Contacts of the strand formed by residues 218 - 223 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131L GLU* 4.8 2.9 - - - -
132L PHE 3.2 16.6 - - - +
133L PHE* 3.5 29.0 - - + -
211L HIS* 2.9 12.9 + - - -
212L GLU* 2.8 46.8 + - + +
213L VAL 3.7 0.2 - - - +
214L ALA* 3.4 27.6 + - + +
217L GLY* 1.3 76.0 - - - +
219L ASN* 1.3 61.5 + - - +
264L ASN* 3.3 26.7 + - - +
265L GLY 2.7 25.1 + - - +
266L SER* 3.0 16.6 + - - +
474L TL 4.3 0.4 - - - -
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Residues in contact with ASN 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L GLU* 3.8 3.1 - - - +
132L PHE* 2.8 54.0 + - + +
134L LEU* 3.9 14.3 - - - +
155L GLU* 5.6 0.2 - - - +
188L ALA* 3.8 11.3 - - - +
192L ARG* 2.9 43.4 - - + +
210L HIS 3.8 3.6 - - - -
211L HIS* 3.5 15.5 + - - +
212L GLU* 3.9 5.1 - - - +
217L GLY* 2.9 26.6 - - - +
218L GLN* 1.3 75.3 + - - +
220L GLU* 1.3 63.4 + - - +
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Residues in contact with GLU 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L GLU* 3.6 16.7 - - - +
130L PRO 3.7 16.2 - - - +
131L GLU* 3.1 10.9 - - + +
132L PHE* 4.0 5.2 - - - -
192L ARG* 4.2 1.7 - - - -
209L HIS* 3.4 4.7 - - - +
210L HIS* 2.9 46.6 + - + +
212L GLU* 3.0 7.8 - - + +
219L ASN* 1.3 77.7 - - - +
221L VAL* 1.3 70.8 + - - +
222L ALA* 4.1 6.1 - - - +
469L MN 2.2 33.7 + - - -
1482L ADP 2.9 32.3 + - - +
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Residues in contact with VAL 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L PRO* 4.5 4.2 - - - +
132L PHE* 4.2 11.4 - - + -
192L ARG* 4.5 11.0 - - + +
195L MET* 4.6 7.4 - - + -
196L CYS* 3.7 31.2 - - - -
199L MET* 3.7 32.3 - - + -
206L VAL* 4.2 9.9 - - + -
208L ALA 3.6 5.8 - - - +
209L HIS* 4.0 4.9 - - + -
220L GLU* 1.3 81.7 - - - +
222L ALA* 1.3 61.8 + - - +
223L THR* 3.6 2.3 + - + -
238L TYR* 2.9 43.8 + - + +
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Residues in contact with ALA 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L PRO 5.9 1.8 - - - -
129L GLU* 5.9 3.4 - - + +
130L PRO* 6.2 0.2 - - - -
206L VAL* 3.6 4.0 - - - +
207L GLU* 2.7 34.7 + - + -
208L ALA* 2.7 30.8 + - + +
210L HIS* 5.7 1.3 - - - +
220L GLU* 4.1 6.1 - - - +
221L VAL* 1.3 71.3 - - - +
223L THR* 1.3 56.5 + - - +
1482L ADP 4.2 40.4 - - - +
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Residues in contact with THR 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L PRO 4.7 10.1 + - - +
130L PRO* 5.4 1.9 - - - +
199L MET* 4.2 10.3 - - - -
204L LEU* 3.9 26.1 - - + +
205L VAL 3.2 12.6 - - - +
206L VAL* 4.3 6.5 - - + -
207L GLU* 3.9 3.8 - - - -
221L VAL* 3.6 4.4 + - + -
222L ALA* 1.3 78.6 - - - +
224L ARG* 1.3 54.7 + - - +
231L LYS* 3.1 25.4 + - - -
235L ILE* 5.8 1.7 - - - +
238L TYR* 4.0 23.2 - - + -
1482L ADP 2.6 29.8 + - - -
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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