Contacts of the helix formed by residues 185 - 201 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165I GLY* 2.7 27.9 + - - +
167I TYR* 3.5 19.4 - - + +
182I GLY* 3.5 21.4 + - - -
183I VAL 3.4 0.8 - - - -
184I ASP* 1.3 82.5 - - - +
186I ALA* 1.3 64.0 + - - +
187I GLY 3.0 5.3 + - - -
188I ALA* 2.8 23.0 + - - +
189I LYS* 3.0 18.9 + - - +
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Residues in contact with ALA 186 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I ASP* 4.8 1.3 - - - +
185I ASN* 1.3 74.1 - - - +
187I GLY* 1.3 54.2 + - - +
189I LYS* 3.1 8.2 + - - +
190I ALA* 2.8 36.6 + - - +
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Residues in contact with GLY 187 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161I ILE 3.5 10.6 - - - +
164I ASP* 3.5 44.2 + - - +
165I GLY* 4.2 2.5 - - - -
185I ASN* 3.0 6.7 + - - -
186I ALA* 1.3 77.7 - - - +
188I ALA* 1.3 56.6 + - - +
190I ALA* 3.6 2.1 - - - +
191I GLY* 3.0 23.4 + - - -
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Residues in contact with ALA 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161I ILE* 3.6 31.0 + - + +
166I GLY* 4.0 11.1 - - - +
182I GLY 4.1 0.9 - - - +
183I VAL* 3.2 29.8 - - - +
185I ASN* 2.8 17.5 + - - +
187I GLY* 1.3 73.6 - - - +
189I LYS* 1.3 65.3 + - - +
191I GLY 3.4 0.5 + - - -
192I LEU* 2.9 26.5 + - - +
361I LEU* 4.1 2.5 - - + -
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Residues in contact with LYS 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I ASP 5.3 2.5 - - - +
185I ASN 3.0 13.6 + - - +
186I ALA* 3.3 12.3 - - - +
188I ALA* 1.3 76.2 - - - +
190I ALA* 1.3 51.3 + - - +
192I LEU* 3.8 0.7 - - - +
193I THR* 2.6 45.4 + - - +
357I VAL* 4.0 1.1 - - + +
358I ASP* 4.4 18.6 - - - +
361I LEU* 3.9 15.4 - - + +
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Residues in contact with ALA 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I ASP* 4.0 15.7 - - - +
186I ALA 2.8 19.1 + - - +
187I GLY 3.6 5.8 - - - +
189I LYS* 1.3 73.5 - - - +
191I GLY* 1.3 57.1 + - - +
193I THR* 3.7 5.7 - - - +
194I PHE* 3.0 30.1 + - - +
250I PHE* 3.6 14.5 - - + -
251I LYS* 4.5 6.3 - - + -
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Residues in contact with GLY 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I LEU* 3.6 32.4 - - - +
161I ILE* 4.3 4.0 - - - -
187I GLY 3.0 15.3 + - - -
188I ALA 3.8 1.3 - - - -
189I LYS 3.3 0.2 - - - -
190I ALA* 1.3 75.0 - - - +
192I LEU* 1.3 63.8 + - - +
194I PHE* 3.4 3.5 + - - +
195I LEU 3.2 16.1 + - - -
250I PHE* 3.7 17.2 - - - -
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Residues in contact with LEU 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161I ILE* 4.1 23.5 - - + +
188I ALA 2.9 17.2 + - - +
189I LYS 3.9 2.0 - - - +
191I GLY* 1.3 72.4 - - - +
193I THR* 1.3 66.5 + - - +
195I LEU* 3.1 29.4 + - + +
196I VAL* 2.9 35.4 + - + +
346I ALA 4.7 6.7 - - - +
347I VAL* 4.3 18.4 - - + +
350I ALA* 4.1 15.3 - - + -
351I ALA* 6.5 0.2 - - + -
357I VAL* 3.8 15.9 - - + +
360I ALA* 5.4 0.7 - - + -
361I LEU* 3.6 32.1 - - + -
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Residues in contact with THR 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I LYS* 2.6 30.4 + - - +
190I ALA* 3.7 7.0 - - - +
192I LEU* 1.3 71.8 - - - +
194I PHE* 1.3 61.6 + - - +
196I VAL* 3.3 4.3 + - - +
197I ASP* 3.1 39.5 + - - +
