Contacts of the strand formed by residues 218 - 223 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131F GLU* 5.0 1.1 - - - -
132F PHE 3.2 15.9 - - - +
133F PHE* 3.4 40.4 - - + -
211F HIS* 3.1 7.7 + - - -
212F GLU* 2.8 56.0 + - + +
214F ALA 3.2 33.4 + - - +
216F ALA 3.6 0.4 - - - -
217F GLY* 1.3 71.2 - - - +
219F ASN* 1.3 69.2 + - - +
264F ASN* 3.5 15.8 - - - +
265F GLY 3.4 20.7 + - - +
266F SER* 3.6 7.0 - - - -
5905F PPQ 4.8 0.2 + - - -
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Residues in contact with ASN 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F GLU* 3.8 1.7 - - - +
132F PHE* 2.7 57.1 + - + +
134F LEU* 4.2 12.1 - - - +
188F ALA* 3.8 8.2 - - - +
192F ARG* 3.0 49.5 - - + +
210F HIS 3.8 4.0 - - - -
211F HIS* 3.7 13.1 + - - +
212F GLU* 3.9 6.1 - - - -
217F GLY* 2.7 30.3 - - - +
218F GLN* 1.3 75.3 - - - +
220F GLU* 1.3 61.7 + - - +
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Residues in contact with GLU 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F GLU* 3.5 30.5 - - - +
130F PRO 4.0 11.2 - - - +
131F GLU* 2.9 24.7 - - + +
132F PHE* 4.2 4.5 - - - -
192F ARG* 4.2 1.4 - - - -
209F HIS* 3.6 1.9 - - - +
210F HIS* 3.2 55.0 + - + +
212F GLU* 4.5 1.5 - - - +
219F ASN* 1.3 78.0 - - - +
221F VAL* 1.3 74.5 + - - +
222F ALA* 4.2 7.8 - - - +
238F TYR* 4.4 0.2 - - - -
469F MN 2.0 38.2 + - - -
4476F ADP 4.0 10.0 + - - -
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Residues in contact with VAL 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F PRO* 4.1 8.3 - - - +
132F PHE* 4.6 12.8 - - + -
192F ARG* 4.8 7.9 - - + -
195F MET* 4.8 13.9 - - + -
196F CYS* 3.9 24.2 - - - -
199F MET* 3.9 21.8 - - + -
206F VAL* 3.9 12.8 - - + -
208F ALA 3.6 3.4 - - - +
209F HIS* 3.9 12.6 - - + -
220F GLU* 1.3 79.9 - - - +
222F ALA* 1.3 65.1 - - - +
223F THR* 3.7 2.4 + - + -
238F TYR* 2.9 41.5 + - + +
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Residues in contact with ALA 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F PRO 5.6 2.7 - - - -
129F GLU* 5.8 1.6 - - + +
130F PRO* 5.7 0.9 - - - -
206F VAL* 3.6 5.5 - - - +
207F GLU* 2.8 31.2 + - + +
208F ALA* 2.6 31.2 + - + +
210F HIS* 5.7 4.9 - - + -
220F GLU* 4.2 9.9 - - - +
221F VAL* 1.3 71.2 - - - +
223F THR* 1.3 62.6 + - - +
4476F ADP 3.9 26.0 - - - +
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Residues in contact with THR 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F PRO 4.3 11.7 + - - +
130F PRO* 5.0 1.6 - - - +
199F MET* 4.5 1.3 - - - -
204F LEU* 4.0 22.5 - - + +
205F VAL 3.3 17.7 - - - +
206F VAL* 4.3 8.7 - - + -
207F GLU* 4.3 3.8 - - - -
221F VAL* 3.7 13.2 + - + -
222F ALA* 1.3 80.0 - - - +
224F ARG* 1.3 62.7 + - - +
231F LYS* 3.3 23.6 + - - -
235F ILE* 5.6 1.9 - - - +
238F TYR* 4.3 19.0 - - + -
4476F 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