Contacts of the helix formed by residues 185 - 201 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165H GLY* 2.7 27.7 + - - +
167H TYR* 3.6 20.0 - - + +
182H GLY* 3.5 20.5 + - - -
183H VAL 3.4 0.8 - - - -
184H ASP* 1.3 83.3 - - - +
186H ALA* 1.3 64.4 + - - +
187H GLY 3.1 5.6 + - - -
188H ALA* 2.8 22.9 + - - +
189H LYS* 3.0 20.4 + - - +
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Residues in contact with ALA 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H ASP* 4.8 2.0 - - - +
185H ASN* 1.3 74.8 - - - +
187H GLY* 1.3 53.9 + - - +
189H LYS* 3.1 11.6 + - - +
190H ALA* 2.7 36.8 + - - +
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Residues in contact with GLY 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161H ILE 3.5 10.3 - - - +
164H ASP* 3.5 44.4 + - - +
165H GLY* 3.9 2.7 - - - -
185H ASN* 3.1 6.7 + - - -
186H ALA* 1.3 77.5 - - - +
188H ALA* 1.3 57.1 + - - +
190H ALA* 3.6 2.3 - - - +
191H GLY* 3.0 23.0 + - - -
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Residues in contact with ALA 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161H ILE* 3.6 29.9 + - + +
166H GLY* 4.0 10.4 - - - +
182H GLY 4.1 0.7 - - - +
183H VAL* 3.2 30.7 - - - +
185H ASN* 2.8 21.3 + - - +
187H GLY* 1.3 69.6 - - - -
189H LYS* 1.3 61.4 + - - +
191H GLY 3.4 0.2 + - - -
192H LEU* 2.9 32.1 + - - +
361H LEU* 4.0 2.4 - - + +
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Residues in contact with LYS 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H ASP* 4.0 23.8 - - - +
185H ASN 3.0 18.5 + - - +
186H ALA* 3.4 10.5 - - - +
188H ALA* 1.3 76.7 - - - +
190H ALA* 1.3 53.0 - - - +
192H LEU* 3.8 0.7 - - - +
193H THR* 2.6 43.5 + - - +
357H VAL* 4.0 1.1 - - + +
358H ASP* 3.7 37.2 - - + +
361H LEU* 3.9 19.5 - - + -
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Residues in contact with ALA 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H ASP* 4.0 15.5 - - - +
186H ALA 2.7 19.9 + - - +
187H GLY 3.6 5.6 - - - +
189H LYS* 1.3 73.1 - - - +
191H GLY* 1.3 57.5 + - - +
193H THR* 3.7 6.3 - - - -
194H PHE* 3.0 29.1 + - - +
250H PHE* 3.6 15.5 - - + -
251H LYS* 4.6 5.8 - - + -
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Residues in contact with GLY 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H LEU* 3.6 32.7 - - - +
161H ILE* 4.2 4.5 - - - -
187H GLY 3.0 14.7 + - - -
188H ALA 3.8 0.9 - - - -
189H LYS 3.3 0.2 - - - -
190H ALA* 1.3 73.8 - - - +
192H LEU* 1.3 66.1 + - - +
194H PHE* 3.5 4.0 + - - +
195H LEU 3.2 16.3 + - - -
250H PHE* 3.7 16.7 - - - -
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Residues in contact with LEU 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H ILE* 4.1 25.3 - - + +
188H ALA 2.9 17.0 + - - +
189H LYS 3.9 1.6 - - - +
191H GLY* 1.3 71.7 - - - +
193H THR* 1.3 66.8 + - - +
195H LEU* 3.0 30.1 + - + +
196H VAL* 2.9 36.4 + - + +
346H ALA 4.7 7.9 - - - +
347H VAL* 4.3 18.8 - - + +
350H ALA* 4.1 14.4 - - + -
351H ALA* 5.9 0.4 - - + +
357H VAL* 3.8 15.9 - - + +
360H ALA* 5.3 0.7 - - + -
361H LEU* 3.6 32.1 - - + -
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Residues in contact with THR 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H LYS* 2.6 31.1 + - - +
190H ALA* 3.7 6.7 - - - +
192H LEU* 1.3 71.0 - - - +
194H PHE* 1.3 63.0 + - - +
196H VAL* 3.3 3.6 + - - +
