Contacts of the strand formed by residues 218 - 223 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D GLU* 4.4 2.6 - - + +
132D PHE 3.2 16.8 - - - +
133D PHE* 3.5 28.0 - - + -
211D HIS* 2.9 12.5 + - - -
212D GLU* 2.8 48.3 + - + +
213D VAL 3.7 0.2 - - - +
214D ALA* 3.4 28.5 + - + +
217D GLY* 1.3 75.1 - - - +
219D ASN* 1.3 62.7 + - - +
264D ASN* 3.3 26.1 + - - +
265D GLY 2.7 24.5 + - - +
266D SER* 3.0 16.5 + - - +
474D TL 4.3 0.4 - - - -
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Residues in contact with ASN 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D GLU* 3.8 3.3 - - - +
132D PHE* 2.8 55.0 + - + -
134D LEU* 3.9 14.1 - - - +
188D ALA* 3.8 11.5 - - - +
192D ARG* 2.9 44.0 - - + +
210D HIS 3.8 3.1 - - - -
211D HIS* 3.5 14.7 + - - +
212D GLU* 3.9 5.0 - - - +
217D GLY* 2.9 26.3 - - - +
218D GLN* 1.3 73.2 + - - +
220D GLU* 1.3 64.7 + - - +
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Residues in contact with GLU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLU* 3.6 16.6 - - - +
130D PRO 3.7 15.5 - - - +
131D GLU* 3.1 11.2 - - + +
132D PHE* 4.0 5.6 - - - -
192D ARG* 4.2 1.4 - - - -
209D HIS* 3.4 4.7 - - - +
210D HIS* 2.9 47.1 + - + +
212D GLU* 3.0 7.2 - - + +
219D ASN* 1.3 77.6 - - - +
221D VAL* 1.3 71.9 + - - +
222D ALA* 4.1 6.0 - - - +
469D MN 2.2 33.7 + - - -
1474D ADP 2.9 33.6 + - - +
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Residues in contact with VAL 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PRO* 4.5 4.0 - - - +
132D PHE* 4.6 10.8 - - + -
192D ARG* 4.5 11.7 - - + +
195D MET* 4.6 7.9 - - + -
196D CYS* 3.7 31.2 - - - -
199D MET* 3.7 32.1 - - + -
206D VAL* 4.2 9.6 - - + -
208D ALA 3.6 5.4 - - - +
209D HIS* 4.0 5.2 - - + -
220D GLU* 1.3 80.8 - - - +
222D ALA* 1.3 62.9 + - - +
223D THR* 3.6 2.2 + - + -
238D TYR* 2.9 44.7 + - + +
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Residues in contact with ALA 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLU* 5.9 4.7 - - + +
130D PRO* 6.2 0.4 - - - -
206D VAL* 3.6 4.7 - - - +
207D GLU* 2.7 34.7 + - + -
208D ALA* 2.7 29.9 + - + +
210D HIS* 5.7 1.5 - - - +
220D GLU* 4.1 7.1 - - - +
221D VAL* 1.3 69.7 - - - +
223D THR* 1.3 56.2 + - - +
1474D ADP 4.2 39.9 - - - +
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Residues in contact with THR 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D PRO 4.7 10.5 + - - +
130D PRO* 5.4 1.9 - - - +
199D MET* 4.2 10.3 - - - -
204D LEU* 3.9 25.5 - - + +
205D VAL 3.2 13.0 - - - +
206D VAL* 4.3 6.7 - - + -
207D GLU* 3.9 3.4 - - - -
221D VAL* 3.6 5.0 + - + -
222D ALA* 1.3 78.2 - - - +
224D ARG* 1.3 56.5 + - - +
231D LYS* 3.1 25.1 + - - -
235D ILE* 5.8 1.4 - - - +
238D TYR* 4.0 23.1 - - + -
1474D ADP 2.6 29.5 + - - -
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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