Contacts of the strand formed by residues 205 - 213 (chain A) in PDB entry 3FZL
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 PHE 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A PHE* 3.2 51.4 - + - -
199A ASP 3.2 18.8 - - - -
200A LEU* 4.0 10.5 - - + -
204A THR* 1.3 75.1 - - - +
206A ASP* 1.3 73.9 + - - +
207A VAL* 3.6 18.4 - - + -
224A GLY* 3.0 1.3 - - - -
225A ASP* 2.7 57.7 + - + +
226A THR* 4.9 0.2 - - - -
228A LEU* 3.9 28.9 - - + +
313A THR* 3.3 29.4 - - - -
316A PRO* 3.7 18.8 - - + -
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Residues in contact with ASP 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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147A PRO* 5.1 4.2 - - - +
149A TYR* 3.6 37.7 + - + -
175A GLU* 5.3 2.4 - - - +
197A ILE* 3.4 2.9 - - - +
199A ASP* 3.0 49.2 + - + +
204A THR* 4.8 12.0 + - - -
205A PHE* 1.3 89.4 + - - +
207A VAL* 1.3 64.3 + - - +
208A SER* 4.9 6.5 + - - +
223A ALA 3.4 8.7 - - - +
224A GLY* 4.0 1.1 - - - -
226A THR* 4.9 8.0 - - - +
382A TRS 5.1 5.0 + - - -
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Residues in contact with VAL 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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196A LEU* 3.9 35.2 - - + -
197A ILE 3.5 5.2 - - - +
198A PHE* 4.4 5.4 - - + -
205A PHE* 3.6 30.1 - - + -
206A ASP* 1.3 73.4 - - - +
208A SER* 1.3 71.2 + - - +
222A THR* 3.6 3.1 - - - +
223A ALA* 2.8 37.0 + - + +
224A GLY* 4.1 0.4 - - - -
316A PRO* 4.1 18.2 - - + +
317A VAL* 4.1 17.0 - - + -
320A ALA* 4.0 14.4 - - + -
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Residues in contact with SER 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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148A ALA* 4.1 13.0 + - - +
149A TYR* 6.1 0.7 - - - -
176A PRO* 3.6 38.5 - - - +
195A VAL 3.6 1.2 - - - +
196A LEU* 3.5 1.9 - - - -
197A ILE* 2.8 39.1 + - - +
206A ASP* 4.9 6.6 + - - +
207A VAL* 1.3 81.9 + - - +
209A ILE* 1.3 63.7 + - - +
210A LEU* 4.9 4.0 - - - -
221A SER 3.5 9.4 - - - -
222A THR* 5.0 1.2 + - - -
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Residues in contact with ILE 209 (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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194A ASN* 4.8 0.9 - - + -
195A VAL 3.3 9.9 - - - +
196A LEU* 3.7 24.2 - - + -
208A SER* 1.3 77.7 - - - +
210A LEU* 1.3 63.5 + - - +
219A VAL* 3.8 2.3 - - - -
220A LYS* 2.8 35.3 + - + -
221A SER* 3.1 25.0 + - - +
320A ALA* 3.6 28.2 - - + +
321A LEU* 3.7 31.2 - - + -
324A ALA* 4.2 2.9 - - + -
326A LEU* 3.8 23.8 - - + -
331A ILE* 4.0 7.9 - - + -
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Residues in contact with LEU 210 (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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176A PRO* 3.8 21.8 - - + +
177A THR* 3.7 22.2 - - - +
180A ALA* 4.5 2.2 - - + -
194A ASN* 3.5 2.1 - - - +
195A VAL* 2.7 42.5 + - + +
197A ILE* 3.6 28.0 - - + -
208A SER* 4.9 2.5 - - - -
209A ILE* 1.3 79.9 - - - +
211A THR* 1.3 64.2 + - - +
212A ILE* 4.8 0.2 - - + -
217A PHE* 3.9 20.9 - - + -
218A GLU 3.1 11.0 - - - +
219A VAL* 3.5 37.7 - - + +
220A LYS* 4.2 1.1 - - - +
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Residues in contact with THR 211 (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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192A GLU* 2.9 49.0 + - + +
193A ARG 3.5 5.2 - - - +
194A ASN* 3.2 13.6 + - - +
210A LEU* 1.3 73.8 - - - +
212A ILE* 1.3 67.2 + - - +
213A GLU* 4.9 1.3 - - + +
216A ILE 3.9 0.3 - - - +
217A PHE* 3.5 2.8 - - - -
218A GLU* 2.8 40.1 + - - +
220A LYS* 3.1 32.0 - - - +
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Residues in contact with ILE 212 (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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180A ALA* 4.2 3.6 - - + -
185A LEU* 4.1 24.5 - - + +
186A ASP* 4.1 16.4 - - + -
191A ALA 4.3 0.9 - - - +
192A GLU* 3.5 0.5 - - - -
193A ARG* 2.7 48.4 + - + +
195A VAL* 3.8 26.0 - - + -
210A LEU* 4.8 3.1 - - + -
211A THR* 1.3 75.3 - - - +
213A GLU* 1.3 60.6 + - - +
214A ASP 5.0 0.4 - - - +
215A GLY* 4.0 19.7 - - - +
216A ILE 3.4 10.5 - - - +
217A PHE* 3.0 41.7 - - + -
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Residues in contact with GLU 213 (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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190A GLY 3.7 19.6 - - - +
191A ALA* 4.7 2.9 - - - -
192A GLU* 3.8 33.9 + - + +
211A THR* 4.3 2.1 - - + +
212A ILE* 1.3 74.4 - - - +
214A ASP* 1.3 77.6 + - - +
215A GLY 3.2 0.9 - - - -
216A ILE* 3.0 34.1 + - - +
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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