Contacts of the helix formed by residues 169 - 183 (chain J) in PDB entry 3KDO
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 SER 169 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D ARG* 3.6 11.6 + - - +
130I GLU* 4.4 0.2 - - - -
134I ARG* 3.5 21.9 + - - -
168J TYR* 1.3 76.3 - - - +
170J PRO* 1.3 71.9 - - - +
171J GLU* 3.3 10.6 + - - +
172J GLU* 2.8 34.6 + - - +
173J PHE* 3.0 27.9 + - - +
199J TYR 3.4 8.1 - - - -
200J ASN* 3.5 2.7 - - - -
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Residues in contact with PRO 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I ARG* 4.5 5.2 - - - +
169J SER* 1.3 91.3 - - - +
171J GLU* 1.3 70.6 + - - +
173J PHE* 3.3 8.4 + - + +
174J GLU 2.8 23.0 + - - -
199J TYR 3.4 12.3 - - - +
200J ASN* 3.5 24.4 - - - +
204J GLU* 3.7 32.3 - - + +
205J ARG* 4.4 7.9 - - + +
208J ILE* 3.4 30.0 - - + +
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Residues in contact with GLU 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I ARG* 3.3 27.0 + - - -
357I TYR* 5.7 0.2 - - - -
358I SER* 3.0 38.9 + - - +
169J SER* 3.3 13.0 + - - +
170J PRO* 1.3 80.2 - - - +
172J GLU* 1.3 65.5 + - + +
174J GLU* 3.1 28.8 + - - +
175J LYS* 3.5 5.7 + - - +
204J GLU* 4.9 2.8 - - - +
208J ILE* 4.6 4.3 - - + -
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Residues in contact with GLU 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D TRP* 3.5 33.4 - - + +
62D TYR* 3.6 3.4 - - - +
63D GLU* 2.9 29.3 + - - +
66D ARG* 2.9 23.9 + - - -
355I LYS* 5.7 0.3 + - - -
168J TYR* 3.4 7.3 - - - +
169J SER* 2.8 36.7 + - - +
171J GLU* 1.3 79.2 - - + +
173J PHE* 1.3 62.8 + - - +
174J GLU 3.4 0.3 + - - -
175J LYS* 3.5 8.0 + - - +
176J LEU 3.5 14.2 + - - -
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Residues in contact with PHE 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D TRP* 3.9 9.8 - + - -
162J PRO* 3.7 16.2 - - + -
168J TYR* 3.8 25.6 - + + -
169J SER 3.0 20.2 + - - +
170J PRO* 3.4 8.1 - - + +
172J GLU* 1.3 75.2 - - - +
174J GLU* 1.3 62.5 + - - +
176J LEU* 3.4 1.9 + - + -
177J ALA* 2.8 33.6 + - + +
188J MET* 3.6 35.9 - - + -
189J KCX 6.3 0.7 - - - -
190J ASP* 5.1 4.7 - - - -
205J ARG* 4.3 26.2 - - + -
208J ILE* 5.0 3.4 - - + -
209J MET* 3.4 41.1 - - + -
226J TRP* 4.6 7.4 - - - -
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Residues in contact with GLU 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170J PRO 2.8 13.5 + - - +
171J GLU* 3.2 19.5 - - - +
173J PHE* 1.3 77.0 - - - +
175J LYS* 1.3 64.7 + - - +
177J ALA* 3.2 4.1 + - - +
178J TYR* 2.9 23.5 + - + +
208J ILE* 3.8 24.5 - - + +
211J LYS* 2.6 43.8 + - - -
212J ILE* 3.8 17.6 - - + +
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Residues in contact with LYS 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D TRP* 6.3 3.4 - - + -
171J GLU 3.5 5.2 + - - +
172J GLU* 3.5 10.5 + - - +
174J GLU* 1.3 83.1 - - - +
176J LEU* 1.3 64.2 + - - +
178J TYR* 3.2 7.2 + - + +
179J ASP* 3.1 54.3 + - - +
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Residues in contact with LEU 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D TRP* 3.6 58.3 - - + -
162J PRO* 4.2 14.6 - - + -
172J GLU 3.5 1.6 + - - -
173J PHE* 3.4 8.0 + - + +
174J GLU 3.3 0.2 - - - -
175J LYS* 1.3 81.1 - - + +
177J ALA* 1.3 63.1 + - - +
