Contacts of the strand formed by residues 215 - 219 (chain B) in PDB entry 6CIM
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 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B VAL* 4.0 2.9 - - - +
210B ILE 4.5 0.2 - - - -
211B ALA* 3.3 3.5 - - - +
212B ARG* 2.9 35.3 + - - -
213B ASN 3.3 1.0 + - - -
214B ASP* 1.3 92.7 + - - +
216B VAL* 1.3 68.3 + - - +
217B TYR* 3.9 20.2 - - + +
235B ARG* 3.3 36.8 - - + -
236B ILE 3.3 9.2 - - - +
237B ARG* 3.7 18.2 + - - +
294B ASP 5.7 0.7 + - - -
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP* 3.8 20.4 - - + +
145B VAL* 3.7 17.5 - - + -
154B VAL* 3.8 28.0 - - + -
210B ILE 3.3 6.7 - - - +
211B ALA* 3.8 17.9 - - + -
215B THR* 1.3 79.2 - - - +
217B TYR* 1.3 63.7 + - - +
218B ILE* 4.1 9.4 + - + +
234B TYR 3.9 0.9 - - - +
235B ARG 3.8 0.2 - - - -
236B ILE* 2.9 56.6 + - + +
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Residues in contact with TYR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL 3.6 1.0 - - - +
209B SER* 3.2 7.4 - - - -
210B ILE* 2.8 56.4 + - + +
212B ARG* 5.4 6.5 - - + -
215B THR* 3.9 15.4 - - + +
216B VAL* 1.3 74.5 - - - +
218B ILE* 1.3 61.0 + - - +
219B LEU* 5.2 1.3 - - + -
233B LEU* 4.0 20.2 - - + -
234B TYR 3.2 5.8 - - - +
235B ARG* 3.6 49.6 + - + -
237B ARG* 5.2 1.2 + - - -
252B LEU* 4.7 8.5 - - + -
292B LEU* 4.4 25.1 - - + -
293B GLY 4.6 3.9 + - - -
294B ASP 5.4 0.9 + - - -
295B ASN* 4.5 3.1 - - - -
296B THR 4.2 14.0 + - - -
297B ILE* 4.0 25.7 - - + +
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B SER* 4.0 6.3 - - - +
156B PHE* 4.2 20.9 - - + -
200B LEU* 6.2 0.9 - - + -
204B LEU* 3.7 29.4 - - + -
207B HIS* 3.9 18.8 - - + +
208B VAL 3.5 0.2 - - - -
209B SER* 3.6 28.7 - - - -
216B VAL* 4.9 11.0 - - + +
217B TYR* 1.3 75.6 - - - +
219B LEU* 1.3 63.1 + - - +
232B ASN 4.0 0.2 - - - +
233B LEU* 3.3 7.6 - - - +
234B TYR* 2.8 52.6 + - + +
236B ILE* 4.9 14.1 - - + -
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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
----------------------------------------------------------
207B HIS* 3.2 2.5 - - - +
208B VAL* 2.9 44.6 + - + +
210B ILE* 3.5 29.4 - - + -
217B TYR* 5.2 2.2 - - + -
218B ILE* 1.3 73.1 - - - +
220B GLY* 1.3 68.3 + - - +
221B GLY 3.4 0.2 + - - -
232B ASN 4.2 0.4 - - - -
233B LEU* 3.5 34.8 - - + -
255B GLY* 4.5 0.2 - - - -
256B ILE* 3.8 25.8 - - + +
258B VAL* 5.4 0.2 - - - -
273B ILE* 3.9 17.5 - - + -
290B VAL* 4.7 6.1 - - + -
299B ILE* 3.8 26.2 - - + -
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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