Contacts of the strand formed by residues 218 - 223 (chain C) in PDB entry 1F1H
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 GLN 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C GLU* 4.8 3.6 - - + -
132C PHE 3.2 16.8 - - - +
133C PHE* 3.5 27.6 - - + -
211C HIS* 2.9 12.2 + - - -
212C GLU* 2.8 46.4 + - + +
213C VAL 3.7 0.2 - - - +
214C ALA* 3.4 27.3 + - + +
216C ALA 3.8 0.2 - - - -
217C GLY* 1.3 75.9 - - - +
219C ASN* 1.3 62.5 + - - +
264C ASN* 3.3 26.3 + - - +
265C GLY 2.7 24.7 + - - +
266C SER* 3.0 16.2 + - - +
474C TL 4.3 0.4 - - - -
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Residues in contact with ASN 219 (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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131C GLU* 3.8 3.5 - - - +
132C PHE* 2.8 53.3 + - + +
134C LEU* 3.9 14.1 - - - +
188C ALA* 3.8 11.2 - - - +
192C ARG* 2.9 44.2 - - + +
210C HIS 3.8 3.8 - - - -
211C HIS* 3.5 16.7 + - - +
212C GLU* 3.9 4.6 - - - +
217C GLY* 2.9 25.8 - - - +
218C GLN* 1.3 74.4 + - - +
220C GLU* 1.3 63.9 + - - +
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Residues in contact with GLU 220 (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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129C GLU* 3.6 16.7 - - - +
130C PRO 3.7 15.5 - - - +
131C GLU* 3.1 9.9 - - + +
132C PHE* 4.0 5.4 - - - -
192C ARG* 4.2 1.3 - - - -
209C HIS* 3.4 4.7 - - - +
210C HIS* 2.9 47.4 + - + +
212C GLU* 3.0 8.0 - - + +
219C ASN* 1.3 77.8 - - - +
221C VAL* 1.3 71.7 + - - +
222C ALA* 4.1 5.7 - - - +
469C MN 2.2 34.2 + - - -
1473C ADP 2.9 33.1 + - - +
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Residues in contact with VAL 221 (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 PRO* 4.5 4.2 - - - +
132C PHE* 4.2 12.3 - - + -
192C ARG* 4.5 11.9 - - + +
195C MET* 4.6 6.7 - - + -
196C CYS* 3.7 30.3 - - - -
199C MET* 3.7 32.3 - - + -
206C VAL* 4.2 9.0 - - + -
208C ALA 3.6 4.7 - - - +
209C HIS* 4.0 5.2 - - + -
220C GLU* 1.3 80.2 - - - +
222C ALA* 1.3 63.4 + - - +
223C THR* 3.6 2.8 + - + -
238C TYR* 2.9 44.8 + - + +
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Residues in contact with ALA 222 (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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128C PRO 5.9 1.6 - - - -
129C GLU* 5.9 3.6 - - + +
206C VAL* 3.6 4.5 - - - +
207C GLU* 2.7 35.2 + - + -
208C ALA* 2.7 30.1 + - + +
210C HIS* 5.7 1.5 - - - +
220C GLU* 4.1 6.5 - - - +
221C VAL* 1.3 71.5 - - - +
223C THR* 1.3 56.2 + - - +
1473C ADP 4.2 39.7 - - - +
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Residues in contact with THR 223 (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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128C PRO 4.7 10.7 + - - +
130C PRO* 5.4 2.3 - - - +
199C MET* 4.2 10.8 - - - -
204C LEU* 3.9 26.5 - - + +
205C VAL 3.2 12.8 - - - +
206C VAL* 4.3 6.1 - - + -
207C GLU* 3.9 3.6 - - - -
221C VAL* 3.6 4.4 + - + -
222C ALA* 1.3 77.9 - - - +
224C ARG* 1.3 55.4 + - - +
231C LYS* 3.1 25.4 + - - -
235C ILE* 5.8 1.4 - - - +
238C TYR* 4.0 22.8 - - + -
1473C ADP 2.6 29.6 + - - -
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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