Contacts of the strand formed by residues 218 - 223 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A GLU* 4.4 3.3 - - - +
132A PHE 3.2 16.4 - - - +
133A PHE* 3.5 28.8 - - + -
211A HIS* 2.9 12.9 + - - -
212A GLU* 2.8 47.1 + - + +
213A VAL 3.7 0.2 - - - +
214A ALA* 3.4 28.2 + - + +
217A GLY* 1.3 75.5 - - - +
219A ASN* 1.3 62.8 + - - +
264A ASN* 3.3 25.5 + - - +
265A GLY 2.7 24.5 + - - +
266A SER* 3.0 16.4 + - - +
474A TL 4.3 0.4 - - - -
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Residues in contact with ASN 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLU* 3.8 3.3 - - - +
132A PHE* 2.8 54.4 + - + +
134A LEU* 3.9 13.6 - - - +
155A GLU* 5.6 0.2 - - - +
188A ALA* 3.8 11.5 - - - +
192A ARG* 2.9 43.4 - - + +
210A HIS 3.8 3.8 - - - -
211A HIS* 3.5 15.4 + - - +
212A GLU* 3.9 5.0 - - - +
217A GLY* 2.9 26.5 - - - +
218A GLN* 1.3 74.7 + - - +
220A GLU* 1.3 64.4 + - - +
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLU* 3.6 16.1 - - - +
130A PRO 3.7 15.5 - - - +
131A GLU* 3.1 10.3 - - + +
132A PHE* 4.0 4.5 - - - -
192A ARG* 4.2 1.0 - - - -
209A HIS* 3.4 4.9 - - - +
210A HIS* 2.9 47.9 + - + +
212A GLU* 3.0 7.8 - - + +
219A ASN* 1.3 78.1 - - - +
221A VAL* 1.3 72.5 + - - +
222A ALA* 4.1 5.9 - - - +
469A MN 2.2 33.5 + - - -
1471A ADP 2.9 33.1 + - - +
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Residues in contact with VAL 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PRO* 4.5 4.0 - - - +
132A PHE* 4.2 11.9 - - + -
192A ARG* 4.5 11.4 - - + +
195A MET* 4.6 7.0 - - + -
196A CYS* 3.7 30.7 - - - -
199A MET* 3.7 32.3 - - + -
206A VAL* 4.2 10.3 - - + -
208A ALA 3.6 5.6 - - - +
209A HIS* 4.0 4.9 - - + -
220A GLU* 1.3 80.5 - - - +
222A ALA* 1.3 63.3 + - - +
223A THR* 3.6 2.0 + - + -
238A TYR* 2.9 44.8 + - + +
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLU* 5.9 5.4 - - + +
206A VAL* 3.6 4.3 - - - +
207A GLU* 2.7 35.2 + - + -
208A ALA* 2.7 31.9 + - + +
210A HIS* 5.7 1.1 - - - +
220A GLU* 4.1 6.1 - - - +
221A VAL* 1.3 71.4 - - - +
223A THR* 1.3 56.3 + - - +
1471A ADP 4.2 39.5 - - - +
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Residues in contact with THR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO 4.7 9.9 + - - +
130A PRO* 5.4 2.5 - - - +
199A MET* 4.2 11.7 - - - -
204A LEU* 3.9 27.0 - - + +
205A VAL 3.2 12.8 - - - +
206A VAL* 4.3 6.3 - - + -
207A GLU* 3.7 4.0 - - - +
221A VAL* 3.6 4.4 + - + -
222A ALA* 1.3 78.6 - - - +
224A ARG* 1.3 54.9 + - - +
231A LYS* 3.1 25.2 + - - -
235A ILE* 5.8 1.7 - - - +
238A TYR* 4.0 21.5 - - + -
1471A 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