Contacts of the strand formed by residues 215 - 221 (chain E) in PDB entry 6CP3
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 VAL 215 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92E LEU* 3.3 10.2 - - - +
93E GLY 2.7 33.1 + - - +
171E ILE* 4.6 6.3 - - + -
182E SER* 2.9 29.2 - - - +
184E PHE* 4.1 16.6 - - + +
201E MET* 3.7 34.1 - - + -
206E VAL* 4.0 7.2 - - + +
207E ILE* 3.7 25.4 - - + -
213E SER* 3.6 1.2 - - - -
214E LYS* 1.3 81.3 - - - +
216E ALA* 1.3 59.1 + - - +
217E LEU* 4.6 4.3 - - + -
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Residues in contact with ALA 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E THR* 3.9 22.7 - - - +
92E LEU* 4.3 9.2 - - + -
93E GLY 4.4 0.4 - - - +
94E ARG 5.3 0.2 - - - +
96E ILE* 5.8 1.3 - - + -
182E SER 2.9 6.7 + - - -
183E VAL* 3.4 10.9 - - + +
184E PHE 2.9 26.7 + - - +
215E VAL* 1.3 75.1 - - - +
217E LEU* 1.3 63.0 - - - +
218E VAL* 5.2 0.2 - - - -
239E ILE* 4.1 29.4 - - + -
243E PHE* 5.4 0.2 - - + -
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Residues in contact with LEU 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLY* 5.9 2.5 - - - -
94E ARG 3.3 12.9 + - - +
95E ILE* 3.8 24.7 - - + -
96E ILE* 3.1 22.6 + - - +
184E PHE* 3.6 37.5 - - + -
198E TYR* 3.8 22.4 - - + -
201E MET* 4.1 21.8 - - + -
207E ILE* 4.1 15.7 - - + -
215E VAL* 4.4 4.0 + - + -
216E ALA* 1.3 74.0 - - - +
218E VAL* 1.3 64.9 + - - +
219E PHE* 3.7 27.8 - - + -
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Residues in contact with VAL 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ILE* 3.3 19.7 - - + +
97E ASN 4.7 5.6 - - - -
183E VAL* 5.1 1.3 - - + -
184E PHE 2.9 10.2 + - - +
185E THR* 3.2 14.0 - - + +
186E GLY 2.9 25.1 + - - -
216E ALA 5.0 2.5 - - - +
217E LEU* 1.3 78.1 - - - +
219E PHE* 1.3 60.6 + - - +
220E GLY 3.8 0.7 + - - +
232E VAL* 3.8 26.0 - - + +
235E THR* 4.0 22.2 - - + -
236E GLY* 4.4 7.6 - - - -
239E ILE* 3.8 28.9 - - + -
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Residues in contact with PHE 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ILE* 4.8 17.3 - - + -
95E ILE* 3.8 29.5 - - + +
96E ILE 3.6 5.8 + - - -
97E ASN* 4.5 13.5 - - - +
103E ILE* 4.9 4.4 - - + +
184E PHE* 3.8 25.1 - + - -
186E GLY* 3.8 2.2 - - - -
189E GLU* 3.7 29.4 - - + -
194E GLY* 3.6 37.0 - - - -
197E LEU* 4.1 13.2 - - + -
198E TYR* 5.4 0.2 - - + -
217E LEU* 3.7 37.2 - - + -
218E VAL* 1.3 73.5 - - - +
220E GLY* 1.3 61.6 + - - +
221E GLN* 3.3 14.0 + - + +
224E GLU* 4.9 0.9 - - - +
232E VAL* 4.6 0.2 - - - -
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Residues in contact with GLY 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E VAL 5.7 2.2 - - - -
186E GLY 2.9 14.9 + - - +
188E GLY 3.0 28.1 + - - -
189E GLU* 3.4 3.8 + - - -
219E PHE* 1.3 70.9 - - - +
221E GLN* 1.3 62.9 + - - +
224E GLU* 4.0 7.4 - - - -
229E ARG* 4.5 1.7 - - - +
232E VAL* 3.6 34.9 - - - +
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Residues in contact with GLN 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ALA 5.3 0.5 - - - +
137A GLY* 3.5 23.3 - - - -
138A ILE* 3.4 34.6 - - + +
103E ILE* 4.1 12.6 - - + +
188E GLY* 4.8 0.2 - - - -
189E GLU* 4.0 8.5 - - - +
191E THR* 4.0 16.3 + - - +
219E PHE* 3.3 11.8 + - + +
220E GLY* 1.3 77.4 - - - +
222E MET* 1.3 66.4 + - - +
223E ASN* 3.1 27.7 + - - +
224E GLU* 3.7 29.4 + - - +
229E ARG* 4.0 9.7 - - - +
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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