Contacts of the strand formed by residues 215 - 221 (chain C) in PDB entry 1P5Q
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 215 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C ARG* 2.4 33.4 + - - -
154C ILE* 3.6 21.1 - - + +
156C THR 3.6 10.5 - - - +
158C GLY* 3.8 14.4 + - - +
211C MSE 3.6 13.0 - - + +
212C GLU* 3.0 40.5 + - - +
213C LYS 2.8 5.8 + - - -
214C GLY* 1.3 72.9 - - - +
216C HIS* 1.3 71.6 + - - +
217C SER* 3.6 12.7 + - - -
247C LEU 4.0 1.0 - - - +
248C HIS* 3.8 2.8 - - - -
249C LEU* 3.2 21.6 + - + +
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Residues in contact with HIS 216 (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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154C ILE* 4.1 0.7 - - - +
155C GLN* 3.6 7.2 + - + -
156C THR* 3.0 53.2 + - + +
214C GLY 3.3 9.1 + - - -
215C GLU* 1.3 78.7 - - - +
217C SER* 1.3 62.8 + - - +
247C LEU 4.1 3.1 - - - -
248C HIS* 3.0 53.0 + + + +
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Residues in contact with SER 217 (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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152C ARG* 4.3 4.9 + - - +
153C ARG 3.7 19.2 + - - -
154C ILE* 4.0 2.0 - - - -
155C GLN* 3.9 7.2 - - - +
211C MSE 3.3 31.7 - - - +
215C GLU* 3.6 16.6 + - - -
216C HIS* 1.3 79.9 + - - +
218C ILE* 1.3 75.8 + - - +
246C GLU* 3.5 4.9 - - - +
247C LEU 2.8 29.7 + - - +
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Residues in contact with ILE 218 (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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151C ILE 4.0 0.3 - - - +
152C ARG* 3.2 3.5 - - - +
153C ARG* 2.6 44.2 + - + +
155C GLN* 3.7 30.7 - - + +
217C SER* 1.3 84.3 + - - +
219C VAL* 1.3 65.3 + - - +
220C TYR* 3.7 32.9 - - + +
244C LYS* 3.8 20.4 - - + +
245C TYR 3.2 10.1 - - - +
246C GLU* 3.6 28.3 - - + +
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Residues in contact with VAL 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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150C ILE* 3.7 9.6 - - + -
151C ILE 3.6 2.2 - - - +
152C ARG* 4.1 9.2 - - + -
204C LEU* 4.4 11.7 - - + -
207C ALA* 3.4 27.1 - - + -
211C MSE 4.1 19.1 - - + -
218C ILE* 1.3 77.3 - - - +
220C TYR* 1.3 67.6 + - - +
221C LEU* 3.6 35.2 - - + -
243C LEU 3.7 1.2 - - - +
244C LYS* 3.3 5.9 - - - +
245C TYR* 2.8 39.3 + - + +
247C LEU* 4.4 6.7 - - + +
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Residues in contact with TYR 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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149C GLY 3.4 6.8 - - - +
150C ILE* 3.4 4.0 - - - -
151C ILE* 2.9 49.2 + - + +
153C ARG* 3.4 39.2 + - + +
218C ILE* 3.7 25.0 - - + +
219C VAL* 1.3 74.7 - - - +
221C LEU* 1.3 60.8 + - - +
243C LEU 3.5 2.7 - - - +
244C LYS* 3.1 40.9 - - + +
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Residues in contact with LEU 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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149C GLY 3.7 0.4 - - - -
150C ILE* 3.5 37.0 - - + -
201C PRO* 4.3 11.9 - - + -
203C GLY* 3.5 21.5 - - - -
204C LEU* 3.8 14.8 - - + +
219C VAL* 3.6 8.3 - - + -
220C TYR* 1.3 74.7 - - - +
222C LYS* 1.3 61.4 + - - +
225C TYR* 4.1 2.7 - - + +
226C ALA* 4.1 15.7 - - + +
242C GLU* 3.3 10.3 - - - +
243C LEU* 2.7 37.6 + - + +
245C TYR* 3.5 38.1 - - + -
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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