Contacts of the strand formed by residues 217 - 222 (chain B) in PDB entry 5IXC
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 THR 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B MET* 4.0 12.4 - - - +
189B LEU* 3.7 18.8 - - + -
190B LYS* 2.9 28.2 + - - +
211B TYR* 4.6 9.4 - - + -
215B LEU* 4.3 16.6 - - + +
216B GLU* 1.3 77.1 - - - +
218B GLU* 1.3 80.0 + - - +
243B PRO* 3.6 1.9 - - - +
244B LEU* 2.7 48.0 + - + +
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Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B VAL 3.7 0.9 - - - +
189B LEU* 3.2 28.4 - - - +
190B LYS 4.2 1.0 + - - -
217B THR* 1.3 93.9 + - - +
219B LEU* 1.3 65.2 + - - +
220B SER* 4.1 6.2 + - - +
241B THR* 4.2 22.5 + - - +
242B VAL 3.2 12.3 - - - +
243B PRO* 4.7 7.2 - - + +
244B LEU* 4.1 3.4 - - - +
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.3 20.4 - - + -
166B VAL* 4.7 4.5 - - + -
187B LEU* 4.5 20.4 - - + -
188B VAL 3.5 13.5 - - - +
189B LEU* 4.0 14.8 - - + -
209B PHE* 4.3 14.8 - - + -
218B GLU* 1.3 75.0 - - - +
220B SER* 1.3 64.9 + - - +
240B LEU 3.8 0.5 - - - +
241B THR* 3.1 3.5 - - - -
242B VAL* 2.7 46.6 + - + +
244B LEU* 4.1 13.7 - - + +
255B MET* 5.0 10.2 - - - +
267B LEU* 5.8 0.2 - - + -
269B LEU* 3.5 36.3 - - + -
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Residues in contact with SER 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU 3.5 0.7 - - - +
187B LEU* 3.3 5.5 - - - +
188B VAL* 2.8 51.2 + - - +
218B GLU* 4.4 7.8 + - - +
219B LEU* 1.3 76.8 - - - +
221B GLY* 1.3 59.3 + - - +
239B TYR* 3.7 25.4 - - - -
240B LEU 3.3 3.8 - - - -
241B THR* 3.2 21.7 - - - +
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Residues in contact with GLY 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLU 3.4 6.7 - - - -
187B LEU* 4.1 13.0 - - - -
219B LEU* 4.2 0.8 - - - +
220B SER* 1.3 74.3 - - - +
222B ARG* 1.3 65.0 + - - +
238B GLY 3.9 0.2 - - - +
239B TYR* 3.6 2.4 - - - -
240B LEU* 2.7 39.9 + - - +
255B MET* 5.3 6.0 - - - -
257B VAL* 4.4 13.2 - - - +
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Residues in contact with ARG 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B GLU 3.6 0.7 - - - +
185B LEU* 4.0 2.5 - - - +
186B GLU* 2.8 71.0 + - - +
221B GLY* 1.3 76.8 - - - +
223B LEU* 1.3 78.0 + - - +
237B ALA* 5.4 6.5 - - + -
238B GLY 3.4 25.6 - - - +
239B TYR* 3.4 41.7 + - + -
257B VAL* 4.1 9.1 - - - +
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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