Contacts of the strand formed by residues 218 - 225 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B GLU* 5.5 0.5 - - - +
131B ASN* 4.6 9.6 + - - +
133B PRO* 3.5 15.1 - - - +
211B PHE 4.0 0.2 - - - +
212B ARG* 3.6 0.9 - - - -
213B ARG* 2.6 75.5 + - - +
216B PRO* 2.8 14.9 + - + +
217B GLU* 1.3 74.3 - - - +
219B ASN* 1.3 68.9 + - - +
220B HIS* 3.7 20.9 + - + -
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Residues in contact with ASN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B THR* 3.2 24.6 - - + +
211B PHE 3.5 2.0 - - - -
212B ARG* 3.2 29.2 + - - +
217B GLU* 2.9 36.8 + - - -
218B GLU* 1.3 79.0 + - - +
220B HIS* 1.3 70.2 + - - +
221B THR* 4.8 6.4 - - + +
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Residues in contact with HIS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PRO* 3.7 12.2 - - + +
134B TYR* 3.0 31.6 - - + +
135B ASN* 3.6 27.5 - - + +
137B ILE* 4.4 7.1 - - + +
209B CYS 3.9 0.7 - - - +
210B THR* 3.3 0.8 - - - -
211B PHE* 2.6 45.2 + - + +
213B ARG* 5.4 0.4 - - - -
218B GLU* 3.7 31.0 + - + +
219B ASN* 1.3 81.3 + - - +
221B THR* 1.3 60.1 + - - +
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Residues in contact with THR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ILE* 3.9 8.4 - - - +
208B TYR* 4.0 18.4 - - - +
209B CYS 3.3 5.8 - - - -
210B THR* 3.1 29.4 - - + +
219B ASN* 4.8 5.6 - - + +
220B HIS* 1.3 81.0 + - - +
222B ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ILE* 3.9 25.4 - - + +
139B GLN* 4.7 10.1 - - + +
208B TYR* 3.0 26.1 - - - +
209B CYS* 2.9 28.9 + - - -
221B THR* 1.3 78.0 + - - +
223B GLU* 1.3 62.5 + - - +
224B LEU* 3.7 1.7 - - - +
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Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ARG* 4.7 8.5 + - - -
139B GLN* 3.1 16.5 + - - +
206B ILE* 4.5 20.4 - - + +
207B PHE 3.6 7.0 - - - +
208B TYR* 4.0 17.1 - - + -
222B ALA* 1.3 75.3 - - - +
224B LEU* 1.3 65.2 + - - +
225B VAL* 4.2 10.3 + - + +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLN* 3.9 20.4 - - + +
140B ARG 4.3 6.7 - - - +
141B ILE* 3.7 13.7 - - + -
153B LEU* 4.0 31.0 - - + -
154B THR 4.1 8.7 - - - +
155B CYS* 4.0 21.8 - - - -
167B TRP* 4.2 9.6 - - + -
205B GLU 3.6 1.9 - - - +
206B ILE* 3.5 6.2 - - - +
207B PHE* 2.9 46.0 + - + +
208B TYR* 3.7 2.5 - - - +
209B CYS 3.7 14.4 - - - +
222B ALA 3.7 13.7 - - - +
223B GLU* 1.3 74.4 - - - +
225B VAL* 1.3 62.2 + - - +
226B ILE 3.9 0.6 + - - -
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLN* 4.8 2.6 - - - +
141B ILE* 3.5 10.4 - - - +
204B ASN* 4.5 13.9 - - + +
205B GLU 3.7 0.9 - - - +
206B ILE* 3.8 33.0 - - + -
223B GLU* 4.2 13.9 + - + +
224B LEU* 1.3 71.2 - - - +
226B ILE* 1.3 73.8 + - - +
227B PRO* 3.2 11.6 - - + +
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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