Contacts of the strand formed by residues 215 - 223 (chain A) in PDB entry 1R8E
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 GLY 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASP* 3.5 5.6 - - - +
129A GLU 2.8 33.1 + - - -
213A PRO 3.7 1.8 + - - -
214A LYS* 1.3 79.8 - - - +
216A ARG* 1.3 60.8 - - - -
217A TYR* 3.5 9.0 - - - -
275A ARG* 4.0 14.4 - - - -
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Residues in contact with ARG 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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126A VAL* 3.3 39.7 + - - +
127A LEU* 3.7 4.2 - - - +
128A ASP* 3.0 29.7 + - - +
215A GLY* 1.3 70.8 - - - -
217A TYR* 1.3 59.9 + - - +
275A ARG* 3.4 9.2 - - - +
276A ILE* 2.9 53.2 + - + +
277A ALA 5.3 7.0 - - - +
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Residues in contact with TYR 217 (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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125A PHE 3.5 0.9 - - - +
126A VAL* 3.2 7.6 - - - -
127A LEU 2.9 35.4 + - - +
129A GLU* 3.8 20.4 - - + -
212A ILE* 3.4 24.3 - - + +
213A PRO* 2.5 48.3 + - - +
215A GLY 3.5 23.8 - - - -
216A ARG* 1.3 76.4 - - - +
218A ALA* 1.3 60.6 + - - +
219A CYS* 3.6 19.5 + - - -
252A TYR* 4.2 14.4 - + - -
273A LYS* 3.9 10.8 - - + -
274A ILE 3.4 11.0 - - - -
275A ARG* 3.4 38.1 - - + +
276A ILE* 4.8 0.7 - - - -
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Residues in contact with ALA 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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124A VAL* 4.6 7.2 - - + -
125A PHE 3.5 4.9 - - - -
126A VAL* 4.3 11.4 - - + -
217A TYR* 1.3 72.2 - - - +
219A CYS* 1.3 57.5 + - - +
236A LEU* 3.8 18.0 - - + +
239A TYR* 4.7 4.3 - - + -
240A ILE* 4.6 8.5 - - + -
273A LYS* 3.3 2.3 - - - -
274A ILE* 2.9 47.7 + - + +
276A ILE* 4.5 13.5 - - + +
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Residues in contact with CYS 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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114A ARG* 5.2 0.2 - - - -
118A TYR* 3.5 19.3 - - - +
123A GLU 3.7 0.3 - - - +
124A VAL* 3.2 7.0 - - - +
125A PHE* 2.6 43.2 + - + +
127A LEU* 3.3 35.2 - - + -
217A TYR* 3.7 11.9 - - - -
218A ALA* 1.3 78.2 - - - +
220A ILE* 1.3 62.9 + - - +
236A LEU* 4.4 2.4 - - - +
271A GLU* 4.5 1.1 - - - -
272A MET 3.2 9.0 - - - +
273A LYS* 3.7 26.9 - - + -
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Residues in contact with ILE 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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118A TYR* 4.3 4.5 - - - -
122A GLY* 3.6 20.6 - - - +
123A GLU 3.7 22.9 - - - +
124A VAL* 3.9 15.9 - - + +
219A CYS* 1.3 80.0 - - - +
221A ALA* 1.3 64.0 + - - +
222A TYR* 4.5 4.6 - - + -
232A ASN* 3.5 51.1 - - + +
235A LYS* 4.0 4.7 - - + -
236A LEU* 4.5 9.9 - - + -
270A VAL 4.1 0.2 - - - +
271A GLU* 3.4 2.8 - - - +
272A MET* 2.9 49.1 + - + +
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Residues in contact with ALA 221 (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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115A GLN* 4.0 15.3 - - - +
118A TYR* 3.5 38.4 - - + +
120A ALA 5.1 0.6 + - - -
121A LEU* 3.3 8.0 - - + -
122A GLY 2.8 25.3 + - - +
123A GLU 4.8 0.8 + - - -
220A ILE* 1.3 75.1 - - - +
222A TYR* 1.3 65.8 + - - +
269A ARG* 4.3 4.0 - - - +
270A VAL 3.2 11.7 - - - +
271A GLU* 4.3 4.3 - - + -
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Residues in contact with TYR 222 (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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121A LEU* 3.7 14.1 - - + -
122A GLY* 4.2 6.5 - - - +
220A ILE* 4.5 10.8 - - + -
221A ALA* 1.3 85.7 - - - +
223A ASN* 1.3 79.0 + - - +
224A PHE* 4.2 4.3 - + - -
228A HIS* 3.7 8.5 - - + +
229A TYR* 3.2 54.6 + - + -
232A ASN* 3.1 40.8 - - + +
269A ARG* 3.3 4.2 - - - +
270A VAL* 2.8 66.1 + - + +
272A MET* 4.3 9.0 - - + +
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Residues in contact with ASN 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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121A LEU* 4.1 14.4 - - - +
222A TYR* 1.3 77.8 - - - +
224A PHE* 1.3 63.4 + - - +
228A HIS* 3.0 30.9 + - + +
258A ILE* 3.5 15.4 - - - +
267A GLU* 3.8 21.3 - - + +
268A TYR 3.3 6.2 + - - +
269A ARG* 2.5 38.8 - - - +
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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