Contacts of the strand formed by residues 218 - 223 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E GLU* 4.4 3.7 - - - +
132E PHE 3.2 16.2 - - - +
133E PHE* 3.5 28.6 - - + -
211E HIS* 2.9 12.7 + - - -
212E GLU* 2.8 47.0 + - + +
214E ALA* 3.4 27.6 + - + +
217E GLY* 1.3 75.9 - - - +
219E ASN* 1.3 62.4 + - - +
264E ASN* 3.3 26.6 + - - +
265E GLY 2.7 24.5 + - - +
266E SER* 3.0 16.4 + - - +
474E TL 4.3 0.4 - - - -
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Residues in contact with ASN 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E GLU* 3.8 3.6 - - - +
132E PHE* 2.8 54.3 + - + +
134E LEU* 3.9 14.4 - - - +
188E ALA* 3.8 11.6 - - - +
192E ARG* 2.9 44.7 - - + +
210E HIS 3.8 3.4 - - - -
211E HIS* 3.5 14.9 + - - +
212E GLU* 3.9 5.0 - - - +
217E GLY* 2.9 26.3 - - - +
218E GLN* 1.3 74.7 + - - +
220E GLU* 1.3 65.8 + - - +
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Residues in contact with GLU 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E GLU* 3.6 16.5 - - - +
130E PRO 3.7 17.0 - - - +
131E GLU* 3.1 10.0 - - + +
132E PHE* 4.0 4.9 - - - -
192E ARG* 4.2 1.3 - - - -
209E HIS* 3.4 4.9 - - - +
210E HIS* 2.9 46.6 + - + +
212E GLU* 3.0 7.2 - - + +
219E ASN* 1.3 77.9 - - - +
221E VAL* 1.3 72.0 + - - +
222E ALA* 4.1 5.5 - - - +
469E MN 2.2 33.2 + - - -
1475E ADP 2.9 33.7 + - - +
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Residues in contact with VAL 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E PRO* 4.5 3.8 - - - +
132E PHE* 4.2 11.8 - - + -
192E ARG* 4.5 11.7 - - + +
195E MET* 4.6 7.0 - - + -
196E CYS* 3.7 30.3 - - - -
199E MET* 3.7 32.3 - - + -
206E VAL* 4.2 8.7 - - + -
208E ALA 3.6 5.8 - - - +
209E HIS* 4.0 4.9 - - + -
220E GLU* 1.3 80.9 - - - +
222E ALA* 1.3 62.4 + - - +
223E THR* 3.6 3.2 + - + -
238E TYR* 2.9 44.9 + - + +
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Residues in contact with ALA 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E PRO 5.9 1.3 - - - -
129E GLU* 5.9 3.6 - - + +
130E PRO* 6.2 0.2 - - - -
206E VAL* 3.6 4.3 - - - +
207E GLU* 2.7 35.2 + - + -
208E ALA* 2.7 30.6 + - + +
210E HIS* 5.7 1.1 - - - +
220E GLU* 4.1 7.1 - - - +
221E VAL* 1.3 69.5 - - - +
223E THR* 1.3 56.0 + - - +
1475E ADP 4.2 39.9 - - - +
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Residues in contact with THR 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E PRO 4.7 10.8 + - - +
130E PRO* 5.4 1.9 - - - +
199E MET* 4.2 11.2 - - - -
204E LEU* 3.9 26.1 - - + +
205E VAL 3.2 12.6 - - - +
206E VAL* 4.3 6.5 - - + -
207E GLU* 3.9 3.1 - - - -
221E VAL* 3.6 4.4 + - + -
222E ALA* 1.3 78.2 - - - +
224E ARG* 1.3 56.5 + - - +
231E LYS* 3.1 23.7 + - - -
235E ILE* 5.8 1.4 - - - +
238E TYR* 4.0 23.7 - - + -
1475E 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