357I VAL* 3.4 29.1 - - + +
358I ASP* 4.7 3.3 + - - -
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Residues in contact with PHE 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I TRP* 3.4 50.0 - + + -
130I GLU* 4.0 15.3 - - + -
133I PRO* 4.4 13.7 - - + -
160I LEU* 4.2 12.6 - - + -
190I ALA 3.0 17.9 + - - +
191I GLY 3.5 4.5 - - - +
193I THR* 1.3 73.9 - - - +
195I LEU* 1.3 67.6 + - - +
197I ASP* 3.0 22.8 + - + +
198I LEU* 3.0 41.5 + - + +
250I PHE* 3.6 26.2 - + + -
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Residues in contact with LEU 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I TRP* 5.6 0.4 - - + -
149I PHE* 4.0 20.2 - - + -
151I LEU* 4.4 12.8 - - + -
157I THR* 3.3 30.7 - - + +
160I LEU* 3.9 22.0 - - + -
161I ILE* 6.3 0.2 - - + -
191I GLY 3.2 4.6 + - - +
192I LEU* 3.1 25.0 + - + +
194I PHE* 1.3 78.8 - - - +
196I VAL* 1.3 63.0 + - + +
198I LEU* 3.2 19.6 + - + +
199I ILE* 3.4 22.4 + - + +
204I MET* 4.0 22.9 - - + -
347I VAL* 4.4 8.5 - - + -
351I ALA* 5.8 2.0 - - + -
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Residues in contact with VAL 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I LEU* 2.9 25.4 + - + +
193I THR 3.5 7.4 - - - +
194I PHE 3.2 0.2 - - - -
195I LEU* 1.3 75.9 - - + +
197I ASP* 1.3 56.4 + - - +
199I ILE* 3.0 12.7 + - + +
200I LYS* 2.8 36.6 + - + +
350I ALA* 3.7 36.6 - - + +
351I ALA* 4.4 7.0 - - + +
357I VAL* 3.7 25.6 - - + -
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Residues in contact with ASP 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I THR* 3.1 29.5 + - - +
194I PHE* 3.0 17.3 + - + +
196I VAL* 1.3 79.8 - - - +
198I LEU* 1.3 55.3 + - + +
200I LYS* 3.9 9.1 - - - +
201I ASN* 2.8 51.9 + - - +
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Residues in contact with LEU 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I TRP* 4.7 12.3 - - + -
132I ILE* 4.8 18.8 - - + -
133I PRO* 5.0 6.3 - - + -
147I LEU* 6.0 0.2 - - + -
194I PHE* 3.0 65.1 - - + +
195I LEU* 3.2 10.9 + - + +
197I ASP* 1.3 77.9 - - + +
199I ILE* 1.3 57.9 + - - +
201I ASN* 3.8 0.6 - - - +
202I LYS 3.6 1.0 + - - -
203I HIS* 2.8 53.4 + - + +
204I MET* 3.0 36.3 + - + -
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Residues in contact with ILE 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I LEU* 3.8 26.9 - - + -
195I LEU* 3.4 22.9 - - + +
196I VAL* 3.0 8.9 + - + +
198I LEU* 1.3 75.9 - - + +
200I LYS* 1.3 64.3 + - - +
201I ASN 3.2 0.2 - - - -
202I LYS* 3.1 14.6 + - - -
204I MET* 3.5 19.2 - - + +
205I ASN* 4.4 0.4 - - - +
206I ALA* 3.6 28.7 - - + +
351I ALA* 3.6 39.9 - - + +
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Residues in contact with LYS 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196I VAL* 2.8 25.4 + - + +
197I ASP* 3.6 13.9 - - - +
199I ILE* 1.3 73.5 - - - +
201I ASN* 1.3 62.0 + - - +
202I LYS* 3.5 2.4 + - - +
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Residues in contact with ASN 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197I ASP* 2.8 39.5 + - - +
200I LYS* 1.3 76.7 - - - +
202I LYS* 1.3 55.8 + - - +
203I HIS* 2.8 47.4 + - + +
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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
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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