Contacts of the strand formed by residues 155 - 161 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C ASN* 4.1 3.6 - - - -
153C GLY 3.9 1.2 + - - -
154C SER* 1.3 77.4 - - - +
156C TRP* 1.3 63.8 + - - -
173C THR 3.3 11.7 - - - -
175C ASN 3.6 8.7 - - - -
191C ASP* 3.7 0.2 - - - +
192C VAL* 2.8 35.1 + - - +
193C TRP* 3.3 19.1 + - - +
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Residues in contact with TRP 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLN* 3.1 25.5 + - - -
107C ASN* 3.4 51.7 - - + +
108C HIS* 3.5 24.2 - + - -
111C PHE* 4.0 11.2 - - + -
151C ASN* 3.1 6.3 + - - +
155C GLY* 1.3 75.0 - - - -
157C THR* 1.3 62.9 + - - +
158C TRP* 3.2 27.6 - + + +
172C SER* 3.4 0.2 - - - -
173C THR* 2.8 39.3 + - - +
175C ASN 3.1 20.3 + - - -
177C GLY 4.3 0.7 - - - -
189C THR* 3.6 16.8 - - + +
190C ALA 3.5 6.3 - - - -
191C ASP* 3.4 50.5 - - + -
192C VAL* 4.3 0.9 - - - -
193C TRP* 3.5 4.9 - - - +
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Residues in contact with THR 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 3.3 30.0 - - + +
147C ALA* 3.9 20.0 - - + -
148C GLY* 3.4 24.9 - - - +
151C ASN* 3.4 10.2 + - - +
156C TRP* 1.3 71.4 - - - +
158C TRP* 1.3 62.9 + - - +
170C ILE* 4.0 7.2 - - + -
171C ASP 3.7 2.0 - - - +
172C SER* 3.1 22.5 + - - +
189C THR* 3.2 2.3 + - - -
190C ALA* 2.8 38.0 + - - -
192C VAL* 4.4 3.3 - - - +
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Residues in contact with TRP 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C PHE* 4.4 7.0 - + - -
107C ASN* 3.2 37.5 - - + -
110C PHE* 3.9 10.5 - + - -
144C PHE* 3.8 5.3 - - - -
156C TRP* 3.2 29.6 - + + +
157C THR* 1.3 75.3 - - - +
159C LEU* 1.3 58.3 - - - +
160C CYS* 3.7 16.4 - - - -
170C ILE* 3.2 10.2 - - - +
171C ASP* 2.8 50.1 + - - +
173C THR* 3.0 29.7 + - + +
177C GLY 3.9 3.6 - - - -
179C PRO* 3.3 32.1 - - + -
186C PRO* 3.6 32.1 - - + -
188C PHE 3.4 6.7 - - - -
189C THR* 3.3 29.2 - - + -
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Residues in contact with LEU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ILE* 4.4 17.9 - - + -
134C PHE* 3.8 28.5 - - + -
140C PHE* 3.9 32.5 - - + -
144C PHE* 4.0 2.8 - - + -
158C TRP* 1.3 74.2 - - - +
160C CYS* 1.3 60.0 + - - +
168C LEU* 4.1 13.0 - - + -
169C LEU 3.6 15.5 - - - +
170C ILE* 4.6 0.7 - - + +
186C PRO* 3.7 2.1 - - - +
187C ILE* 2.8 51.9 + - + +
188C PHE* 2.9 27.7 + - + +
218C TRP* 5.2 1.6 - - + -
221C VAL* 4.8 3.1 - - + -
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Residues in contact with CYS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C TRP* 3.7 22.7 - - - -
159C LEU* 1.3 79.0 - - - +
161C VAL* 1.3 64.5 + - - +
162C ASP 4.1 0.2 - - - -
168C LEU* 3.2 9.6 - - - +
169C LEU* 2.8 44.8 + - + +
171C ASP* 4.6 5.6 - - - -
179C PRO* 3.9 24.5 - - - -
184C LEU* 4.0 22.4 - - + -
185C ARG 3.4 6.3 - - - +
186C PRO* 4.0 9.4 - - - -
187C ILE* 5.0 0.7 - - - -
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Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C CYS* 1.3 73.2 - - - +
162C ASP* 1.3 74.7 + - - +
163C PRO* 3.4 5.9 - - + +
166C LYS* 4.4 6.5 - - - +
167C GLU 3.4 7.0 - - - +
168C LEU* 3.7 22.0 - - + -
169C LEU* 4.5 0.7 - - - -
184C LEU* 3.9 2.4 - - - -
185C ARG* 2.8 37.7 + - + +
187C ILE* 4.0 14.8 - - + -
225C TYR* 3.9 17.9 - - + -
228C ALA* 3.9 27.4 - - + +
229C THR* 3.8 20.0 - - + -
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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