E ILE* 3.4 21.3 + - + +
204E MET* 4.0 22.4 - - + -
347E VAL* 4.4 8.5 - - + -
351E ALA* 5.8 2.5 - - + -
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Residues in contact with VAL 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E LEU* 2.9 24.8 + - + +
193E THR 3.5 7.2 - - - +
195E LEU* 1.3 75.9 - - + +
197E ASP* 1.3 53.3 + - - +
199E ILE* 3.0 13.2 + - + +
200E LYS* 2.8 59.1 + - + +
350E ALA* 3.7 36.8 - - + +
351E ALA* 4.4 6.1 - - - +
357E VAL* 3.8 26.0 - - + -
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Residues in contact with ASP 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E THR* 3.1 29.2 + - - +
194E PHE* 3.0 17.8 + - + +
196E VAL* 1.3 78.0 - - - +
198E LEU* 1.3 54.3 + - + +
200E LYS* 3.9 19.0 + - + +
201E ASN* 2.8 50.5 + - - +
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Residues in contact with LEU 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E TRP* 4.7 13.2 - - + -
132E ILE* 4.8 17.9 - - + -
133E PRO* 5.0 6.3 - - + -
147E LEU* 5.5 0.4 - - + -
194E PHE* 3.0 66.1 + - + +
195E LEU* 3.3 10.0 + - + +
197E ASP* 1.3 77.2 - - + +
199E ILE* 1.3 58.6 + - - +
201E ASN 3.8 0.3 + - - -
202E LYS 3.7 0.9 + - - -
203E HIS* 2.9 53.2 + - + -
204E MET* 3.0 37.3 + - + -
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Residues in contact with ILE 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA* 5.5 8.6 - - + -
87A ASP* 5.3 7.1 - - - +
151E LEU* 3.8 26.9 - - + -
195E LEU* 3.4 23.1 - - + +
196E VAL* 3.0 9.6 + - + +
198E LEU* 1.3 75.0 - - + +
200E LYS* 1.3 65.8 + - - +
202E LYS* 3.1 14.6 + - - -
204E MET* 3.5 19.6 - - + +
205E ASN* 4.4 0.7 - - - +
206E ALA* 3.6 28.7 - - + +
351E ALA* 3.6 40.2 - - + +
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Residues in contact with LYS 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA* 6.5 1.3 - - - -
83A ALA* 5.0 16.3 - - + +
84A ALA* 5.5 17.9 - - + +
196E VAL* 2.8 36.5 + - + +
197E ASP* 3.5 19.4 + - - +
199E ILE* 1.3 77.4 - - - +
201E ASN* 1.3 63.1 + - - +
202E LYS 3.5 2.3 + - - -
353E GLY* 6.3 2.9 - - - -
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Residues in contact with ASN 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1246C SER* 4.2 5.2 + - - -
1377C PRO* 5.6 12.1 - - - +
197E ASP* 2.8 38.7 + - - +
198E LEU 3.8 0.2 - - - -
199E ILE 3.2 0.2 - - - -
200E LYS* 1.3 76.8 - - - +
202E LYS* 1.3 56.4 + - - +
203E HIS* 2.8 47.3 + - + +
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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