Contacts of the strand formed by residues 218 - 223 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H GLU* 4.4 3.1 - - - +
132H PHE 3.2 16.8 - - - +
133H PHE* 3.5 27.9 - - + -
211H HIS* 2.9 12.2 + - - -
212H GLU* 2.8 47.2 + - + +
213H VAL 3.7 0.4 - - - +
214H ALA* 3.4 27.4 + - + +
216H ALA 3.8 0.2 - - - -
217H GLY* 1.3 74.7 - - - +
219H ASN* 1.3 62.1 + - - +
264H ASN* 3.3 25.7 + - - +
265H GLY 2.7 24.3 + - - +
266H SER* 3.0 16.9 + - - +
474H TL 4.3 0.4 - - - -
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Residues in contact with ASN 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H GLU* 3.8 3.5 - - - +
132H PHE* 2.8 54.9 + - + +
134H LEU* 3.9 14.0 - - - +
155H GLU* 5.6 0.2 - - - +
188H ALA* 3.8 10.6 - - - +
192H ARG* 2.9 43.6 - - + +
210H HIS 3.8 3.6 - - - -
211H HIS* 3.5 15.4 + - - +
212H GLU* 3.9 5.1 - - - +
217H GLY* 2.9 26.4 - - - +
218H GLN* 1.3 73.8 + - - +
220H GLU* 1.3 64.1 + - - +
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Residues in contact with GLU 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H GLU* 3.6 16.5 - - - +
130H PRO 3.7 16.2 - - - +
131H GLU* 3.1 10.1 - - + +
132H PHE* 4.0 5.2 - - - -
192H ARG* 4.2 1.6 - - - -
209H HIS* 3.4 5.4 - - - +
210H HIS* 2.9 46.9 + - + +
212H GLU* 3.0 8.1 - - + +
219H ASN* 1.3 79.0 - - - +
221H VAL* 1.3 70.2 + - - +
222H ALA* 4.1 6.0 - - - +
469H MN 2.2 33.6 + - - -
1478H ADP 2.9 33.1 + - - +
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Residues in contact with VAL 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H PRO* 4.5 3.8 - - - +
132H PHE* 4.2 11.8 - - + -
192H ARG* 4.5 11.7 - - + +
195H MET* 4.6 7.0 - - + -
196H CYS* 3.7 30.5 - - - -
199H MET* 3.7 32.5 - - + -
206H VAL* 4.2 9.6 - - + -
208H ALA 3.6 5.8 - - - +
209H HIS* 4.0 4.9 - - + -
220H GLU* 1.3 81.6 - - - +
222H ALA* 1.3 61.7 + - - +
223H THR* 3.6 1.9 + - + -
238H TYR* 2.9 45.4 + - + +
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Residues in contact with ALA 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H GLU* 5.9 5.4 - - + +
130H PRO* 6.2 0.2 - - - -
206H VAL* 3.6 4.5 - - - +
207H GLU* 2.7 34.1 + - + -
208H ALA* 2.7 30.4 + - + +
210H HIS* 5.7 1.3 - - - +
220H GLU* 4.1 6.5 + - + +
221H VAL* 1.3 72.1 - - - +
223H THR* 1.3 57.7 + - - +
1478H ADP 4.2 39.7 - - - +
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Residues in contact with THR 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H PRO 4.7 10.5 + - - +
130H PRO* 5.4 2.1 - - - +
199H MET* 4.2 11.2 - - - -
204H LEU* 3.9 26.2 - - + +
205H VAL 3.2 11.7 - - - +
206H VAL* 4.3 6.5 - - + -
207H GLU* 3.9 3.8 - - - -
221H VAL* 3.6 4.2 + - + -
222H ALA* 1.3 77.4 - - - +
224H ARG* 1.3 55.7 + - - +
231H LYS* 3.1 26.4 + - - -
235H ILE* 5.8 1.2 - - - +
238H TYR* 4.0 22.8 - - + -
1478H ADP 2.6 30.1 + - - -
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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