Contacts of the helix formed by residues 177 - 192 (chain M) in PDB entry 1FNP
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 GLY 177 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M PHE* 4.3 7.6 - - - -
91M PHE 3.8 12.8 - - - -
175M PRO 3.6 3.4 + - - -
176M TYR* 1.3 74.4 - - - +
178M ILE* 1.3 68.7 + - - +
179M PHE 3.6 1.1 - - - -
180M SER* 3.5 12.7 + - - -
181M HIS* 3.2 23.4 + - - +
600M SPO 3.6 14.7 - - - +
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Residues in contact with ILE 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73M PHE* 5.1 3.6 - - + -
88M LEU* 4.2 21.5 - - + +
89M PHE* 4.0 32.3 + - + +
91M PHE 4.6 0.4 + - - -
177M GLY* 1.3 72.5 - - - -
179M PHE* 1.3 77.4 + - + +
181M HIS* 3.0 25.7 + - - -
182M LEU* 3.4 10.4 - - - +
600M SPO 3.5 28.5 - - + -
801M BCL 3.4 55.0 - - + -
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Residues in contact with PHE 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169L TYR* 3.4 36.0 + + - +
174L MET* 3.9 18.8 - - + -
260L VAL* 5.9 0.9 - - + -
263L TRP* 3.4 42.6 - + + -
89M PHE* 3.0 39.9 + + + +
90M PHE* 3.8 41.3 - + + -
178M ILE* 1.3 87.4 - - + +
180M SER* 1.3 59.5 + - - +
182M LEU* 3.2 13.2 - - + +
183M ASP* 3.0 31.6 + - - +
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Residues in contact with SER 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M PHE 4.5 1.4 + - - -
90M PHE 5.6 2.4 + - - -
91M PHE 4.8 1.1 - - - -
92M SER* 2.9 35.6 + - - -
94M GLU* 4.0 8.3 - - - -
175M PRO* 3.7 10.1 - - - +
177M GLY* 3.5 17.0 + - - -
178M ILE 3.3 0.2 - - - -
179M PHE* 1.3 79.4 - - - +
181M HIS* 1.3 60.1 + - - +
183M ASP* 3.1 11.4 + - - +
184M TRP* 2.8 28.4 + - - +
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Residues in contact with HIS 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174M VAL* 3.9 7.6 - - + -
175M PRO* 3.8 18.4 - - - +
177M GLY 3.2 14.2 + - - +
178M ILE* 3.0 24.6 + - - -
180M SER* 1.3 80.8 + - - +
182M LEU* 1.3 65.0 + - + +
184M TRP* 3.7 9.2 - - - +
185M THR* 2.9 27.4 + - - -
600M SPO 3.4 27.1 - - + -
801M BCL 2.2 82.9 + + + +
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Residues in contact with LEU 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166L ASN* 4.7 2.0 - - - +
168L HIS* 3.2 36.3 + - + +
169L TYR* 4.9 5.6 - - + +
174L MET* 4.0 26.5 - - + -
178M ILE 3.4 17.9 - - - +
179M PHE* 3.2 17.9 + - + +
181M HIS* 1.3 80.7 + - + +
183M ASP* 1.3 59.9 + - - +
185M THR* 2.9 18.9 + - - -
186M ASN 3.1 10.4 + - - -
801M BCL 3.6 58.3 - - + +
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Residues in contact with ASP 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166L ASN* 3.8 9.4 + - - +
169L TYR* 3.1 31.1 + - - -
179M PHE* 3.0 19.1 + - - +
180M SER* 3.1 11.2 + - - +
182M LEU* 1.3 75.5 - - - +
184M TRP* 1.3 58.4 + - - +
185M THR 3.2 0.2 + - - -
186M ASN* 3.2 4.8 + - - +
187M ASN* 2.8 34.1 + - - +
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Residues in contact with TRP 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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159M LEU* 3.7 32.3 - - + -
163M ARG* 4.9 0.9 - - - -
171M SER 4.9 2.9 + - - -
172M GLU 3.5 23.0 + - - -
173M ALA 3.1 15.7 + - - -
174M VAL* 3.7 23.8 - - + -
175M PRO* 3.6 28.7 - - + -
180M SER 2.8 15.2 + - - +
181M HIS* 3.7 5.8 - - - +
183M ASP* 1.3 75.2 - - - +
185M THR* 1.3 67.1 + - - +
187M ASN* 3.4 6.6 + - - +
188M PHE* 2.9 61.9 + + - +
801M BCL 4.2 8.1 - - + -
802M BCL 4.1 18.8 - - + -
