Contacts of the strand formed by residues 222 - 232 (chain A) in PDB entry 5FJV
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 CYS 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A LYS* 3.8 7.2 - - - +
219A TYR 3.3 12.8 + - - +
221A CYS* 1.3 124.1 - - - +
223A ALA* 1.3 66.8 + - - +
224A GLU* 3.2 21.7 + - - +
226A TYR* 4.6 2.9 - - + +
300A EPJ 4.3 31.2 - - + -
146B HIS* 5.5 13.0 - - - +
148B VAL* 4.5 12.3 - - - -
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Residues in contact with ALA 223 (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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218A LYS* 3.1 29.6 - - - +
222A CYS* 1.3 72.6 - - - +
224A GLU* 1.3 76.8 + - + +
225A ILE* 4.6 2.6 - - - +
146B HIS* 5.8 4.6 + - + -
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Residues in contact with GLU 224 (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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181A ASP* 3.4 34.1 - - + +
218A LYS* 3.8 10.6 - - - -
219A TYR 4.3 0.2 + - - -
222A CYS* 3.2 15.1 + - - +
223A ALA* 1.3 100.1 + - + +
225A ILE* 1.3 63.1 + - - +
226A TYR* 2.4 38.7 + - - +
300A EPJ 5.2 0.3 - - - -
108B ARG* 3.4 11.8 + - - +
138B HIS* 3.8 23.2 + - + -
140B PHE* 4.7 4.7 - - - -
146B HIS* 5.4 3.8 + - - -
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Residues in contact with ILE 225 (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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181A ASP* 3.3 2.6 + - - +
182A LYS* 2.8 46.8 + - + +
183A ALA 5.8 0.2 - - - +
216A SER* 3.8 16.6 - - - +
217A LYS 3.0 14.8 - - - +
218A LYS* 4.2 16.2 - - + -
223A ALA 4.6 3.4 - - - +
224A GLU* 1.3 80.7 - - - +
226A TYR* 1.3 62.6 + - - +
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Residues in contact with TYR 226 (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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122A TYR* 4.5 4.9 - - - +
177A SER 4.5 3.8 - - - +
178A TRP 4.2 2.2 - - - -
179A THR 3.6 9.2 - - - -
180A TYR 3.4 11.0 - - - +
181A ASP* 3.2 36.6 - - + -
216A SER* 3.9 2.6 - - - -
217A LYS 2.9 22.6 + - - +
219A TYR* 3.5 31.6 + + + +
222A CYS* 4.6 5.1 - - + +
224A GLU* 2.4 54.8 + - + +
225A ILE* 1.3 73.5 - - - +
227A PRO* 1.3 71.3 - - + +
228A ASP 3.9 0.2 + - - -
300A EPJ 3.5 58.4 - + + -
108B ARG* 3.8 4.2 + - - -
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Residues in contact with PRO 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 5.5 1.9 + - - -
176A GLY* 4.2 10.0 - - - -
177A SER* 4.4 8.0 + - - +
180A TYR 4.5 3.8 - - - +
181A ASP* 3.9 3.4 - - - -
182A LYS* 3.3 26.2 - - + +
185A ILE* 3.8 14.1 - - + +
186A ASP* 3.2 30.3 - - - +
187A LEU* 4.1 13.2 - - + +
214A TYR* 3.3 17.3 - - + +
215A ASN 3.4 7.9 - - - +
216A SER* 4.4 2.8 - - - +
219A TYR* 5.1 0.2 + - - -
225A ILE 3.6 0.9 - - - +
226A TYR* 1.3 92.9 - - + +
228A ASP* 1.3 61.0 + - - +
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Residues in contact with ASP 228 (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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122A TYR* 5.2 1.8 - - + -
174A LYS* 3.8 23.5 - - - -
175A PHE 3.3 16.2 - - - +
176A GLY* 4.3 2.5 - - - -
187A LEU* 4.1 9.7 - - - +
214A TYR* 3.5 1.2 - - - -
215A ASN* 3.0 48.6 + - - +
216A SER* 4.3 0.9 + - - -
217A LYS* 5.5 2.6 - - - +
219A TYR* 3.5 17.9 + - - +
226A TYR 4.3 0.3 - - - +
227A PRO* 1.3 75.7 - - - +
229A VAL* 1.3 68.4 + - - +
230A THR* 2.9 24.3 + - - -
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Residues in contact with VAL 229 (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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62A PHE* 4.1 16.8 - - + -
175A PHE* 3.0 30.5 + - - +
187A LEU* 3.6 24.8 - - + +
189A GLN* 4.1 28.7 - - + -
213A THR 3.5 15.9 - - - +
214A TYR* 4.5 7.4 - - - -
228A ASP* 1.3 78.4 - - - +
230A THR* 1.3 60.5 + - - +
231A TYR* 3.2 42.4 - - + +
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Residues in contact with THR 230 (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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172A LYS* 4.3 18.6 - - + +
173A MET 3.4 11.7 - - - +
174A LYS* 3.3 27.0 - - + +
211A THR 3.5 1.0 - - - +
212A GLY* 3.7 1.2 - - - -
213A THR* 2.9 44.2 + - - +
215A ASN* 4.5 6.5 + - - -
228A ASP* 2.9 17.7 + - - -
229A VAL* 1.3 72.7 - - - +
231A TYR* 1.3 70.2 + - - +
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Residues in contact with TYR 231 (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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62A PHE* 4.1 14.0 + + - -
63A GLY* 3.8 8.7 - - - -
64A LEU* 3.4 50.5 + - + -
171A CYS 4.0 0.7 - - - +
172A LYS* 3.1 9.9 - - - +
173A MET* 2.7 48.7 + - + +
175A PHE* 4.2 3.4 - + - -
189A GLN* 4.6 7.0 + - - +
196A LEU* 3.7 31.9 - - + -
211A THR 3.1 11.9 - - - -
212A GLY* 3.8 9.0 - - - -
229A VAL* 3.2 35.4 - - + +
230A THR* 1.3 79.0 - - - +
232A ALA* 1.3 59.7 + - - +
233A PHE* 3.9 18.6 - + + -
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Residues in contact with ALA 232 (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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170A ASN* 4.2 20.0 - - - +
171A CYS 4.6 0.2 - - - -
172A LYS* 4.7 3.1 - - + +
209A ASN 3.3 2.0 - - - +
210A ALA* 3.1 5.5 - - - -
211A THR* 2.7 59.6 + - + +
213A THR* 5.6 1.5 - - + +
230A THR 4.2 0.2 + - - -
231A TYR* 1.3 72.3 - - - +
233A PHE* 1.3 62.6 + - - +
234A VAL* 5.1 1.3 - - + -
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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