Contacts of the strand formed by residues 270 - 274 (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 GLU 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B GLN* 4.1 0.3 - - - +
266B THR* 3.0 33.3 + - - +
267B ASN* 2.7 56.5 + - + +
268B ASN 3.1 2.4 - - - +
269B ASP* 1.3 79.5 - - - +
271B PHE* 1.3 63.9 + - - +
289B LEU* 3.6 22.9 - - + +
290B VAL 3.2 8.1 - - - +
291B SER* 4.3 10.0 + - - +
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Residues in contact with PHE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 3.5 21.1 - - + -
211B ALA 5.2 6.3 - - - -
212B ARG* 6.3 0.4 - - + -
263B LEU* 3.7 18.8 - - + -
264B THR 3.3 11.0 - - - +
265B GLN* 3.1 55.0 - - + -
266B THR* 4.3 0.9 - - - -
269B ASP* 4.7 6.7 - - - -
270B GLU* 1.3 78.7 - - - +
272B VAL* 1.3 63.8 + - - +
289B LEU* 3.2 5.9 - - - +
290B VAL* 2.8 49.8 + - + +
292B LEU* 3.4 32.8 - - + -
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE 3.8 0.9 - - - +
263B LEU* 3.5 4.9 - - - +
264B THR* 2.9 42.7 + - + +
266B THR* 3.5 26.0 - - + -
271B PHE* 1.3 77.3 - - - +
273B ILE* 1.3 64.5 + - - +
274B VAL* 3.5 25.6 + - + +
288B SER 3.4 9.9 - - - +
289B LEU* 3.9 15.5 - - + -
302B MET* 3.8 21.5 - - + -
350B CYS* 4.7 12.1 - - + -
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Residues in contact with ILE 273 (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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208B VAL* 4.5 11.7 - - + -
210B ILE* 4.9 0.4 - - + -
219B LEU* 3.9 20.9 - - + -
256B ILE* 3.5 33.4 - - + -
258B VAL* 5.0 1.6 - - + -
261B ALA* 4.0 24.9 - - + -
262B ILE 3.4 4.7 - - - +
263B LEU* 3.7 24.9 - - + -
271B PHE 4.4 0.2 + - - -
272B VAL* 1.3 71.6 - - - +
274B VAL* 1.3 62.3 + - - +
275B GLY 5.0 0.2 - - - +
284B ARG* 5.0 7.4 + - - +
286B VAL 4.6 0.2 - - - +
287B CYS* 3.4 5.5 - - - +
288B SER* 2.8 45.7 + - - +
290B VAL* 4.5 15.5 - - + -
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Residues in contact with VAL 274 (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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261B ALA* 4.0 0.3 - - - -
262B ILE* 2.9 44.6 + - + +
264B THR* 5.6 1.1 - - + -
272B VAL* 3.5 23.1 - - + +
273B ILE* 1.3 76.3 - - - +
275B GLY* 1.3 66.4 + - - +
284B ARG* 5.8 0.2 - - - -
286B VAL 4.9 1.1 - - - -
287B CYS* 3.7 22.0 - - - -
307B TRP* 5.4 2.5 - - + -
327B ILE* 3.9 32.1 - - + -
329B LEU* 5.3 4.7 - - + -
348B LEU* 4.1 22.7 - - + -
350B CYS* 5.4 4.5 - - - -
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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