197H ASP* 3.1 39.6 + - - +
357H VAL* 3.4 28.8 - - + +
358H ASP* 4.7 3.3 + - - -
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Residues in contact with PHE 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H TRP* 3.4 50.7 - + + -
130H GLU* 4.0 15.5 - - + -
133H PRO* 4.4 13.5 - - + -
160H LEU* 4.2 12.6 - - + -
190H ALA 3.0 18.1 + - - +
191H GLY 3.5 4.3 - - - +
193H THR* 1.3 73.9 - - - +
195H LEU* 1.3 66.7 + - - +
197H ASP* 3.0 23.1 + - + +
198H LEU* 3.0 41.3 + - + +
250H PHE* 3.6 27.4 - + + -
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Residues in contact with LEU 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H TRP* 5.6 0.4 - - + -
149H PHE* 4.0 20.0 - - + -
151H LEU* 4.4 15.3 - - + -
157H THR* 3.3 31.9 - - + +
160H LEU* 3.9 23.1 - - + -
161H ILE* 6.3 0.2 - - + -
191H GLY 3.2 5.0 + - - +
192H LEU* 3.0 24.3 + - + +
194H PHE* 1.3 77.6 - - - +
196H VAL* 1.3 64.1 + - + +
198H LEU* 3.2 18.4 + - + +
199H ILE* 3.4 16.2 + - + +
204H MET* 4.0 22.7 - - + -
347H VAL* 4.4 7.9 - - + -
351H ALA* 5.8 6.5 - - + -
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Residues in contact with VAL 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192H LEU* 2.9 25.8 + - + +
193H THR 3.5 7.4 - - - +
194H PHE 3.2 0.2 - - - -
195H LEU* 1.3 76.6 - - + +
197H ASP* 1.3 54.7 + - - +
199H ILE* 2.8 21.2 - - + +
200H LYS* 2.8 37.3 + - + +
350H ALA* 3.7 36.3 - - + +
351H ALA* 4.4 3.1 - - - +
357H VAL* 3.7 25.6 - - + -
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Residues in contact with ASP 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193H THR* 3.1 28.7 + - - +
194H PHE* 3.0 17.3 + - + +
196H VAL* 1.3 80.1 - - - +
198H LEU* 1.3 55.1 + - + +
200H LYS* 3.9 9.2 - - - +
201H ASN* 2.8 51.2 + - - +
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Residues in contact with LEU 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H TRP* 4.7 13.5 - - + -
132H ILE* 4.8 17.5 - - + -
133H PRO* 5.0 6.1 - - + -
147H LEU* 5.5 0.7 - - + -
194H PHE* 3.0 66.0 - - + +
195H LEU* 3.2 10.4 + - + +
197H ASP* 1.3 78.1 - - + +
199H ILE* 1.3 59.8 + - - +
201H ASN 3.8 0.2 - - - -
202H LYS 3.6 1.6 + - - -
203H HIS* 2.8 53.5 + - + +
204H MET* 3.0 34.1 + - + -
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Residues in contact with ILE 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H LEU* 4.1 19.7 - - + -
195H LEU* 3.5 15.7 - - + +
196H VAL* 2.8 31.2 + - + +
198H LEU* 1.3 78.8 - - + +
200H LYS* 1.3 67.0 + - + +
202H LYS* 3.1 14.0 + - - -
204H MET* 3.4 34.2 - - + +
206H ALA* 4.5 12.1 - - + +
351H ALA* 3.1 35.2 - - + +
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Residues in contact with LYS 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196H VAL* 2.8 24.1 + - + +
197H ASP* 3.6 13.7 - - - +
199H ILE* 1.3 79.0 - - + +
201H ASN* 1.3 61.1 + - - +
202H LYS* 3.3 3.0 + - - +
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Residues in contact with ASN 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197H ASP* 2.8 39.3 + - - +
200H LYS* 1.3 76.1 - - - +
202H LYS* 1.3 55.8 - - - +
203H HIS* 2.8 47.9 + - + +
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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
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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