Contacts of the strand formed by residues 218 - 225 (chain A) in PDB entry 3FN3
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 GLU 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ASN* 3.1 21.6 + - - +
133A PRO* 3.6 14.6 - - - +
211A PHE 3.3 6.2 - - - +
212A ARG* 3.4 1.0 - - - -
213A ARG* 2.8 55.8 + - - +
216A PRO* 4.4 3.7 - - + +
217A GLU* 1.3 77.4 - - - +
219A ASN* 1.3 64.2 + - - +
220A HIS* 3.5 32.3 + - + +
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Residues in contact with ASN 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A THR* 3.6 15.3 - - + +
211A PHE 3.5 2.7 - - - -
212A ARG* 2.9 41.3 + - - +
217A GLU* 2.6 25.9 + - - +
218A GLU* 1.3 74.4 - - - +
220A HIS* 1.3 78.9 + - - +
221A THR* 4.6 7.0 - - + -
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Residues in contact with HIS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PRO* 3.3 20.7 - - + +
134A TYR* 3.1 47.3 - - + +
135A ASN* 3.8 16.5 - - + +
137A ILE* 4.0 6.1 - - + -
211A PHE* 2.6 44.1 + - - +
218A GLU* 3.5 20.5 + - + -
219A ASN* 1.3 87.3 + - - +
221A THR* 1.3 59.3 + - - +
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Residues in contact with THR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ILE* 3.7 5.9 - - - +
208A TYR* 4.1 13.7 - - - +
209A CYS 3.1 8.3 - - - -
210A THR* 2.8 37.7 + - + +
219A ASN* 4.6 5.8 - - + -
220A HIS* 1.3 80.4 - - - +
222A ALA* 1.3 67.5 + - - +
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ILE* 3.4 34.6 - - + +
139A GLN* 4.1 15.7 - - - +
155A CYS* 4.7 1.1 - - - -
208A TYR* 3.6 6.1 - - - -
209A CYS* 3.1 32.6 + - - -
221A THR* 1.3 78.0 + - - +
223A GLU* 1.3 62.1 + - - +
224A LEU* 3.7 2.1 - - + +
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLN* 3.3 16.5 + - - +
206A ILE* 3.6 29.9 - - + +
207A PHE 3.9 1.3 - - - -
208A TYR* 3.5 29.8 + - + -
221A THR 4.3 0.4 + - - -
222A ALA* 1.3 73.2 - - - +
224A LEU* 1.3 63.0 + - - +
225A VAL* 4.1 13.7 + - - +
136B LYS* 5.3 3.1 + - - -
186B ARG* 4.9 9.3 + - - -
187B GLU* 5.7 0.5 - - - +
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLN* 4.1 20.0 - - + +
140A ARG 4.4 0.2 - - - +
141A ILE* 4.3 17.5 - - + -
153A LEU* 3.9 37.0 - - + -
154A THR 4.1 8.5 - - - +
155A CYS* 3.6 13.2 - - - -
167A TRP* 4.0 7.2 - - + -
205A GLU 3.8 0.5 - - - +
206A ILE* 3.3 6.1 - - - +
207A PHE* 2.8 48.8 + - - +
209A CYS* 3.6 35.0 - - - +
222A ALA* 3.7 8.5 - - + +
223A GLU* 1.3 75.6 - - - +
225A VAL* 1.3 62.7 + - - +
226A ILE* 4.0 0.4 + - - -
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLN* 5.2 1.8 - - - +
141A ILE* 3.5 11.8 - - - +
204A ASN* 3.9 24.7 - - - +
205A GLU 3.7 4.3 - - - +
206A ILE* 4.4 9.0 - - + -
223A GLU* 4.1 13.6 + - - +
224A LEU* 1.3 76.2 - - - +
226A ILE* 1.3 77.7 + - - +
227A PRO* 3.2 12.1 - - + +
138B ASN* 4.6 4.0 + - - -
186B ARG* 3.5 37.5 - - - +
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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