Contacts of the helix formed by residues 176 - 189 (chain M) in PDB entry 6FF7
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 176 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171M ARG 5.5 2.4 - - - +
173M LEU 5.2 0.6 + - - -
175M LEU* 1.3 77.8 - - - +
177M PRO* 1.3 63.7 - - - +
178M GLU* 4.2 3.1 - - - -
179M SER* 3.7 33.3 + - - -
180M ALA* 4.4 5.4 + - - +
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Residues in contact with PRO 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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176M SER* 1.3 73.8 - - - +
178M GLU* 1.3 61.5 + - - +
179M SER 3.5 0.7 + - - -
180M ALA* 3.7 6.6 + - + +
181M GLU* 3.6 15.4 + - - +
209M PHE* 4.7 13.7 - - + -
212M LYS* 4.0 39.5 - - + +
213M ALA* 4.2 9.4 - - + +
218M TYR* 5.4 4.0 - - - +
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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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176M SER* 3.4 3.4 - - - -
177M PRO* 1.3 77.5 - - - +
179M SER* 1.3 60.3 + - - +
180M ALA 3.4 0.2 - - - -
181M GLU* 3.6 9.5 - - + +
182M GLU* 2.9 31.4 + - - +
216M SER* 6.0 6.1 - - - -
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Residues in contact with SER 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170M ARG* 4.8 17.7 - - - -
171M ARG* 5.4 2.2 - - - -
176M SER* 3.7 25.6 - - - -
177M PRO 3.3 1.0 - - - -
178M GLU* 1.3 77.9 - - - +
180M ALA* 1.3 57.7 + - - +
182M GLU* 3.5 3.6 + - - +
183M TYR* 2.9 30.8 + - - +
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Residues in contact with ALA 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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171M ARG* 3.8 31.9 - - + +
176M SER 4.4 4.6 + - - +
177M PRO 3.7 8.1 + - - +
178M GLU 3.4 0.4 - - - -
179M SER* 1.3 78.1 - - - +
181M GLU* 1.3 57.6 + - - +
183M TYR* 3.9 3.8 - - - +
184M ILE* 2.9 29.2 + - - +
199M ARG* 4.2 16.0 - - + +
202M THR* 6.3 2.0 - - - -
203M VAL* 5.3 9.9 - - + +
218M TYR* 6.1 0.4 - - - -
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Residues in contact with GLU 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 PRO 3.6 11.0 + - - +
178M GLU* 3.2 13.9 + - + +
179M SER 3.2 0.6 - - - -
180M ALA* 1.3 77.0 - - - +
182M GLU* 1.3 61.0 + - - +
184M ILE* 3.3 5.4 + - - +
185M GLU* 2.9 28.2 + - - +
216M SER* 6.5 1.1 - - - -
218M TYR* 4.4 24.4 - - + +
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Residues in contact with GLU 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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149M TRP* 6.0 5.8 - - + -
178M GLU 2.9 16.0 + - - +
179M SER* 4.0 4.0 - - - +
181M GLU* 1.3 76.7 - - - +
183M TYR* 1.3 57.8 + - - +
185M GLU* 3.3 7.0 + - - +
186M TYR* 2.9 29.5 + - - +
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Residues in contact with TYR 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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149M TRP* 6.5 1.6 - - + -
167M ARG* 4.4 28.7 - - + +
170M ARG* 5.9 4.3 - - + -
171M ARG* 5.6 2.2 - - + +
179M SER 2.9 19.4 + - - +
180M ALA* 4.1 7.2 - - - +
182M GLU* 1.3 76.9 - - - +
184M ILE* 1.3 57.4 + - - +
186M TYR* 3.8 5.8 - - - +
187M LEU* 2.9 30.1 + - - +
199M ARG* 5.3 2.9 - - + -
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Residues in contact with ILE 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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180M ALA 2.9 21.2 + - - +
181M GLU* 3.6 7.0 - - - +
182M GLU 3.2 0.2 - - - -
183M TYR* 1.3 74.9 - - - +
185M GLU* 1.3 60.5 + - - +
187M LEU* 3.7 4.3 - - - +
188M LYS* 2.9 30.1 + - - +
196M ALA* 4.5 11.2 - - - +
199M ARG* 3.8 21.8 - - + -
200M LEU* 5.0 4.0 - - + +
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Residues in contact with GLU 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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181M GLU 2.9 16.5 + - - +
182M GLU* 3.7 7.4 - - - +
184M ILE* 1.3 77.9 - - - +
186M TYR* 1.3 58.8 + - - +
188M LYS* 3.5 12.9 + - - +
189M SER* 3.6 12.3 + - - -
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Residues in contact with TYR 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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153M LEU* 4.9 17.5 - - + -
182M GLU 2.9 17.2 + - - +
183M TYR* 4.0 6.3 - - - +
185M GLU* 1.3 76.1 - - - +
187M LEU* 1.3 62.0 + - - +
189M SER* 3.6 16.7 + - - +
190M SER* 4.2 4.0 + - - -
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Residues in contact with LEU 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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163M GLU* 6.0 7.4 - - + -
167M ARG* 5.7 5.4 - - + -
183M TYR 2.9 18.9 + - - +
184M ILE* 3.9 5.4 - - - +
185M GLU 3.3 0.2 - - - -
186M TYR* 1.3 75.4 - - - +
188M LYS* 1.3 64.4 + - - +
189M SER 3.2 0.9 - - - -
190M SER* 3.4 19.2 + - - -
192M ARG 3.9 11.4 - - - +
195M GLU* 3.8 30.7 - - + +
196M ALA* 4.2 8.6 + - - +
199M ARG* 6.0 0.2 - - + -
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Residues in contact with LYS 188 (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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184M ILE 2.9 17.7 + - - +
185M GLU* 3.9 8.3 - - - +
186M TYR 3.3 0.4 - - - -
187M LEU* 1.3 75.8 - - - +
189M SER* 1.3 60.7 + - - +
190M SER 3.2 7.7 + - - +
192M ARG 5.2 2.4 - - - +
196M ALA* 4.0 17.9 - - + +
225M CYS* 5.0 15.3 - - + -
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Residues in contact with SER 189 (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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185M GLU 3.6 8.9 + - - -
186M TYR* 3.6 13.8 + - - -
187M LEU 3.2 1.0 - - - -
188M LYS* 1.3 75.7 - - - +
190M SER* 1.3 63.1 + - - +
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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