Contacts of the strand formed by residues 296 - 299 (chain W) in PDB entry 1XDM
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 LYS 296 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23W VAL* 3.7 34.3 - - + +
24W ALA* 3.4 29.2 + - - +
25W ASN* 4.5 1.4 - - - +
26W GLY* 4.5 10.0 - - - +
265W PRO 3.4 20.5 + - - +
266W GLY* 4.1 1.1 - - - -
267W ILE* 2.7 34.1 + - - +
295W TRP* 1.3 72.3 - - - +
297W LEU* 1.3 56.8 - - - +
298W SER* 3.6 1.8 - - - +
339W LYS* 5.1 4.9 - - - +
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Residues in contact with LEU 297 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253W VAL* 4.5 2.9 - - + -
256W LEU* 4.4 5.2 - - + -
267W ILE* 3.4 12.1 - - + -
269W PHE* 3.5 28.7 - - + -
283W LEU* 3.0 20.9 - - - +
286W ILE* 3.8 20.2 - - + -
287W ASN* 3.2 32.7 - - - +
293W LYS* 3.7 42.2 - - + -
295W TRP* 3.1 31.2 + - + +
296W LYS* 1.3 69.6 - - - +
298W SER* 1.3 60.9 + - - +
338W ALA* 4.1 4.8 + - - +
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Residues in contact with SER 298 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W VAL* 3.6 10.5 - - - -
26W GLY* 6.1 0.2 - - - -
27W LYS 2.7 28.7 + - - -
28W GLY* 2.9 12.5 - - - -
267W ILE 2.8 7.7 + - - -
268W CYS* 3.4 24.0 - - - -
269W PHE* 3.1 24.3 + - - +
283W LEU* 3.8 10.9 - - - +
296W LYS* 3.6 1.1 - - - -
297W LEU* 1.3 75.8 - - - +
299W PHE* 1.3 75.5 + - - +
338W ALA* 4.5 7.5 - - - +
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Residues in contact with PHE 299 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26W GLY 4.1 2.0 - - - -
28W GLY* 3.2 36.1 - - - -
29W ILE 2.8 32.7 + - - -
72W SER 3.7 14.4 - - - -
73W ILE* 4.1 4.9 - - + -
268W CYS* 3.2 12.3 - - - +
269W PHE 3.3 7.6 - - - -
283W LEU* 3.6 7.2 - - + -
298W SER* 1.3 89.8 + - - +
300W SER* 1.3 58.2 + - - +
301W TYR* 3.4 36.3 - + + -
305W LEU* 4.0 21.1 - - + -
331W ALA* 4.5 2.2 - - - -
334W ASN* 3.4 50.5 - - + -
335W CYS* 3.8 5.2 - - - -
338W ALA* 4.3 1.6 - - + -
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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