Contacts of the helix formed by residues 174 - 187 (chain M) in PDB entry 6K71
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 TYR 174 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173M ASP* 1.3 81.2 - - + +
175M THR* 1.3 58.4 + - + +
177M GLU* 3.3 17.4 + - - +
178M GLU* 2.9 28.4 + - - +
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Residues in contact with THR 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M ASP* 3.8 14.8 + - - +
174M TYR* 1.3 78.9 - - + +
176M TYR* 1.3 58.5 + - - +
178M GLU* 3.3 18.1 - - - +
179M LEU* 2.9 35.6 + - - +
220P PRO* 5.0 2.0 - - + +
221P ILE* 3.4 21.4 + - - +
222P ILE* 6.2 0.9 - - - -
234P VAL* 5.2 10.3 - - + -
238P TYR* 3.4 25.0 + - - +
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Residues in contact with TYR 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M ASP* 3.1 12.7 + - + +
175M THR* 1.3 82.3 + - - +
177M GLU* 1.3 65.5 + - + +
179M LEU* 3.2 9.5 + - - +
180M LEU* 2.8 53.9 + - + +
184M PHE* 5.5 5.8 - + - -
189P GLN* 4.1 9.9 - - - -
197P GLU* 4.6 3.5 + - - -
200P ALA* 3.3 34.7 - - + +
201P LYS* 3.7 3.3 + - - +
204P TYR* 3.5 33.8 - + + -
221P ILE* 3.6 44.6 - - + -
223P PRO* 3.7 14.6 - - + -
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Residues in contact with GLU 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M ASP 3.6 8.6 + - - +
174M TYR* 3.3 20.1 + - + +
176M TYR* 1.3 84.6 - - + +
178M GLU* 1.3 59.7 + - - +
180M LEU* 3.6 17.3 - - + +
181M ASN* 2.9 37.1 + - - +
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Residues in contact with GLU 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174M TYR 2.9 14.1 + - - +
175M THR* 3.3 24.3 - - - +
177M GLU* 1.3 74.6 - - - +
179M LEU* 1.3 67.4 + - + +
181M ASN* 4.1 2.2 - - - +
182M ARG* 3.0 35.5 + - + +
183M VAL* 4.6 1.1 - - + +
231P ASN* 6.0 1.8 - - - -
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Residues in contact with LEU 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M THR* 2.9 21.3 + - - +
176M TYR* 3.4 6.7 - - - +
178M GLU* 1.3 77.9 - - + +
180M LEU* 1.3 62.4 + - - +
181M ASN 3.1 0.2 + - - -
183M VAL* 2.9 55.9 + - + -
184M PHE* 3.2 21.8 + - + -
223P PRO* 2.3 66.2 - - + +
230P TYR* 3.5 3.6 - - + -
231P ASN* 2.8 31.4 - - - +
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Residues in contact with LEU 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M TYR* 2.8 52.1 + - + +
177M GLU* 3.3 18.1 + - + +
179M LEU* 1.3 71.5 - - - +
181M ASN* 1.3 76.5 + - - +
184M PHE* 3.6 23.3 - - + +
185M ASN* 4.3 4.3 - - - +
197P GLU* 5.4 12.3 - - + -
201P LYS* 6.6 0.2 - - + -
204P TYR* 5.8 0.9 - - + -
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Residues in contact with ASN 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177M GLU* 2.9 22.8 + - - +
178M GLU* 4.2 2.4 - - - +
180M LEU* 1.3 91.0 - - - +
182M ARG* 1.3 69.8 + - + +
185M ASN* 2.6 49.3 + - - +
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Residues in contact with ARG 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178M GLU* 3.0 25.6 + - + +
181M ASN* 1.3 82.7 - - + +
183M VAL* 1.3 68.8 + - + +
185M ASN* 3.8 4.4 - - - +
186M ILE* 3.0 44.5 + - + +
230P TYR* 5.2 4.5 - - - +
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Residues in contact with VAL 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178M GLU* 4.6 2.0 - - + +
179M LEU* 2.9 37.2 + - + +
182M ARG* 1.3 72.7 - - + +
184M PHE* 1.3 66.7 + - + +
186M ILE* 5.2 0.4 - - - -
187M MET* 2.6 42.2 + - + +
188M ARG 3.4 19.5 - - - +
192P ILE* 5.4 3.1 - - + -
223P PRO 5.4 2.7 - - - +
228P LEU* 5.5 0.2 - - + -
230P TYR* 2.6 62.8 - - + +
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Residues in contact with PHE 184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M TYR* 5.5 6.1 - + - -
179M LEU* 3.2 44.7 + - + -
180M LEU* 3.6 18.4 - - + +
183M VAL* 1.3 78.3 - - + +
185M ASN* 1.3 66.0 + - - +
187M MET 3.6 9.9 - - - +
188M ARG 4.1 13.5 - - - -
189P GLN* 5.9 1.1 - - - -
191P LYS 5.1 1.3 - - - -
192P ILE* 3.5 47.8 - - + -
196P LYS* 4.9 14.6 - - + -
200P ALA* 5.9 5.2 - - + -
223P PRO* 4.7 12.6 - - + -
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Residues in contact with ASN 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180M LEU 4.3 4.2 - - - +
181M ASN* 2.6 43.8 + - - +
182M ARG* 3.9 5.1 - - - +
184M PHE* 1.3 79.9 - - - +
186M ILE* 1.3 65.8 + - + +
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Residues in contact with ILE 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182M ARG* 3.0 34.1 + - + +
183M VAL* 4.3 0.7 - - - +
185M ASN* 1.3 87.7 - - + +
187M MET* 1.3 80.5 + - + +
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Residues in contact with MET 187 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183M VAL* 2.6 29.2 + - + +
184M PHE 3.6 11.8 - - - +
186M ILE* 1.3 92.9 - - + +
188M ARG* 1.3 69.8 + - - +
228P LEU* 3.5 33.4 - - + +
230P TYR* 5.0 15.9 - - + -
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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