Contacts of the strand formed by residues 185 - 191 (chain F) in PDB entry 4F2N
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 ARG 185 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C GLY 5.4 1.0 + - - -
23F TYR* 3.6 71.7 - - + +
25F THR* 4.6 0.9 - - - +
160F CYS* 4.1 1.8 - - - -
161F VAL* 2.8 51.7 + - + +
163F PRO* 3.8 38.1 - - + +
166F LYS* 6.0 1.6 - - - +
180F LEU* 5.3 0.4 - - + -
183F GLY 4.3 2.4 + - - +
184F LEU* 1.3 76.0 - - - +
186F PRO* 1.3 68.9 - - - +
187F ILE* 3.5 2.7 + - + +
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Residues in contact with PRO 186 (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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23F TYR* 5.0 4.3 + - - -
25F THR* 3.5 27.7 + - + +
106F PHE* 4.6 2.5 - - + -
110F PHE* 3.6 20.7 - - + -
158F TRP* 3.7 36.3 - - + -
160F CYS* 3.8 15.2 - - - -
179F PRO* 4.7 6.5 - - + -
180F LEU* 3.7 18.6 - - + +
184F LEU 3.4 11.4 - - - +
185F ARG* 1.3 86.5 - - - +
187F ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 187 (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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23F TYR* 5.9 1.8 - - - +
110F PHE* 3.6 12.3 - - - -
114F CYS* 4.3 4.3 - - - -
126F LEU* 4.3 20.6 - - + -
159F LEU* 2.8 37.9 + - + +
160F CYS* 4.8 0.2 - - - -
161F VAL* 3.8 23.1 - - + -
168F LEU* 3.7 26.2 - - + -
185F ARG* 3.9 4.0 - - + +
186F PRO* 1.3 79.8 - - - +
188F PHE* 1.3 63.1 + - + +
220F PHE* 4.7 12.8 - - - +
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Residues in contact with PHE 188 (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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110F PHE* 3.6 8.1 - - - -
114F CYS* 3.8 22.4 - - + -
115F LEU* 5.0 3.4 - - + -
140F PHE* 5.0 2.0 - + - -
144F PHE* 3.5 37.2 - + - -
158F TRP* 3.4 7.3 - - - -
159F LEU* 3.0 43.5 + - + +
187F ILE* 1.3 79.6 - - + +
189F THR* 1.3 80.6 + - - +
212F LEU* 4.3 13.0 - - + -
213F TRP* 3.7 20.6 - + - -
216F VAL* 3.7 44.4 - - + -
218F TRP* 4.9 8.1 - + + -
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Residues in contact with THR 189 (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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107F ASN 4.2 2.2 - - - +
110F PHE* 3.8 12.6 - - + -
111F PHE* 3.4 45.3 - - + +
114F CYS* 3.8 2.8 - - - +
156F TRP* 3.5 22.8 - - + +
157F THR 3.2 12.3 + - - -
158F TRP* 3.4 27.2 - - + -
188F PHE* 1.3 99.3 - - - +
190F ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 190 (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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111F PHE* 3.8 5.2 - - - -
144F PHE* 3.6 23.9 - - + -
156F TRP* 3.6 6.3 - - - -
157F THR* 2.9 30.8 + - - -
188F PHE* 4.7 0.2 - - + -
189F THR* 1.3 73.0 + - - +
191F ASP* 1.3 63.1 + - - +
192F VAL* 3.5 3.0 + - + +
208F TYR* 4.7 0.2 - - - +
209F LEU* 3.9 14.1 - - + -
212F LEU* 3.5 25.8 - - + -
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Residues in contact with ASP 191 (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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58F HIS* 2.7 30.7 + - - -
108F HIS* 3.3 9.7 + - - -
111F PHE* 3.6 21.1 - - + -
155F GLY 3.5 0.9 - - - +
156F TRP* 3.4 30.7 - - + -
190F ALA* 1.3 68.3 - - - +
192F VAL* 1.3 58.8 + - - +
193F TRP* 3.1 37.5 + - - +
195F HIS* 3.6 3.3 + - - -
196F ALA* 3.6 17.4 - - + +
208F TYR* 2.8 29.3 + - - -
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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