Contacts of the strand formed by residues 289 - 294 (chain D) 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 ILE 289 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288D VAL* 1.3 81.5 - - - +
290D HIS* 1.3 64.9 + - - +
300D CYS* 3.1 5.7 - - - -
301D LEU* 2.7 46.6 + - + +
398D PHE* 3.3 33.4 - - + -
401D ALA* 3.7 20.9 - - + +
402D ALA* 3.5 38.4 - - + +
405D CYS* 3.8 22.7 - - + -
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Residues in contact with HIS 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D ARG* 3.9 18.2 - - + +
288D VAL* 4.3 3.1 + - + +
289D ILE* 1.3 79.7 - - - +
291D GLU* 1.3 96.1 + - - +
292D GLN* 3.8 9.0 - - + -
298D GLU* 3.0 32.1 + - + +
299D VAL 3.3 8.5 - - - -
300D CYS* 3.3 26.9 - - - -
398D PHE* 3.5 10.0 - - - +
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Residues in contact with GLU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D HIS* 1.3 92.4 + - - +
292D GLN* 1.3 63.7 + - - +
293D VAL* 3.2 33.3 + - + +
298D GLU* 3.5 5.0 - - - +
299D VAL* 2.9 31.3 + - - +
393D GLN 4.1 1.7 - - - +
394D LEU* 3.8 5.9 - - + -
395D SER* 2.8 43.3 + - - -
398D PHE* 2.9 30.5 - - + +
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Residues in contact with GLN 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D HIS* 3.8 7.5 - - + -
291D GLU* 1.3 77.3 - - - +
293D VAL* 1.3 63.5 + - - +
294D ASN* 2.8 34.0 + - - +
295D HIS* 4.5 7.6 - - - +
296D ARG 5.4 0.2 - - - -
297D TRP 3.5 5.8 + - - +
298D GLU* 3.1 41.8 + - + +
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Residues in contact with VAL 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D GLU* 3.2 27.8 + - + +
292D GLN* 1.3 71.1 - - - +
294D ASN* 1.3 74.2 + - - +
297D TRP* 3.1 8.9 + - + +
299D VAL* 4.8 4.0 - - + -
391D THR 4.8 0.2 - - - +
392D CYS* 3.5 28.3 - - - -
393D GLN 3.3 35.7 - - - +
394D LEU* 4.0 12.8 - - + -
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Residues in contact with ASN 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D GLN* 2.8 29.5 + - - -
293D VAL* 1.3 89.4 + - - +
295D HIS* 1.3 69.4 + - + +
296D ARG* 2.4 47.3 + - - +
297D TRP* 3.2 17.1 + - - +
390D SER* 5.4 3.8 - - - -
391D THR 3.3 24.4 + - - -
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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