Contacts of the strand formed by residues 221 - 225 (chain C) in PDB entry 4B5G
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 221 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C SER* 4.7 9.1 + - - +
8C ASN* 4.0 13.7 + - - +
35C GLN* 4.5 2.1 - - - +
148C GLY 3.3 7.2 - - - +
149C ASP* 3.9 18.0 + - - +
203C THR* 2.8 38.7 + - + +
219C ARG* 3.5 9.9 + - - +
220C ILE* 1.3 82.4 - - - +
222C TYR* 1.3 65.4 + - - +
247C HIS* 3.0 32.7 + - - -
248C ALA 4.9 4.5 - - - +
250C LEU* 3.4 23.5 - - + +
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Residues in contact with TYR 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C SER* 4.1 2.1 + - - -
146C VAL 3.5 0.8 - - - +
147C CYS* 3.3 2.4 - - - -
148C GLY 2.9 31.5 + - - -
150C TRP* 3.4 28.9 - + + +
152C ILE 2.4 31.2 + - - -
153C ALA* 3.8 0.9 - - - -
154C HIS* 3.2 22.3 + - + +
158C ASP* 5.1 0.2 + - - -
179C ILE* 4.1 18.2 - - + +
190C ASP* 3.6 28.3 - - - +
219C ARG* 3.6 25.7 + - - +
220C ILE 3.5 12.1 - - - -
221C ASP* 1.3 81.1 - - - +
223C GLN* 1.3 67.0 + - - +
224C MET* 3.5 33.2 - - + +
250C LEU* 4.1 3.4 - - - -
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Residues in contact with GLN 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ILE* 3.1 35.5 + - - +
5C ILE 4.2 0.4 - - - -
6C SER* 3.9 7.3 - - - +
145C VAL* 3.6 14.0 - - + +
146C VAL 3.3 6.1 - - - -
147C CYS* 4.0 16.8 - - + -
189C THR 3.6 1.4 - - - +
190C ASP* 5.2 1.8 + - - -
191C MET* 3.4 18.9 + - + +
192C TRP 6.1 0.4 - - - +
222C TYR* 1.3 79.3 - - - +
224C MET* 1.3 65.3 + - - +
225C VAL* 3.2 12.5 + - - +
250C LEU* 3.2 31.4 + - + +
252C VAL* 3.5 20.6 - - + +
254C TYR* 3.1 22.0 + - - +
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Residues in contact with MET 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ILE 3.6 0.3 - - - +
146C VAL* 2.9 40.4 + - + +
150C TRP* 3.5 31.9 - - + -
179C ILE* 4.2 11.9 - - + -
182C VAL* 4.6 10.5 - - + -
183C ILE* 3.8 26.0 - - + -
188C TRP* 3.3 36.3 - - + -
189C THR 3.5 2.9 - - - +
190C ASP* 3.7 24.7 - - + -
222C TYR* 3.5 32.8 - - + -
223C GLN* 1.3 70.1 - - - +
225C VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ILE 3.6 4.3 - - - +
145C VAL* 4.3 6.3 - - + +
188C TRP* 3.7 6.2 - - - -
189C THR* 2.9 32.7 + - - +
191C MET* 3.7 21.8 - - + -
223C GLN 3.2 18.2 - - - +
224C MET* 1.3 76.1 - - - +
226C THR* 1.3 75.8 + - - +
229C LEU* 3.6 25.4 - - + -
230C ALA* 3.5 17.0 - - + +
254C TYR* 3.2 25.8 - - + +
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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