Contacts of the strand formed by residues 204 - 208 (chain A) 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 VAL 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ILE* 4.3 14.8 - - + -
179A TYR* 3.4 28.7 - - + +
182A MET* 3.3 18.6 - - + +
184A PHE* 4.5 14.8 - - + -
195A MET* 5.7 0.2 - - - -
198A LEU* 3.8 22.4 - - + +
199A PRO 5.0 0.7 - - - +
202A ILE* 3.3 18.7 - - + +
203A ASN* 1.3 83.6 - - - +
205A TYR* 1.3 69.8 + - - +
271A GLY* 3.3 8.8 - - - -
272A GLN* 2.9 25.6 + - - +
275A ILE* 3.6 4.8 - - - +
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Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A MET 2.8 9.2 + - - +
183A VAL* 3.1 28.5 - - + -
184A PHE* 2.7 29.8 + - - +
185A TYR* 5.2 3.4 - - - -
204A VAL* 1.3 77.0 - - - +
206A ALA* 1.3 59.8 + - - +
207A THR* 3.2 26.2 + - - -
251A LEU* 4.3 18.8 + - + -
255A TYR* 3.7 14.1 - - + +
269A GLN* 2.8 40.7 + - + +
270A TYR 3.8 7.0 - - - -
272A GLN 3.4 23.6 - - - +
273A LYS* 4.3 8.1 - - + -
275A ILE* 3.9 20.5 - - + +
276A SER* 3.9 24.6 - - - -
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PHE* 3.4 9.4 - - + -
195A MET* 3.6 43.1 - - + -
198A LEU* 4.1 5.4 - - + -
205A TYR* 1.3 79.0 - - - +
207A THR* 1.3 64.9 + - - +
208A THR 4.3 0.2 - - - -
269A GLN* 3.3 4.9 - - - +
270A TYR* 2.7 45.7 + - - +
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Residues in contact with THR 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PHE* 2.7 11.2 + - - +
185A TYR* 3.7 25.2 - - + -
186A ILE* 3.0 25.5 + - - +
205A TYR* 3.2 30.5 + - - -
206A ALA* 1.3 72.1 + - - +
208A THR* 1.3 62.0 + - - +
233A TYR* 3.0 16.9 + - + +
255A TYR* 3.8 23.2 - - + +
258A VAL* 6.5 0.2 - - + -
267A VAL* 3.9 12.1 - - + -
268A MET 3.4 15.3 - - - +
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Residues in contact with THR 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ILE* 3.6 11.4 - - + -
191A SER* 3.4 36.1 - - - +
192A GLY* 3.6 10.1 - - - -
195A MET* 3.9 27.4 - - + -
207A THR* 1.3 77.8 - - - +
209A ALA* 1.3 64.5 + - - +
210A ALA 3.7 2.3 + - - -
233A TYR* 4.1 2.7 - - - -
267A VAL* 3.3 11.1 - - - +
268A MET* 3.0 31.0 + - - +
270A TYR* 3.4 20.3 - - + -
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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