Contacts of the strand formed by residues 218 - 223 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G GLU* 5.0 1.8 - - + -
132G PHE 3.2 15.5 - - - +
133G PHE* 3.4 41.0 - - + -
211G HIS* 3.1 8.2 + - - -
212G GLU* 2.8 54.9 + - + +
214G ALA 3.2 33.2 + - - +
216G ALA 3.6 0.2 - - - -
217G GLY* 1.3 71.2 - - - +
219G ASN* 1.3 68.6 - - - +
264G ASN* 3.5 15.0 - - - +
265G GLY 3.4 21.1 + - - +
266G SER* 3.6 6.4 - - - -
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Residues in contact with ASN 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G GLU* 3.8 1.6 - - - +
132G PHE* 2.7 58.8 + - + +
134G LEU* 4.2 12.3 - - - +
188G ALA* 3.8 8.3 - - - +
192G ARG* 3.0 48.1 - - + +
210G HIS 3.8 3.6 - - - -
211G HIS* 3.7 13.7 + - - +
212G GLU* 3.9 5.8 - - - -
217G GLY* 2.7 30.3 - - - +
218G GLN* 1.3 76.2 - - - +
220G GLU* 1.3 61.9 + - - +
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Residues in contact with GLU 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G GLU* 3.5 29.0 - - - +
130G PRO 4.0 11.7 - - - +
131G GLU* 2.9 24.3 - - + +
132G PHE* 4.2 4.9 - - - -
192G ARG* 4.2 1.2 - - - -
209G HIS* 3.6 2.6 - - - +
210G HIS* 3.2 54.0 + - + +
212G GLU* 4.5 1.8 - - - +
219G ASN* 1.3 77.6 - - - +
221G VAL* 1.3 73.2 + - - +
222G ALA* 4.2 7.8 - - - +
238G TYR* 4.4 0.2 - - - -
469G MN 2.0 37.0 + - - -
4477G ADP 4.0 10.6 + - - -
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Residues in contact with VAL 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G PRO* 4.1 8.3 - - - +
132G PHE* 4.6 12.8 - - + -
192G ARG* 4.8 7.6 - - + -
195G MET* 4.8 14.6 - - + -
196G CYS* 3.9 24.9 - - - -
199G MET* 3.9 20.6 - - + -
206G VAL* 3.9 12.6 - - + -
208G ALA 3.6 3.8 - - - +
209G HIS* 3.9 12.1 - - + -
220G GLU* 1.3 80.1 - - - +
222G ALA* 1.3 63.6 + - - +
223G THR* 3.7 3.1 + - + -
238G TYR* 2.9 42.0 + - + +
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Residues in contact with ALA 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G PRO 5.6 2.0 - - - -
129G GLU* 5.8 2.0 - - + +
130G PRO* 5.7 0.9 - - - -
206G VAL* 3.6 6.1 - - - +
207G GLU* 2.8 32.7 + - + +
208G ALA* 2.6 31.0 + - + +
210G HIS* 5.7 4.9 - - + +
220G GLU* 4.2 9.9 - - - +
221G VAL* 1.3 72.0 - - - +
223G THR* 1.3 60.9 + - - +
4477G ADP 3.9 25.8 - - - +
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Residues in contact with THR 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G PRO 4.3 12.4 + - - +
130G PRO* 5.0 2.1 - - - +
199G MET* 4.5 1.3 - - - -
204G LEU* 4.0 22.5 - - + +
205G VAL 3.3 15.9 - - - +
206G VAL* 4.3 8.7 - - + -
207G GLU* 4.3 4.0 - - - -
221G VAL* 4.2 12.4 + - + -
222G ALA* 1.3 80.3 - - - +
224G ARG* 1.3 62.0 + - - +
231G LYS* 3.3 23.8 + - - -
235G ILE* 5.6 1.6 - - - +
238G TYR* 4.3 18.7 - - + -
4477G 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