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Residues in contact with THR 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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168L HIS* 3.7 16.4 - - + -
302L BCL 4.0 6.7 - - + -
181M HIS 2.9 14.7 + - - -
182M LEU* 2.9 11.0 + - - -
184M TRP* 1.3 86.5 - - - +
186M ASN* 1.3 62.2 + - - +
188M PHE* 3.4 4.0 + - - +
189M SER 3.4 14.0 + - - -
801M BCL 3.6 33.4 - - + +
802M BCL 3.5 43.6 - - + +
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Residues in contact with ASN 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162L TYR* 2.6 39.2 + - - -
166L ASN* 3.6 38.3 - - - +
168L HIS* 3.9 1.1 - - + -
182M LEU 3.1 5.2 + - - +
183M ASP* 3.7 6.4 + - - +
185M THR* 1.3 73.2 - - - +
187M ASN* 1.3 68.7 + - - +
189M SER* 3.1 6.4 + - - -
190M LEU* 3.1 36.3 + - - +
802M BCL 3.4 18.5 - - + +
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Residues in contact with ASN 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 ASP 2.8 19.2 + - - +
184M TRP* 3.6 8.2 - - - +
186M ASN* 1.3 79.6 - - - +
188M PHE* 1.3 58.2 + - - +
190M LEU* 3.3 13.1 + - - +
191M VAL* 3.0 43.7 + - - +
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Residues in contact with PHE 188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163M ARG* 3.3 41.5 - - - -
172M GLU* 5.5 0.9 - - - -
184M TRP* 2.9 44.6 + + + +
185M THR 3.5 6.7 - - - +
186M ASN 3.2 0.2 - - - -
187M ASN* 1.3 79.0 + - - +
189M SER* 1.3 61.8 + - - +
191M VAL* 3.4 2.0 + - - -
192M HIS* 2.9 51.3 + + - -
195M LEU* 4.0 15.7 - - + -
283M ILE* 4.0 23.1 - - + -
286M SER* 3.8 20.9 - - - -
802M BCL 3.7 20.2 - - + -
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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
----------------------------------------------------------
162L TYR* 5.1 1.7 + - - -
185M THR 3.4 3.2 + - - -
186M ASN 3.1 9.5 + - - -
188M PHE* 1.3 78.1 - - - +
190M LEU* 1.3 64.8 + - - +
192M HIS 3.1 9.2 + - - -
193M GLY 3.3 0.2 + - - -
194M ASN* 2.9 29.3 + - - -
195M LEU* 2.9 36.3 + - - -
802M BCL 3.5 37.8 - - - +
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Residues in contact with LEU 190 (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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162L TYR* 3.1 34.1 - - + +
186M ASN* 3.1 31.6 + - - +
187M ASN* 3.6 14.1 - - - +
189M SER* 1.3 82.8 - - - +
191M VAL* 1.3 62.5 + - + +
192M HIS 3.3 1.4 + - - -
193M GLY* 3.5 9.2 + - - -
194M ASN* 4.5 3.3 + - + +
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Residues in contact with VAL 191 (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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187M ASN* 3.0 37.5 + - - +
188M PHE* 4.0 4.0 - - - +
189M SER 3.3 0.2 - - - -
190M LEU* 1.3 78.1 - - + +
192M HIS* 1.3 75.9 + - + +
193M GLY 3.5 1.1 + - - -
291M ASP 3.7 8.3 - - - +
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Residues in contact with HIS 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163M ARG* 3.2 30.5 + - - -
167M MET* 5.3 1.3 - - + -
172M GLU* 5.0 1.4 + - - -
188M PHE* 2.9 45.0 + + - +
189M SER 3.1 3.8 + - - +
191M VAL* 1.3 93.8 - - + +
193M GLY* 1.3 55.7 + - - +
194M ASN 3.5 1.8 - - - -
195M LEU* 4.4 6.3 - - + -
286M SER* 3.5 9.0 - - - -
287M GLY* 3.5 29.3 + - - -
290M VAL 4.2 1.2 + - - -
291M ASP* 3.5 14.4 + - - +
292M ASN* 3.2 6.9 - - - -
293M TRP* 2.7 47.2 + - + -
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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
------------------------------------------------------------
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