Contacts of the strand formed by residues 297 - 302 (chain J) in PDB entry 1XFB
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 ALA 297 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24J VAL* 3.7 37.5 - - + +
266J PRO 3.0 18.3 + - - +
267J GLY* 3.8 1.6 - - - -
268J VAL 2.8 24.4 + - - -
296J TRP* 1.3 74.6 - - - +
298J LEU* 1.3 63.3 + - - +
299J THR* 3.8 8.1 - - + -
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Residues in contact with LEU 298 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254J VAL* 4.3 5.4 - - + -
257J LEU* 3.9 13.2 - - + -
268J VAL* 3.6 18.6 - - + -
270J PHE* 4.0 10.5 - - + -
284J LEU* 3.3 4.2 - - - +
287J ILE* 3.4 25.1 - - + -
288J ASN* 2.8 35.4 + - - +
294J ARG* 3.5 40.4 - - + +
296J TRP* 3.4 33.6 + - + +
297J ALA* 1.3 78.0 - - - +
299J THR* 1.3 62.9 + - - +
339J ALA 4.2 1.3 + - - +
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Residues in contact with THR 299 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J VAL* 4.3 20.6 - - + +
25J ALA 5.0 0.7 - - - +
26J PRO* 6.2 0.2 - - + -
27J GLY 5.5 1.1 - - - +
28J LYS 3.0 29.8 + - - +
29J GLY* 3.5 2.1 - - - -
30J ILE* 5.7 0.2 - - - +
268J VAL 3.2 9.8 + - - -
269J THR* 4.2 9.2 - - - +
270J PHE* 3.1 31.6 + - - -
284J LEU* 3.8 8.8 - - - +
297J ALA* 4.3 5.8 - - + -
298J LEU* 1.3 80.9 - - - +
300J PHE* 1.3 83.5 + - - +
339J ALA* 3.8 22.4 - - + +
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Residues in contact with PHE 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J LYS 4.1 1.8 - - - -
29J GLY* 3.2 25.1 - - - -
30J ILE* 2.8 52.4 + - - +
73J CYS 3.5 14.1 - - - -
74J ILE* 4.2 6.7 - - + -
269J THR* 3.9 5.1 - - - -
270J PHE 3.6 4.9 - - - -
284J LEU* 3.7 9.9 - - + -
299J THR* 1.3 94.1 + - - +
301J SER* 1.3 58.6 + - - +
302J TYR* 3.3 39.3 - + + -
306J LEU* 3.8 16.8 - - + -
332J ALA 4.4 4.9 - - - -
335J ASN* 3.5 42.8 - - + -
336J GLY* 3.9 3.6 - - - -
339J ALA* 4.4 1.3 - - + -
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Residues in contact with SER 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ILE* 3.4 27.9 - - - +
32J ALA* 4.5 1.1 - - - +
78J ILE* 3.7 5.7 - - - +
186J ILE* 4.9 0.2 - - - +
230J LYS* 3.3 37.9 + - - +
269J THR* 3.2 33.9 + - - -
270J PHE 2.7 13.3 + - - +
271J LEU* 3.8 4.9 - - - -
272J SER 4.3 0.2 + - - -
300J PHE* 1.3 70.3 - - - +
302J TYR* 1.3 61.6 + - - +
303J GLY 4.1 0.3 + - - -
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Residues in contact with TYR 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ILE 3.3 7.3 + - - +
31J LEU* 4.2 0.5 - - - +
32J ALA* 2.9 27.0 + - - -
233J MET* 3.2 16.9 - - + +
270J PHE* 3.5 22.2 - - + -
271J LEU 4.1 1.1 - - - -
272J SER* 3.5 22.4 - - - -
280J ALA* 3.1 41.5 + - + -
284J LEU* 3.5 9.8 - - + +
300J PHE* 3.3 27.1 - + + -
301J SER* 1.3 75.7 - - - +
303J GLY* 1.3 62.0 + - - +
305J ALA* 3.4 19.7 - - + -
306J LEU* 3.7 24.2 - - + +
335J ASN* 3.5 31.2 - - - -
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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