Contacts of the helix formed by residues 169 - 182 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C ARG* 3.5 15.2 + - - +
168F TYR* 1.3 76.6 - - - +
170F PRO* 1.3 67.7 - - - +
171F GLU* 3.1 22.5 + - - +
172F GLU* 2.7 36.0 + - - +
173F PHE* 2.8 26.9 + - - +
199F TYR 3.6 4.9 - - - -
200F ASN* 3.6 2.0 - - - -
134J ARG* 3.3 14.8 + - - -
357J TYR* 5.8 0.3 - - - -
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Residues in contact with PRO 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F SER* 1.3 87.3 - - - +
171F GLU* 1.3 71.0 + - - +
173F PHE* 3.1 10.2 + - + +
174F GLU* 2.7 31.0 + - - +
199F TYR 3.3 16.8 - - - +
200F ASN* 3.6 16.1 - - - +
204F GLU* 3.7 32.1 - - + +
205F ARG* 5.1 1.1 - - + +
208F ILE* 3.3 29.9 - - + +
134J ARG* 4.2 5.2 - - - +
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Residues in contact with GLU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F SER* 3.1 8.5 + - - +
170F PRO* 1.3 85.7 - - - +
172F GLU* 1.3 60.8 + - + +
174F GLU* 3.5 9.6 + - - +
175F LYS* 3.5 19.4 + - - +
208F ILE* 5.0 1.6 - - + -
134J ARG* 2.8 45.3 + - - -
357J TYR* 5.5 1.3 - - + -
358J SER* 3.3 32.5 + - - +
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Residues in contact with GLU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C TRP* 3.8 29.4 - - + +
62C TYR* 3.5 5.4 - - - +
63C GLU* 2.8 37.5 + - - +
66C ARG* 3.2 11.1 + - - -
168F TYR* 3.2 8.8 - - - +
169F SER* 2.7 42.3 + - - +
171F GLU* 1.3 75.9 - - + +
173F PHE* 1.3 62.7 + - - +
175F LYS* 3.4 8.4 + - - +
176F LEU* 3.1 23.0 + - - +
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Residues in contact with PHE 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C TRP* 4.3 6.7 - - - -
162F PRO* 3.9 24.5 - - + -
168F TYR* 3.9 24.5 - + + -
169F SER 2.8 14.4 + - - +
170F PRO* 3.2 13.2 - - + +
172F GLU* 1.3 76.2 - - - +
174F GLU* 1.3 59.7 + - - +
176F LEU* 3.3 3.4 + - + +
177F ALA* 2.9 30.2 + - + +
188F MET* 3.9 19.1 - - + -
189F KCX 6.3 0.9 - - - -
190F ASP* 5.2 2.2 - - - -
200F ASN* 4.5 0.7 - - - +
205F ARG* 4.2 31.6 - - + -
208F ILE* 4.5 8.5 - - + -
209F MET* 3.5 42.0 - - + -
226F TRP* 4.3 13.2 - - - -
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Residues in contact with GLU 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F PRO 2.7 16.3 + - - +
171F GLU* 3.7 10.2 - - - +
172F GLU 3.3 0.2 - - - -
173F PHE* 1.3 74.2 - - - +
175F LYS* 1.3 64.2 + - - +
177F ALA* 3.8 2.9 - - - +
178F TYR* 3.1 23.8 + - + +
208F ILE* 3.4 35.6 - - + +
211F LYS* 3.4 29.8 + - - +
212F ILE* 3.7 22.4 - - + +
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Residues in contact with LYS 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C TRP* 6.4 1.8 - - + -
171F GLU 3.5 8.8 + - - +
172F GLU* 3.4 10.2 + - - +
174F GLU* 1.3 81.6 - - - +
176F LEU* 1.3 62.9 + - - +
178F TYR* 3.6 4.1 + - - +
179F ASP* 3.1 60.7 + - - +
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Residues in contact with LEU 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C TRP* 3.4 44.4 - - + -
162F PRO* 4.0 17.3 - - + -
172F GLU 3.1 16.6 + - - +
173F PHE* 3.3 4.7 + - + +
175F LYS* 1.3 76.7 - - + +
177F ALA* 1.3 60.6 + - - +
179F ASP* 3.4 5.2 + - + +
180F LEU* 2.9 47.2 + - + +
188F MET* 4.4 4.0 - - + -
395F LEU* 3.4 31.6 - - + -
401F PRO* 3.5 25.8 - - + -
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Residues in contact with ALA 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F PHE* 2.9 19.1 + - + +
174F GLU* 3.8 5.2 - - - +
176F LEU* 1.3 75.3 - - - +
178F TYR* 1.3 60.0 + - - +
181F LEU* 2.9 35.5 + - - +
188F MET* 3.9 24.4 - - + +
209F MET* 3.8 29.8 - - + -
212F ILE* 4.4 8.1 - - + -
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Residues in contact with TYR 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F GLU* 3.1 17.0 + - + +
175F LYS* 3.8 5.6 - - - +
177F ALA* 1.3 76.2 - - - +
179F ASP* 1.3 69.3 - - - +
181F LEU* 4.3 0.5 - - - +
182F SER* 2.6 53.0 + - - -
212F ILE* 4.1 21.7 - - + +
215F LYS* 3.0 33.9 - - + +
216F VAL* 3.9 14.8 - - + -
219F GLU* 2.5 29.1 + - - -
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Residues in contact with ASP 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F LYS* 3.1 53.4 + - - +
176F LEU* 3.8 6.7 - - - +
178F TYR* 1.3 89.6 - - - +
180F LEU* 1.3 63.8 + - + +
182F SER* 4.4 0.7 - - - -
183F ASN* 2.7 35.5 + - - +
401F PRO* 5.3 4.0 - - + +
402F ALA* 4.3 20.6 - - + +
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Residues in contact with LEU 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F VAL* 3.7 29.8 - - + -
176F LEU* 2.9 43.3 + - + +
177F ALA 3.9 1.8 - - - +
179F ASP* 1.3 75.2 - - - +
181F LEU* 1.3 65.9 + - - +
183F ASN 3.0 12.8 + - - -
184F GLY 3.6 0.5 + - - -
185F ALA* 3.2 25.1 + - + +
188F MET* 3.8 20.0 - - + -
394F THR* 3.8 16.2 - - + -
395F LEU* 4.9 1.6 - - + -
401F PRO* 3.5 40.4 - - + +
405F ALA* 4.0 8.5 - - + +
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Residues in contact with LEU 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177F ALA 2.9 20.3 + - - +
180F LEU* 1.3 73.7 - - - +
182F SER* 1.3 59.9 + - - +
183F ASN 3.1 1.4 + - - -
184F GLY 3.9 1.9 + - - -
185F ALA* 3.6 24.5 - - + +
187F TYR 3.9 11.2 - - - +
188F MET* 3.6 26.5 - - + -
209F MET* 3.9 28.5 - - + -
212F ILE* 4.4 10.5 - - + -
213F ILE* 4.8 2.9 - - + -
216F VAL* 3.7 19.5 - - + +
220F THR* 4.9 0.7 - - - +
224F LYS* 3.0 55.5 + - + -
225F THR 4.7 3.1 - - - +
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Residues in contact with SER 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F TYR* 2.6 44.0 + - - -
179F ASP* 4.2 1.3 - - - -
181F LEU* 1.3 76.9 - - - +
183F ASN* 1.3 73.5 + - - +
184F GLY 3.7 0.9 - - - -
216F VAL* 3.7 19.5 - - - +
219F GLU* 5.1 1.2 + - - -
220F THR* 4.5 14.3 - - - +
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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