Contacts of the strand formed by residues 223 - 230 (chain J) in PDB entry 3FFC
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 HIS 223 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176J TRP 3.4 3.3 - - - +
177J VAL* 3.4 6.2 - - - -
178J ASN* 2.9 44.6 + - - +
179J GLY 5.6 2.7 - - - -
221J ARG 4.0 0.8 + - - +
222J ASN* 1.3 71.3 - - - +
224J PHE* 1.3 64.6 + - - +
225J ARG* 3.7 25.1 - - + +
254J GLU* 3.0 48.9 + - + +
255J ALA 4.0 2.9 - - - -
256J TRP* 3.3 37.8 - + + -
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Residues in contact with PHE 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J VAL* 5.0 1.9 - - - +
159J LEU* 3.5 23.1 - - + -
175J TRP* 4.7 4.7 - - + -
176J TRP 3.7 1.6 - - - -
177J VAL* 3.9 14.6 - - + -
210J LEU* 3.7 20.0 - - + -
212J VAL* 3.8 34.3 - - + -
216J PHE* 3.7 33.0 - + - -
217J TRP* 3.4 36.8 - + - -
222J ASN* 3.9 22.9 - - + -
223J HIS* 1.3 73.6 - - - +
225J ARG* 1.3 60.3 + - - +
226J CYS 4.2 0.6 + - - -
253J ALA 4.2 0.2 - - - +
254J GLU* 3.2 2.6 - - - +
255J ALA* 2.8 46.1 + - - +
257J GLY 4.5 1.3 - - - -
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Residues in contact with ARG 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175J TRP* 3.6 5.9 - - - -
176J TRP* 2.7 81.2 + - + +
179J GLY* 6.2 0.8 - - - -
223J HIS* 3.7 22.4 + - + +
224J PHE* 1.3 73.6 - - - +
226J CYS* 1.3 66.7 + - - +
227J GLN* 2.9 32.4 + - - +
250J ILE* 4.5 2.4 - - - +
252J SER* 3.6 25.8 + - - -
253J ALA 3.5 10.8 - - - +
254J GLU* 4.1 10.1 - - + -
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Residues in contact with CYS 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J VAL* 4.1 1.7 - - - +
143J VAL* 3.6 19.9 - - + +
161J CYS* 2.0 52.0 - - + -
173J LEU* 3.3 25.8 - - - -
174J SER 3.9 1.8 - - - -
175J TRP* 4.0 12.3 - - + -
225J ARG* 1.3 73.2 - - - +
227J GLN* 1.3 59.5 + - - +
228J VAL* 4.3 0.4 - - - -
252J SER* 3.1 7.1 - - - -
253J ALA* 2.7 34.9 + - + +
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Residues in contact with GLN 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172J GLU 3.6 1.1 + - - +
173J LEU* 3.3 2.8 - - - +
174J SER* 2.8 50.8 + - - +
176J TRP* 3.6 34.7 - - + +
225J ARG* 2.9 37.5 + - - +
226J CYS* 1.3 74.7 - - - +
228J VAL* 1.3 68.2 + - - +
229J GLN* 4.4 8.1 - - - +
250J ILE* 3.6 35.7 - - + +
252J SER* 3.9 4.5 - - - -
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Residues in contact with VAL 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J PRO* 3.5 24.0 - - + -
141J VAL* 3.4 29.6 - - + -
163J ALA* 3.7 17.7 - - + -
171J VAL* 3.8 26.7 - - + -
172J GLU 3.7 5.4 - - - +
173J LEU* 3.8 17.3 - - + +
226J CYS* 5.0 1.1 - - - -
227J GLN* 1.3 77.9 - - - +
229J GLN* 1.3 63.8 + - - +
230J PHE* 3.5 1.7 + - - +
250J ILE* 3.4 4.2 - - - -
251J VAL* 2.9 37.2 + - - +
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Residues in contact with GLN 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170J HIS 3.7 0.7 - - - +
171J VAL* 3.1 6.8 - - - +
172J GLU* 2.9 49.0 + - + +
227J GLN* 4.0 9.3 - - - +
228J VAL* 1.3 71.0 - - - +
230J PHE* 1.3 78.9 + - - +
231J TYR* 3.3 37.9 + - + +
248J THR* 3.4 13.7 - - - +
249J GLN* 3.4 11.9 - - - +
250J ILE* 3.7 25.2 - - + +
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Residues in contact with PHE 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J VAL* 4.1 4.3 - - + -
137J PHE 3.2 24.0 - - - -
138J PRO* 3.9 16.6 - - + -
139J PRO* 3.4 26.9 - - + -
166J PHE* 4.4 1.3 - - + -
167J TYR 3.7 15.9 - - - -
168J PRO* 4.2 14.8 - - + -
170J HIS* 3.6 3.6 - - + -
171J VAL* 3.6 18.6 - - + -
228J VAL 3.5 1.6 + - - +
229J GLN* 1.3 81.4 - - - +
231J TYR* 1.3 69.4 + - - +
232J GLY* 3.5 25.8 - - - -
246J PRO* 3.7 13.2 - - + -
247J VAL 3.5 16.2 - - - -
248J THR* 3.1 2.9 - - - +
249J GLN* 2.8 41.4 + - + +
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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