Contacts of the strand formed by residues 267 - 272 (chain B) in PDB entry 4B92
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 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ILE* 4.0 26.0 - - + -
243B ILE* 3.5 19.1 - - + +
245B LEU* 3.9 21.8 - - + -
257B ILE* 4.1 17.9 - - + +
260B ALA* 4.1 6.3 - - + -
261B LYS* 3.1 31.0 - - + +
265B LYS* 2.7 23.9 + - + +
266B VAL* 1.3 76.5 - - - +
268B LEU* 1.3 79.7 + - - +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ILE* 5.0 4.0 - - + -
242B PRO* 5.5 2.2 - - + -
243B ILE 2.8 13.0 + - - +
244B TYR* 3.5 21.5 - - + -
245B LEU* 3.0 20.3 + - - +
261B LYS* 5.1 0.9 - - - -
266B VAL* 4.2 5.6 - - + -
267B VAL* 1.3 85.3 - - - +
269B ALA* 1.3 65.5 + - - +
320B ASN* 3.2 31.9 - - + +
384B LEU* 3.2 30.5 - - + -
470B THR* 5.6 0.4 - - + -
471B VAL* 3.3 28.5 - - + -
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B TYR* 4.5 4.0 + - - +
245B LEU* 3.5 10.3 - - + +
248B VAL* 4.5 0.4 - - + -
257B ILE* 4.2 21.1 - - + -
268B LEU* 1.3 82.0 - - - +
270B GLU* 1.3 62.6 + - - +
318B THR 3.7 20.9 - - - +
319B LEU* 3.8 14.6 - - + -
320B ASN* 2.8 36.9 + - - +
321B ILE* 3.3 2.4 + - - +
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Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B THR* 2.7 23.7 + - - -
66B SER* 3.8 10.9 - - - -
189B ARG* 2.9 34.5 + - - -
244B TYR* 2.6 39.0 + - + +
245B LEU 2.8 16.4 + - - +
246B VAL* 4.1 8.1 - - - +
247B ASN* 3.2 18.4 + - - +
248B VAL* 3.2 9.9 + - - +
269B ALA* 1.3 76.8 - - - +
271B THR* 1.3 73.0 + - - +
272B THR* 5.8 0.7 - - + +
319B LEU* 5.0 1.8 - - - -
320B ASN 5.0 0.2 - - - +
321B ILE* 3.2 14.8 - - + +
323B ALA* 4.1 4.6 - - + +
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Residues in contact with THR 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL 2.6 30.9 + - - +
270B GLU* 1.3 79.5 - - - +
272B THR* 1.3 78.1 + - - +
275B HIS* 3.3 12.1 - - - +
276B ALA* 4.2 7.6 - - + -
310B LEU* 4.3 3.8 - - + +
314B LEU* 4.0 27.6 - - + -
319B LEU* 3.9 23.1 - - + +
321B ILE 3.0 8.9 + - - +
322B VAL* 3.4 5.4 - - + -
323B ALA* 3.0 21.7 + - - -
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Residues in contact with THR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER* 6.3 0.2 - - - -
247B ASN* 3.6 34.8 - - - +
270B GLU* 5.8 1.1 - - - +
271B THR* 1.3 83.1 + - - +
273B THR* 1.3 59.6 + - - +
274B ALA* 3.7 6.8 + - - +
275B HIS* 2.5 35.6 + - + +
276B ALA* 3.0 29.8 + - - +
322B VAL* 3.9 4.0 - - - -
323B ALA* 3.1 12.8 - - + +
324B SER 4.3 7.2 - - - -
325B ASP* 3.8 17.7 - - + +
348B VAL* 6.4 1.1 - - - -
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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