Contacts of the strand formed by residues 182 - 187 (chain M) in PDB entry 3FKS
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 182 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92M LEU* 4.9 0.7 - - - +
171M ILE* 6.3 0.4 - - - -
175M ALA* 4.6 12.8 + - - +
178M HIS* 4.9 2.8 + - - +
180M GLY 4.7 1.6 + - - -
181M PHE* 1.3 79.6 + - - +
183M VAL* 1.3 65.6 + - - +
214M LYS 3.4 10.4 + - - -
215M VAL* 3.1 20.4 - - - +
216M ALA* 2.8 25.6 + - - +
251M VAL* 5.1 0.2 - - - -
252M LEU* 3.2 34.4 - - - +
254M PHE* 5.0 6.5 - - - -
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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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182M SER* 1.3 78.3 - - - +
184M PHE* 1.3 56.1 + - - +
185M THR* 4.1 7.2 - - - +
215M VAL* 5.0 0.2 - - - -
216M ALA* 3.6 13.5 - - + +
218M VAL* 4.9 4.3 - - + -
236M GLY* 3.5 26.7 - - - +
239M ILE* 4.4 5.8 - - + -
240M ALA* 4.0 17.9 - - + +
243M PHE* 4.0 28.7 - - + -
251M VAL* 4.5 4.7 - - + -
252M LEU 2.8 10.8 + - - +
253M LEU* 3.1 20.6 - - + +
254M PHE* 2.7 32.3 + - - -
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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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164M THR* 6.6 0.2 - - + -
167M ILE* 4.4 24.7 - - + -
168M GLN* 6.5 0.7 - - + -
171M ILE* 4.1 17.9 - - + -
182M SER 4.2 0.6 - - - -
183M VAL* 1.3 73.0 - - - +
185M THR* 1.3 78.7 + - - +
186M GLY* 4.2 3.6 - - - -
197M LEU* 3.4 36.6 - - + -
201M MET* 5.9 0.9 - - + -
215M VAL* 4.6 6.5 - - + +
216M ALA 3.0 7.5 + - - -
217M LEU* 3.6 19.9 - - + -
218M VAL* 2.8 28.9 + - - +
219M PHE* 4.0 17.5 - + - -
254M PHE* 3.4 33.4 - + + -
256M ASP* 4.6 8.5 - - + -
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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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183M VAL* 4.1 1.6 - - - +
184M PHE* 1.3 80.8 - - - +
186M GLY* 1.3 63.1 + - - +
187M VAL* 3.6 18.0 + - + +
218M VAL* 3.3 15.9 - - + +
232M VAL* 3.5 25.1 - - + +
233M ALA* 4.3 5.7 + - - +
236M GLY* 3.7 22.3 - - - -
253M LEU* 4.0 10.9 - - - +
254M PHE 2.7 15.7 + - - +
255M ILE* 4.7 9.0 - - + +
256M ASP 3.1 25.5 + - - +
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Residues in contact with GLY 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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184M PHE* 4.2 4.3 - - - -
185M THR* 1.3 71.5 - - - +
187M VAL* 1.3 61.9 + - - +
218M VAL 2.7 16.8 + - - -
219M PHE* 3.6 22.1 - - - -
220M GLY* 2.8 32.1 + - - -
221M GLN* 3.6 8.2 - - - +
232M VAL* 4.3 2.1 - - - +
256M ASP 3.4 6.7 - - - -
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Residues in contact with VAL 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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185M THR* 3.8 22.9 - - + +
186M GLY* 1.3 75.4 - - - +
188M GLY* 1.3 64.5 + - - +
189M GLU 3.3 0.7 - - - -
220M GLY 4.1 1.6 - - - -
229M ARG* 3.6 25.6 - - + +
232M VAL* 3.8 6.3 - - + -
233M ALA* 3.9 23.6 - - + -
255M ILE* 4.3 13.9 - - + -
256M ASP 2.7 9.1 + - - -
257M ASN 2.6 44.5 + - - +
258M ILE* 5.4 0.4 - - - -
260M ARG* 3.2 12.7 - - + +
261M PHE* 4.3 7.2 - - + +
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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
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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