Contacts of the strand formed by residues 267 - 272 (chain B) in PDB entry 5M5X
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 ASN 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B PHE 4.5 0.2 - - - +
263B SER* 4.7 0.9 - - - -
264B TRP* 3.0 30.0 + - + +
266B LYS* 1.3 94.9 + - - +
268B GLU* 1.3 62.9 + - - +
269B TYR* 3.8 30.1 + - + +
337B VAL* 5.4 4.2 - - + +
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Residues in contact with GLU 268 (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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225B ARG* 5.0 12.1 + - - +
261B ARG* 6.4 1.1 - - + -
262B PHE 3.5 12.1 - - - +
263B SER* 4.1 4.9 + - - +
266B LYS 3.6 12.3 - - - +
267B ASN* 1.3 75.0 - - - +
269B TYR* 1.3 67.8 + - - +
270B LEU* 4.2 18.2 + - + +
24S G 3.9 31.8 + - - +
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Residues in contact with TYR 269 (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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260B PHE 3.8 4.0 - - - +
261B ARG* 3.8 2.8 - - - -
262B PHE* 3.1 62.1 + + + -
264B TRP* 3.6 21.8 - + + -
267B ASN* 3.8 29.1 + - + +
268B GLU* 1.3 80.2 - - - +
270B LEU* 1.3 63.3 + - - +
271B VAL* 3.6 11.9 + - + +
334B PHE* 3.5 22.7 - + + -
337B VAL* 3.2 42.0 - - + +
338B PHE* 5.0 0.4 - + - -
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Residues in contact with LEU 270 (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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225B ARG* 5.7 1.6 - - - +
229B TYR* 4.6 4.3 - - - +
259B THR* 4.2 6.5 - - + -
261B ARG* 3.2 50.3 - - - +
268B GLU* 4.6 20.4 - - + +
269B TYR* 1.3 72.3 - - - +
271B VAL* 1.3 61.5 + - - +
272B PRO* 4.1 4.7 - - - +
333B LYS* 4.5 10.6 + - - -
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Residues in contact with VAL 271 (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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259B THR* 3.2 3.6 - - - +
260B PHE* 2.8 39.5 + - + +
262B PHE* 3.6 21.1 - - + -
269B TYR* 4.1 5.6 - - + +
270B LEU* 1.3 77.4 - - - +
272B PRO* 1.3 74.4 - - + +
275B MET* 4.0 15.5 - - - -
276B ILE* 3.6 34.1 - - + -
330B LEU* 4.3 4.5 - - + -
333B LYS* 5.5 4.0 - - - +
334B PHE* 3.5 29.4 - - + -
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Residues in contact with PRO 272 (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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257B GLN* 4.5 13.5 - - - +
258B VAL 4.6 1.1 - - - +
259B THR* 4.1 10.5 - - + -
260B PHE* 3.9 1.4 - - - -
270B LEU 4.1 4.3 - - - +
271B VAL* 1.3 96.7 - - + +
273B VAL* 1.3 64.9 + - - +
274B VAL 3.6 3.6 - - - +
275B MET* 3.7 35.0 - - + -
276B ILE* 3.7 18.5 + - - +
313B PHE* 4.6 14.4 - - + -
316B ARG* 6.1 3.4 - - - +
317B TYR* 5.4 1.8 - - + -
333B LYS* 5.0 4.9 - - - +
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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