Contacts of the strand formed by residues 155 - 161 (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 GLY 155 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151F ASN* 3.9 3.6 - - - -
153F GLY 4.0 0.2 + - - -
154F SER* 1.3 77.5 - - - +
156F TRP* 1.3 64.8 - - - -
173F THR 3.2 11.7 - - - -
175F ASN 3.6 8.5 - - - -
191F ASP* 3.5 0.2 - - - +
192F VAL* 2.8 35.7 + - - +
193F TRP* 3.2 20.3 + - - +
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Residues in contact with TRP 156 (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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104F GLN* 2.9 27.6 + - - -
107F ASN* 3.4 51.9 - - + +
108F HIS* 3.5 24.9 - + - -
111F PHE* 4.0 11.2 - - + -
151F ASN* 3.2 7.0 + - - +
155F GLY* 1.3 75.2 - - - -
157F THR* 1.3 61.4 + - - +
158F TRP* 3.2 26.7 - + + +
172F SER* 3.3 0.5 - - - -
173F THR* 2.7 39.5 + - - +
175F ASN 3.1 21.9 + - - -
177F GLY 4.1 0.4 - - - -
189F THR* 3.5 17.5 - - + +
190F ALA 3.6 4.7 - - - -
191F ASP* 3.4 50.3 - - + -
192F VAL* 4.2 0.7 - - - -
193F TRP* 3.6 3.8 - - - +
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Residues in contact with THR 157 (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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144F PHE* 3.4 37.9 - - + +
147F ALA* 3.8 26.2 - - + -
148F GLY* 3.2 23.5 + - - -
151F ASN* 3.9 4.9 + - - -
156F TRP* 1.3 75.4 - - - +
158F TRP* 1.3 63.5 + - - +
170F ILE* 4.1 5.2 - - + -
171F ASP 3.6 2.2 - - - -
172F SER* 3.6 10.0 + - - +
189F THR* 3.2 4.7 + - - -
190F ALA* 2.9 36.5 + - - -
192F VAL* 4.1 3.6 - - - +
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Residues in contact with TRP 158 (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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106F PHE* 4.3 8.7 - + - -
107F ASN* 3.2 39.9 - - + -
110F PHE* 4.1 9.4 - + - -
144F PHE* 3.9 5.1 - - - -
156F TRP* 3.2 26.3 - + + +
157F THR* 1.3 77.5 - - - +
159F LEU* 1.3 59.9 + - - +
160F CYS* 3.7 16.4 - - - -
170F ILE* 3.2 11.3 - - - +
171F ASP 2.8 43.6 + - - +
173F THR* 3.0 25.3 + - + -
177F GLY 3.9 4.9 - - - -
179F PRO* 3.3 33.4 - - + +
186F PRO* 3.7 33.7 - - + -
188F PHE 3.4 7.2 - - - -
189F THR* 3.4 27.8 - - + -
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Residues in contact with LEU 159 (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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126F LEU* 5.5 0.4 - - + -
130F ILE* 4.4 20.6 - - + -
134F PHE* 4.0 21.1 - - + -
140F PHE* 3.7 41.1 - - + -
144F PHE* 4.0 3.0 - - + -
158F TRP* 1.3 72.6 - - - +
160F CYS* 1.3 60.0 + - - +
168F LEU* 4.2 12.3 - - + -
169F LEU 3.5 13.0 - - - +
170F ILE* 4.4 0.7 - - + +
186F PRO* 3.8 1.2 - - - +
187F ILE* 2.8 50.8 + - + +
188F PHE* 3.0 29.2 + - + +
218F TRP* 5.3 3.1 - - + -
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Residues in contact with CYS 160 (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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158F TRP* 3.7 17.9 - - - -
159F LEU* 1.3 79.0 - - - +
161F VAL* 1.3 62.7 + - - +
162F ASP 4.0 0.2 + - - -
168F LEU* 3.3 9.1 - - - +
169F LEU* 2.9 38.3 + - + +
171F ASP* 4.8 3.6 - - + -
179F PRO* 3.7 30.1 - - - -
184F LEU* 4.1 22.4 - - + -
185F ARG 3.3 9.9 - - - +
186F PRO* 3.8 15.7 - - - -
187F ILE* 4.2 1.1 - - - +
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Residues in contact with VAL 161 (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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160F CYS* 1.3 74.7 - - - +
162F ASP* 1.3 72.8 + - - +
163F PRO* 3.4 12.6 - - + +
166F LYS* 4.7 12.3 - - + +
167F GLU 3.5 6.5 - - - +
168F LEU* 3.7 21.3 - - + -
184F LEU* 3.8 2.6 - - - -
185F ARG* 2.8 44.2 + - + +
187F ILE* 3.8 19.7 - - + -
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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