Contacts of the strand formed by residues 185 - 191 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D TYR* 3.5 66.1 - - + +
25D THR* 4.6 1.3 - - - +
160D CYS* 4.0 1.3 - - - -
161D VAL* 2.8 42.6 + - - +
163D PRO* 3.7 31.8 - - + +
180D LEU* 6.2 0.2 - - + -
183D GLY 4.6 2.4 + - - +
184D LEU* 1.3 76.5 - - - +
186D PRO* 1.3 68.4 - - - +
187D ILE* 3.6 2.1 + - - +
227D ARG 4.1 2.6 + - - -
228D ALA* 2.9 43.7 + - + +
230D LYS* 4.5 8.7 + - - -
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Residues in contact with PRO 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D TYR* 5.1 0.2 + - - -
25D THR* 3.6 20.9 + - + +
106D PHE* 4.7 2.9 - - + -
110D PHE* 3.6 19.5 - - + -
158D TRP* 3.6 36.8 - - + -
159D LEU 3.7 6.7 - - - +
160D CYS* 3.8 9.8 - - - -
179D PRO* 4.5 7.4 - - + -
180D LEU* 3.6 16.4 - - + +
184D LEU 3.5 10.8 - - - +
185D ARG* 1.3 86.2 - - - +
187D ILE* 1.3 62.4 + - - +
224D MET* 3.8 14.9 - - - +
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Residues in contact with ILE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D PHE* 3.5 13.7 - - - -
114D CYS* 4.3 1.7 - - - -
126D LEU* 4.3 5.4 - - + -
159D LEU* 2.8 35.2 + - + +
160D CYS 4.7 0.2 - - - +
161D VAL* 3.9 10.5 - - + -
168D LEU* 3.7 26.9 - - + -
185D ARG 3.8 9.0 - - - +
186D PRO* 1.3 78.2 - - - +
188D PHE* 1.3 58.3 + - - +
220D PHE* 4.6 0.2 - - - -
221D VAL* 3.3 42.2 - - + +
224D MET* 3.8 17.3 - - + +
225D TYR* 3.7 38.4 - - + +
228D ALA* 4.3 2.5 - - + -
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Residues in contact with PHE 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D PHE* 3.6 8.6 - - - -
114D CYS* 3.7 22.9 - - + -
115D LEU* 4.9 2.7 - - + -
140D PHE* 5.1 2.9 - + - -
144D PHE* 3.5 35.7 - + - -
158D TRP* 3.5 6.8 - - - +
159D LEU* 2.9 40.6 + - + +
187D ILE* 1.3 79.0 - - - +
189D THR* 1.3 81.0 + - - +
212D LEU* 4.4 13.0 - - + -
213D TRP* 3.8 20.4 - + - -
216D VAL* 3.6 37.2 - - + -
218D TRP* 4.9 3.8 - + + -
221D VAL* 3.9 22.9 - - + -
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Residues in contact with THR 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASN 4.2 2.2 - - - +
110D PHE* 3.6 19.3 - - + -
111D PHE* 3.3 37.0 - - + +
114D CYS* 3.8 2.9 - - - +
156D TRP* 3.4 25.5 - - + +
157D THR 3.2 12.3 + - - -
158D TRP* 3.5 26.8 - - + -
188D PHE* 1.3 98.9 - - - +
190D ALA* 1.3 65.9 + - - +
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Residues in contact with ALA 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PHE* 3.7 5.8 - - - -
144D PHE* 3.6 24.2 - - + -
156D TRP* 3.5 2.4 - - - -
157D THR* 2.9 31.0 + - - +
188D PHE* 4.6 0.4 - - + -
189D THR* 1.3 77.1 + - - +
191D ASP* 1.3 63.9 + - - +
192D VAL* 3.4 3.6 + - + +
209D LEU* 3.9 13.0 - - + -
212D LEU* 3.6 25.4 - - + -
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Residues in contact with ASP 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D HIS* 2.7 30.8 + - - -
108D HIS* 3.4 9.9 + - - -
111D PHE* 3.6 25.8 - - + -
155D GLY 3.6 0.5 - - - +
156D TRP* 3.4 30.0 - - + -
190D ALA* 1.3 71.1 - - - +
192D VAL* 1.3 58.6 + - - +
193D TRP* 3.1 31.1 + - - +
195D HIS* 3.6 3.5 + - - -
196D ALA* 3.5 14.3 - - + +
208D TYR* 2.8 31.2 + - - -
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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