Contacts of the strand formed by residues 288 - 294 (chain B) in PDB entry 1ZXN
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 288 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B VAL* 4.9 4.7 - - + -
272B ASP* 5.5 6.3 - - - +
275B LEU* 3.2 35.2 - - + -
287B LYS* 1.3 81.7 - - - +
289B ILE* 1.3 79.0 + - - +
290B HIS* 4.2 3.5 + - + +
300B CYS* 4.6 17.3 - - + -
301B LEU 3.6 8.7 - - - +
302B THR* 4.2 3.8 - - - +
363B PHE* 6.2 0.7 - - + -
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Residues in contact with ILE 289 (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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288B VAL* 1.3 79.7 - - - +
290B HIS* 1.3 63.5 + - - +
299B VAL 3.9 0.3 - - - +
300B CYS* 3.1 5.5 - - - -
301B LEU* 2.8 45.2 + - + +
398B PHE* 3.2 44.8 - - + +
401B ALA* 3.3 22.4 - - + +
402B ALA* 3.2 33.4 - - + -
405B CYS* 3.6 27.4 - - + -
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Residues in contact with HIS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ARG* 3.5 23.6 - - + +
288B VAL* 4.2 4.2 + - + +
289B ILE* 1.3 78.9 - - - +
291B GLU* 1.3 83.2 + - - +
292B GLN* 3.9 17.7 - - + -
298B GLU* 3.1 28.2 + - + +
299B VAL 3.4 6.5 - - - -
300B CYS* 3.4 27.1 - - - -
397B LYS* 6.1 0.3 - - - +
398B PHE* 3.6 7.8 - - - -
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Residues in contact with GLU 291 (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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290B HIS* 1.3 91.6 + - - +
292B GLN* 1.3 63.4 + - - +
293B VAL* 3.3 29.1 + - + +
299B VAL* 3.0 30.9 + - + +
393B GLN 5.2 0.2 - - - +
394B LEU* 3.4 9.7 - - - +
395B SER* 2.7 52.4 + - - +
398B PHE* 3.3 23.2 - - + +
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Residues in contact with GLN 292 (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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290B HIS* 3.9 8.3 - - + -
291B GLU* 1.3 73.3 - - - +
293B VAL* 1.3 67.5 + - - +
294B ASN* 3.4 20.3 + - - +
295B HIS* 5.9 1.1 - - - -
297B TRP 3.6 6.7 - - - +
298B GLU* 3.7 30.5 + - + +
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Residues in contact with VAL 293 (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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291B GLU* 3.9 34.1 - - + +
292B GLN* 1.3 72.9 - - - +
294B ASN* 1.3 75.7 + - - +
297B TRP* 3.0 16.3 + - + +
299B VAL* 4.4 9.4 - - + -
392B CYS* 3.8 30.1 - - - -
393B GLN 3.7 21.8 - - - +
394B LEU* 4.5 5.8 - - + -
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Residues in contact with ASN 294 (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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292B GLN* 3.3 16.3 - - - +
293B VAL* 1.3 90.5 - - - +
295B HIS* 1.3 68.8 + - + +
296B ARG* 2.8 34.4 + - - +
297B TRP* 3.0 30.3 + - - +
390B SER* 5.3 2.1 + - - -
391B THR* 2.9 29.3 + - - -
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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