Contacts of the strand formed by residues 218 - 223 (chain I) in PDB entry 1FPY
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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I GLU* 5.0 1.6 - - + -
132I PHE 3.2 15.7 - - - +
133I PHE* 3.4 41.0 - - + -
211I HIS* 3.1 8.0 + - - -
212I GLU* 2.8 55.4 + - + +
214I ALA 3.2 34.0 + - - +
216I ALA 3.6 0.2 - - - -
217I GLY* 1.3 70.5 - - - +
219I ASN* 1.3 69.5 + - - +
264I ASN* 3.5 15.4 - - - +
265I GLY 3.4 21.2 + - - +
266I SER* 3.6 6.8 - - - -
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Residues in contact with ASN 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131I GLU* 3.8 1.4 - - - +
132I PHE* 2.7 57.7 + - + +
134I LEU* 4.2 12.1 - - - +
188I ALA* 3.8 7.6 - - - +
192I ARG* 3.0 49.0 - - + +
210I HIS 3.8 3.6 - - - -
211I HIS* 3.7 13.1 + - - +
212I GLU* 3.9 5.4 - - - -
217I GLY* 2.7 30.3 - - - +
218I GLN* 1.3 75.8 - - - +
220I GLU* 1.3 61.5 + - - +
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Residues in contact with GLU 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I GLU* 3.5 30.1 - - - +
130I PRO 4.0 11.9 - - - +
131I GLU* 2.9 24.9 - - + +
132I PHE* 4.2 4.9 - - - -
192I ARG* 4.2 1.7 - - - -
209I HIS* 3.6 2.8 - - - +
210I HIS* 3.2 54.2 + - + +
212I GLU* 4.5 1.3 - - - +
219I ASN* 1.3 78.0 - - - +
221I VAL* 1.3 74.0 + - - +
222I ALA* 4.2 7.4 - - - +
238I TYR* 4.4 0.2 - - - -
469I MN 2.0 38.2 + - - -
4479I ADP 4.0 9.9 + - - -
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Residues in contact with VAL 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I PRO* 4.1 8.3 - - - +
132I PHE* 4.6 12.6 - - + -
192I ARG* 4.8 8.1 - - + -
195I MET* 4.8 14.4 - - + -
196I CYS* 3.9 25.6 - - - -
199I MET* 3.9 21.1 - - + -
206I VAL* 3.9 12.3 - - + -
208I ALA 3.6 3.1 - - - +
209I HIS* 3.9 12.3 - - + -
220I GLU* 1.3 80.3 - - - +
222I ALA* 1.3 65.1 + - - +
223I THR* 3.7 2.2 + - + -
238I TYR* 2.9 41.7 + - + +
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Residues in contact with ALA 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I PRO 5.6 2.0 - - - -
129I GLU* 5.8 2.0 - - + +
130I PRO* 5.7 0.9 - - - -
206I VAL* 3.6 6.6 - - - +
207I GLU* 2.8 32.3 + - + +
208I ALA* 2.6 30.1 + - + +
210I HIS* 5.7 5.1 - - + -
220I GLU* 4.2 10.8 - - - +
221I VAL* 1.3 71.4 - - - +
223I THR* 1.3 61.5 + - - +
4479I ADP 3.9 25.8 - - - +
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Residues in contact with THR 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I PRO 4.3 11.6 + - - +
130I PRO* 5.0 2.1 - - - +
199I MET* 4.5 1.6 - - - -
204I LEU* 4.0 22.9 - - + +
205I VAL 3.3 15.9 - - - +
206I VAL* 4.3 8.3 - - + -
207I GLU* 4.3 4.0 - - - -
221I VAL* 4.2 13.0 + - + -
222I ALA* 1.3 80.0 - - - +
224I ARG* 1.3 63.0 + - - +
231I LYS* 3.3 23.3 + - - -
235I ILE* 5.6 1.6 - - - +
238I TYR* 4.3 18.8 - - + -
4479I ADP 3.0 23.4 + - - -
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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