Contacts of the strand formed by residues 212 - 220 (chain A) in PDB entry 1FR8
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 ASP 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ARG* 2.8 33.6 + - - -
171A TYR 3.3 4.7 - - - -
172A THR* 3.1 21.5 + - + +
173A PRO* 3.8 12.4 - - + +
178A SER* 4.2 12.1 + - - +
180A HIS 3.3 16.0 + - - +
181A LYS* 3.3 13.5 - - + +
182A VAL 3.0 22.0 + - - +
211A LEU* 1.3 68.9 - - - +
213A TYR* 1.3 57.1 + - - +
243A TYR* 2.5 29.8 + - - -
245A TYR* 4.7 1.4 - - - -
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Residues in contact with TYR 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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169A GLY 4.0 5.6 - - - -
170A ARG* 2.6 23.0 + - - -
171A TYR* 2.8 60.4 + + + +
182A VAL* 3.0 18.4 - - + +
184A ILE* 4.0 11.2 - - + -
203A HIS* 2.9 53.0 + + - -
206A LEU* 3.3 43.1 - - + -
207A GLN* 3.4 7.8 - - - +
211A LEU* 2.9 28.6 + - + -
212A ASP* 1.3 73.8 - - - +
214A GLY* 1.3 60.9 + - - +
215A ILE* 3.8 15.0 - - + -
245A TYR* 4.5 0.9 - - - -
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Residues in contact with GLY 214 (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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168A GLY 5.3 0.2 - - - -
169A GLY 3.3 8.7 - - - -
170A ARG* 3.7 6.7 - - - -
182A VAL 3.1 5.7 + - - -
183A ALA* 3.7 1.7 - - - -
184A ILE* 3.0 25.8 + - - +
213A TYR* 1.3 78.0 - - - +
215A ILE* 1.3 67.0 + - - +
216A TYR* 3.8 7.1 - - - -
245A TYR* 3.5 18.7 + - - -
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Residues in contact with ILE 215 (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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168A GLY 3.4 4.2 + - - +
169A GLY 3.2 17.4 + - - +
184A ILE* 3.9 13.0 - - + +
186A ILE* 4.5 12.3 - - + -
198A TRP* 3.9 36.6 - - + -
199A LEU* 4.4 3.8 - - + -
203A HIS* 3.8 20.0 - - + +
206A LEU* 4.1 3.6 - - + -
213A TYR* 3.8 18.6 - - + -
214A GLY* 1.3 79.6 - - - +
216A TYR* 1.3 72.9 + - - +
217A VAL* 4.7 2.2 - - + -
390A LEU 3.9 0.7 - - - +
391A TYR* 3.5 27.1 - - + -
392A THR* 2.9 24.1 + - - -
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Residues in contact with TYR 216 (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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168A GLY 5.9 0.2 - - - -
170A ARG* 4.9 4.3 - - + +
183A ALA* 4.2 1.8 - - + -
184A ILE 2.9 15.9 + - - +
185A ILE* 3.7 14.3 - - + -
186A ILE* 2.9 28.4 + - - +
214A GLY* 3.8 17.3 - - - -
215A ILE* 1.3 79.2 - - - +
217A VAL* 1.3 64.7 + - - +
218A ILE* 3.8 13.3 + - + +
235A GLY* 5.4 0.9 - - - -
238A GLU 5.0 0.2 - - - -
239A ALA* 3.9 20.2 - - + -
242A ASP* 3.2 32.8 + - - +
245A TYR* 2.6 48.6 + + - -
387A ARG* 4.8 1.4 + - - -
392A THR* 3.5 24.9 - - + -
394A ILE* 4.2 16.6 - - + -
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ILE* 3.7 14.8 - - + +
188A PHE* 3.2 46.0 - - + -
195A LEU* 4.2 19.7 - - + -
215A ILE* 4.7 1.1 - - + -
216A TYR* 1.3 74.0 - - - +
218A ILE* 1.3 61.5 + - - +
219A ASN 3.3 2.8 + - - -
391A TYR* 3.4 35.4 - - + -
392A THR 2.7 14.0 + - - +
393A LYS* 3.6 11.0 - - + +
394A ILE 3.0 23.4 + - - -
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Residues in contact with ILE 218 (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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185A ILE* 3.9 13.5 - - + -
186A ILE 2.9 11.2 + - - +
187A PRO* 3.8 1.0 - - - +
188A PHE* 2.8 30.3 + - - +
216A TYR* 4.2 11.7 - - + +
217A VAL* 1.3 76.1 - - - +
219A ASN* 1.3 57.6 + - - +
220A GLN 3.8 0.9 + - - -
231A LEU* 3.3 54.6 - - + +
234A VAL* 4.1 15.9 - - + -
235A GLY* 3.8 22.9 - - - -
394A ILE* 3.6 33.7 - - + +
396A VAL* 4.3 2.9 - - + -
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Residues in contact with ASN 219 (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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188A PHE* 3.2 27.6 - - + +
189A ARG* 3.9 6.8 - - - -
190A ASN 4.7 0.7 + - - -
217A VAL 3.3 4.1 + - - +
218A ILE* 1.3 70.0 - - - +
220A GLN* 1.3 68.6 + - - +
221A ALA* 3.4 1.0 + - - +
231A LEU* 4.4 2.2 - - - -
393A LYS* 3.6 33.0 - - - +
394A ILE 2.9 13.2 + - - +
395A THR* 3.1 34.6 + - - +
396A VAL* 3.0 26.9 + - - +
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Residues in contact with GLN 220 (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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188A PHE 3.0 12.9 + - - +
189A ARG* 3.2 39.7 + - - +
218A ILE 3.8 1.6 + - - -
219A ASN* 1.3 75.3 + - - +
221A ALA* 1.3 65.8 + - - +
222A GLY 3.5 7.6 + - - +
224A SER* 3.6 7.7 + - - -
225A MET 2.7 28.1 + - - -
226A PHE* 3.5 8.5 - - + -
227A ASN 3.0 22.5 + - - -
231A LEU* 3.3 26.3 - - + +
312A TRP* 4.6 1.2 - - - -
396A VAL 4.0 3.4 - - - -
398A ILE* 3.7 27.8 - - + +
399A GLY 5.3 0.8 + - - -
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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