179J ASP* 3.3 6.0 + - + +
180J LEU* 3.0 41.4 + - + +
188J MET* 4.6 4.9 - - + -
395J LEU* 4.1 9.6 - - + -
401J PRO* 3.7 37.0 - - + -
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Residues in contact with ALA 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J PHE* 2.8 23.9 + - + +
174J GLU* 3.6 5.2 - - - +
176J LEU* 1.3 76.4 - - - +
178J TYR* 1.3 63.2 + - - +
180J LEU* 4.0 0.3 - - - +
181J LEU* 3.1 31.7 + - - +
188J MET* 4.0 21.9 - - + +
209J MET* 3.8 30.3 - - + -
212J ILE* 4.4 5.2 - - + -
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Residues in contact with TYR 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174J GLU* 2.9 16.8 + - + +
175J LYS* 3.2 6.9 + - + +
177J ALA* 1.3 76.4 - - - +
179J ASP* 1.3 71.0 + - - +
182J SER* 2.7 53.3 + - - -
212J ILE* 4.0 21.9 - - + +
215J LYS* 3.4 35.7 + - + -
216J VAL* 3.5 22.1 - - + +
219J GLU* 2.5 30.4 + - - -
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Residues in contact with ASP 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175J LYS* 3.1 52.3 + - - +
176J LEU* 3.7 8.4 - - + +
177J ALA 3.3 0.2 - - - -
178J TYR* 1.3 89.9 - - - +
180J LEU* 1.3 64.0 + - + +
182J SER* 3.4 2.5 + - - -
183J ASN* 2.8 34.2 + - - +
401J PRO* 5.7 0.7 - - + -
402J ALA* 4.5 20.4 - - + +
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Residues in contact with LEU 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160J VAL* 3.8 10.8 - - + -
176J LEU* 3.0 26.9 + - + +
179J ASP* 1.3 77.2 - - - +
181J LEU* 1.3 60.3 - - - +
183J ASN* 3.2 9.2 + - - -
184J GLY 3.5 0.7 + - - -
185J ALA* 3.1 28.5 + - + +
188J MET* 3.6 38.6 - - + -
394J THR* 4.0 15.3 - - + -
395J LEU* 3.6 22.2 - - + -
401J PRO* 3.6 39.0 - - + +
402J ALA 4.2 0.2 - - - +
405J ALA* 4.0 10.0 - - + +
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Residues in contact with LEU 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177J ALA 3.1 21.3 + - - +
180J LEU* 1.3 76.6 - - - +
182J SER* 1.3 61.7 + - - +
183J ASN 3.4 0.2 + - - -
184J GLY 3.6 1.7 + - - -
185J ALA* 3.5 21.4 - - + +
186J ASP 4.0 3.1 - - - +
187J TYR* 3.7 33.9 - - - +
188J MET* 3.9 9.2 - - + +
209J MET* 4.0 26.7 - - + -
212J ILE* 4.2 13.5 - - + -
213J ILE* 4.7 4.7 - - + -
216J VAL* 3.7 18.7 - - + +
220J THR* 5.2 0.7 - - - +
224J LYS* 3.1 45.7 + - + -
225J THR 4.5 1.1 - - - +
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Residues in contact with SER 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J TYR* 2.7 51.8 + - - -
179J ASP* 3.7 5.6 - - - -
180J LEU 3.2 0.2 - - - -
181J LEU* 1.3 77.8 - - - +
183J ASN* 1.3 64.3 + - - +
184J GLY 3.5 0.9 + - - -
216J VAL* 3.7 13.0 - - - +
219J GLU* 4.8 1.6 + - - -
220J THR* 4.6 15.0 - - - +
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Residues in contact with ASN 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179J ASP* 2.8 29.6 + - - +
180J LEU 3.2 3.1 + - - -
181J LEU 3.2 0.6 - - - -
182J SER* 1.3 84.4 - - - +
184J GLY* 1.3 55.0 + - - +
185J ALA 3.7 0.4 - - - -
402J ALA* 3.3 33.3 - - - +
405J ALA* 3.5 8.3 - - + +
406J ARG* 2.4 64.9 + - + +
409J ARG* 4.5 0.3 - - - +
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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
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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