Contacts of the strand formed by residues 218 - 225 (chain C) in PDB entry 3SBW
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 GLU 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C GLU* 5.3 1.9 - - - +
133C PRO* 3.6 18.1 - - - +
134C TYR* 4.4 2.1 + - - -
211C PHE 3.2 5.5 - - - +
212C ARG* 3.6 1.2 - - - -
213C ARG* 3.1 72.3 + - + +
216C PRO 4.1 0.4 - - - +
217C GLU* 1.3 80.4 - - - +
219C ASN* 1.3 61.8 + - - +
220C HIS* 3.4 36.9 + - + +
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Residues in contact with ASN 219 (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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210C THR* 3.8 17.9 - - + +
211C PHE 3.5 2.2 - - - -
212C ARG* 3.2 38.5 + - - +
217C GLU* 3.3 30.9 + - - +
218C GLU* 1.3 74.8 - - - +
220C HIS* 1.3 68.8 + - - +
221C THR* 4.0 3.8 + - - +
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Residues in contact with HIS 220 (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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133C PRO* 4.1 3.8 - - + -
134C TYR* 2.9 35.1 + - + +
135C ASN* 3.6 29.7 - - + +
137C ILE* 3.9 7.7 - - + +
209C CYS 3.7 1.6 - - - +
210C THR* 3.5 0.7 - - - +
211C PHE* 2.9 42.6 + - + +
218C GLU* 3.4 41.4 + - + +
219C ASN* 1.3 81.6 - - - +
221C THR* 1.3 62.9 + - - +
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Residues in contact with THR 221 (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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137C ILE* 4.2 7.1 - - - +
208C TYR* 3.6 25.4 - - + -
209C CYS 3.3 7.9 - - - +
210C THR* 2.7 29.8 + - - +
219C ASN* 4.0 3.5 + - - +
220C HIS* 1.3 71.8 - - - +
222C ALA* 1.3 75.4 + - - +
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Residues in contact with ALA 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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137C ILE* 3.6 35.9 - - + +
139C GLN* 4.6 11.9 - - - +
155C CYS* 4.8 0.9 - - - -
208C TYR* 3.2 5.5 - - - -
209C CYS* 2.9 39.2 + - - -
221C THR* 1.3 80.4 - - - +
223C GLU* 1.3 62.5 + - - +
224C LEU* 4.2 1.3 - - - +
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Residues in contact with GLU 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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139C GLN* 2.9 18.4 + - - +
206C ILE* 3.6 36.4 - - + +
207C PHE 3.3 4.7 - - - +
208C TYR* 3.8 21.6 + - + -
222C ALA* 1.3 74.2 - - - +
224C LEU* 1.3 67.2 + - - +
225C VAL* 3.5 24.3 + - + +
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Residues in contact with LEU 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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139C GLN* 3.8 22.2 - - + +
140C ARG 4.1 8.3 - - - +
141C ILE* 4.1 16.6 - - + -
153C LEU* 4.0 27.1 - - + -
154C THR 3.9 20.4 - - - +
155C CYS* 3.6 24.0 - - - -
167C TRP* 4.2 9.9 - - + -
205C GLU 3.7 1.6 - - - +
206C ILE* 3.6 1.6 - - - -
207C PHE* 2.8 49.4 + - + +
209C CYS* 4.1 7.9 - - - +
222C ALA* 4.2 1.3 - - + +
223C GLU* 1.3 83.7 - - - +
225C VAL* 1.3 61.9 + - - +
226C ILE* 5.7 0.7 - - + -
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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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139C GLN* 5.1 0.2 + - - -
141C ILE* 3.4 18.2 - - - +
204C ASN* 4.1 23.1 - - + +
205C GLU 3.5 8.5 - - - +
206C ILE* 4.6 7.6 - - + -
223C GLU* 3.5 28.7 - - + +
224C LEU* 1.3 78.5 - - - +
226C ILE* 1.3 68.7 + - - +
227C PRO* 3.4 4.5 - - - +
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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