Contacts of the strand formed by residues 217 - 222 (chain B) in PDB entry 4FGU
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 TYR 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B GLU* 5.9 2.5 - - + -
215B SER* 3.6 16.4 - - - -
216B SER* 1.3 94.0 + - - +
218B ALA* 1.3 61.9 + - - +
231B ASP* 3.6 5.7 - - - +
232B TRP* 2.9 29.9 + - + +
264B THR* 3.2 61.6 + - + +
265B SER* 4.4 3.9 + - - -
304B LEU* 4.2 4.9 - - + -
305B THR* 3.4 24.9 - - - +
306B PRO* 3.4 30.4 - - + +
307B SER* 4.7 1.3 - - - -
1D NAG 5.2 6.5 - - + +
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 3.8 24.5 - - - +
217B TYR* 1.3 75.3 - - - +
219B CYS* 1.3 61.2 + - - +
228B TYR* 4.3 10.5 - - + -
230B GLY 3.7 11.9 - - - +
231B ASP* 4.2 1.6 - - - +
232B TRP* 4.3 0.9 - - - -
303B ASP 3.1 15.0 - - - +
304B LEU* 3.4 7.1 - - - +
305B THR* 2.8 19.1 + - + +
307B SER* 4.6 1.7 - - - +
310B VAL* 3.8 21.8 - - + -
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Residues in contact with CYS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ALA* 1.3 74.3 - - - +
220B TYR* 1.3 95.2 + - + +
221B TYR 3.7 0.9 - - - -
228B TYR* 3.8 6.9 - - - -
229B LEU 3.6 2.8 + - - -
230B GLY 2.8 34.6 + - - +
231B ASP 2.9 40.8 - - - -
232B TRP* 3.1 26.2 - - + -
235B VAL* 3.8 0.7 - - - -
302B LEU* 3.5 11.0 - - - +
303B ASP 3.7 1.3 - - - -
304B LEU* 4.1 2.9 - - + -
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Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASN 3.9 14.8 - - - -
89B ARG* 4.6 2.2 - - + -
90B PRO* 3.4 34.5 - - + -
219B CYS* 1.3 93.1 - - + +
221B TYR* 1.3 62.4 + - - +
229B LEU* 2.9 36.6 + - + +
230B GLY* 4.9 1.8 - - - -
232B TRP* 3.9 16.5 - + - -
235B VAL* 3.0 34.2 - - + +
239B GLU* 3.1 27.0 + - - -
299B VAL* 3.7 28.4 - - + +
301B HIS* 4.3 12.8 - - - -
302B LEU* 3.0 18.2 + - + -
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Residues in contact with TYR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PRO* 4.8 1.9 - - - +
219B CYS 3.7 0.8 - - - -
220B TYR* 1.3 73.7 - - - +
222B ASP* 1.3 69.1 + - - +
223B GLU* 3.3 17.9 - - + +
226B SER* 3.7 8.1 - - - -
227B THR* 3.0 42.2 - - - -
228B TYR* 3.7 34.0 - + + -
301B HIS* 3.5 19.4 + - - +
303B ASP* 3.5 23.1 + - - +
313B THR 5.4 0.2 - - - -
314B ILE* 3.9 26.1 + - + +
317B ARG* 3.4 56.0 - - + +
318B LYS* 4.1 8.7 - - - +
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Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ILE* 3.7 12.0 - - - +
90B PRO* 5.0 9.8 - - + +
91B ASN* 5.1 4.2 + - - +
220B TYR 3.5 0.8 + - - -
221B TYR* 1.3 74.8 - - - +
223B GLU* 1.3 64.5 + - - +
224B LYS* 3.6 11.3 + - - +
225B ARG* 2.8 44.8 + - + -
226B SER* 3.0 21.5 + - - -
227B THR 3.0 19.9 + - - +
229B LEU* 3.9 19.4 - - + +
301B HIS* 5.7 2.6 - - - -
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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