Contacts of the strand formed by residues 296 - 301 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23Y VAL* 3.4 27.4 - - + +
24Y ALA* 2.5 29.6 + - - +
25Y ASN* 4.3 5.3 - - - +
26Y GLY* 4.6 5.5 - - - +
265Y PRO 3.4 18.6 + - - +
266Y GLY* 3.3 4.7 - - - -
267Y ILE* 2.6 34.8 + - - +
295Y TRP* 1.3 71.7 - - - +
297Y LEU* 1.3 56.5 + - - +
298Y SER* 3.7 2.0 + - - +
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Residues in contact with LEU 297 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253Y VAL* 4.9 2.2 - - + -
256Y LEU* 3.8 5.4 - - + -
267Y ILE* 3.3 35.7 - - + -
269Y PHE* 3.5 23.3 - - + -
283Y LEU* 3.0 9.8 - - + +
286Y ILE* 3.9 25.1 - - + +
287Y ASN* 3.0 35.0 + - - +
293Y LYS* 3.9 39.3 - - + -
295Y TRP* 3.2 15.7 + - + +
296Y LYS* 1.3 70.3 - - - +
298Y SER* 1.3 62.0 + - - +
338Y ALA* 4.0 5.1 + - - +
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Residues in contact with SER 298 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Y VAL* 4.0 7.0 - - - -
26Y GLY 5.8 0.2 - - - -
27Y LYS 3.0 11.5 + - - -
28Y GLY* 2.9 27.4 - - - -
267Y ILE 2.8 8.5 + - - -
268Y CYS* 3.7 24.0 - - - -
269Y PHE* 3.1 19.6 + - - +
283Y LEU* 3.3 25.1 - - - +
296Y LYS* 3.7 2.4 - - - -
297Y LEU* 1.3 73.7 - - - +
299Y PHE* 1.3 70.4 + - - +
338Y ALA* 4.6 5.3 - - - +
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Residues in contact with PHE 299 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Y GLY 3.9 12.8 - - - -
28Y GLY* 3.1 40.6 - - - -
29Y ILE 2.7 32.6 + - - -
72Y SER 3.7 10.8 - - - -
73Y ILE* 4.0 9.6 - - + -
268Y CYS* 3.9 5.2 - - - +
269Y PHE 3.5 6.1 - - - -
283Y LEU* 3.4 16.8 - - + -
298Y SER* 1.3 86.1 + - - +
300Y SER* 1.3 54.2 + - - +
301Y TYR* 3.2 35.7 - + + -
305Y LEU* 3.7 32.8 - - + -
331Y ALA 4.4 2.7 - - - -
334Y ASN* 3.9 26.0 - - + -
335Y CYS 4.4 2.7 - - - -
338Y ALA* 4.8 0.4 - - + -
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Residues in contact with SER 300 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Y ILE* 3.2 34.1 - - - +
31Y ALA* 4.5 3.5 - - - +
77Y ILE* 4.3 3.3 - - - +
185Y ILE* 4.8 3.2 - - - +
229Y LYS* 3.2 40.9 + - - +
268Y CYS* 3.4 25.3 + - - -
269Y PHE 3.0 8.0 + - - -
270Y LEU* 4.1 5.7 - - - +
299Y PHE* 1.3 73.2 - - - +
301Y TYR* 1.3 63.2 + - - +
302Y GLY 4.3 0.2 + - - -
303Y ARG* 5.2 3.3 + - - -
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Residues in contact with TYR 301 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Y ILE 3.2 5.3 + - - -
30Y LEU* 3.5 6.9 - - - +
31Y ALA* 2.7 30.7 + - - -
232Y MET* 3.5 14.8 - - + +
269Y PHE* 3.0 26.9 - - - +
270Y LEU 4.1 0.2 - - - -
271Y SER* 3.5 23.8 - - - +
279Y ALA* 2.6 36.1 + - + -
283Y LEU* 3.5 8.5 - - - +
299Y PHE* 3.2 22.0 - + + -
300Y SER* 1.3 76.4 - - - +
302Y GLY* 1.3 55.9 + - - +
303Y ARG* 5.0 0.7 - - - +
304Y ALA* 3.5 21.5 - - + -
305Y LEU* 3.6 19.0 - - + +
334Y ASN* 3.3 40.2 - - - -
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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