Contacts of the strand formed by residues 218 - 223 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131K GLU* 5.0 1.3 - - + -
132K PHE 3.2 15.5 - - - +
133K PHE* 3.4 41.7 - - + -
211K HIS* 3.1 8.3 + - - -
212K GLU* 2.8 55.5 + - + +
214K ALA 3.2 32.4 + - - +
216K ALA 3.6 0.4 - - - -
217K GLY* 1.3 71.0 - - - +
219K ASN* 1.3 69.8 + - - +
264K ASN* 3.5 15.8 - - - +
265K GLY 3.4 20.9 + - - +
266K SER* 3.6 6.6 - - - -
5910K PPQ 4.8 0.2 + - - -
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Residues in contact with ASN 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131K GLU* 3.8 1.4 - - - +
132K PHE* 2.7 58.5 + - + +
134K LEU* 4.2 12.0 - - - +
188K ALA* 3.8 8.1 - - - +
192K ARG* 3.0 47.5 - - + +
210K HIS 3.8 4.3 - - - -
211K HIS* 3.7 13.7 + - - +
212K GLU* 3.9 5.4 - - - -
217K GLY* 2.7 30.8 - - - +
218K GLN* 1.3 76.5 - - - +
220K GLU* 1.3 62.3 + - - +
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Residues in contact with GLU 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129K GLU* 3.5 30.2 - - - +
130K PRO 4.0 11.4 - - - +
131K GLU* 2.9 23.9 - - + +
132K PHE* 4.2 5.2 - - - -
192K ARG* 4.2 1.0 - - - -
209K HIS* 3.6 2.6 - - - +
210K HIS* 3.2 53.9 + - + +
212K GLU* 4.5 1.8 - - - +
219K ASN* 1.3 77.8 - - - +
221K VAL* 1.3 73.9 + - - +
222K ALA* 4.2 7.6 - - - +
238K TYR* 4.4 0.2 - - - -
469K MN 2.0 37.4 + - - -
4481K ADP 4.0 10.0 + - - -
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Residues in contact with VAL 221 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K PRO* 4.1 8.3 - - - +
132K PHE* 4.6 13.0 - - + -
192K ARG* 4.8 7.6 - - + -
195K MET* 4.8 14.1 - - + -
196K CYS* 3.9 25.4 - - - -
199K MET* 3.9 21.5 - - + -
206K VAL* 3.9 12.3 - - + -
208K ALA 3.6 3.4 - - - +
209K HIS* 3.9 12.8 - - + -
220K GLU* 1.3 81.7 - - - +
222K ALA* 1.3 64.8 + - - +
223K THR* 3.7 2.8 + - + -
238K TYR* 2.9 41.3 + - + +
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Residues in contact with ALA 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K PRO 5.6 1.8 - - - -
129K GLU* 5.8 2.7 - - + +
130K PRO* 5.7 0.4 - - - -
206K VAL* 3.6 6.1 - - - +
207K GLU* 2.8 32.2 + - + +
208K ALA* 2.6 30.9 + - + +
210K HIS* 5.7 4.4 - - + -
220K GLU* 4.2 11.0 - - - +
221K VAL* 1.3 71.5 - - - +
223K THR* 1.3 61.4 + - - +
4481K ADP 3.9 26.0 - - - +
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Residues in contact with THR 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K PRO 4.3 11.7 + - - +
130K PRO* 5.0 1.7 - - - +
199K MET* 4.5 1.8 - - - -
204K LEU* 4.0 22.3 - - + +
205K VAL 3.3 15.3 - - - +
206K VAL* 4.3 8.3 - - + -
207K GLU* 4.3 3.6 - - - -
221K VAL* 4.2 11.3 + - + -
222K ALA* 1.3 80.5 - - - +
224K ARG* 1.3 63.0 + - - +
231K LYS* 3.3 23.6 + - - -
235K ILE* 5.6 1.7 - - - +
238K TYR* 4.3 20.6 - - + -
4481K ADP 3.0 24.1 + - - -
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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