Contacts of the strand formed by residues 297 - 302 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24K VAL* 3.7 38.4 - - + +
266K PRO 3.0 18.3 + - - +
267K GLY* 3.8 1.3 - - - -
268K VAL 2.8 24.3 + - - -
296K TRP* 1.3 75.2 - - - +
298K LEU* 1.3 63.1 + - - +
299K THR* 3.8 7.4 - - + -
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Residues in contact with LEU 298 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254K VAL* 4.3 5.8 - - + -
257K LEU* 3.9 13.7 - - + -
268K VAL* 3.6 17.3 - - + -
270K PHE* 4.0 11.4 - - + -
284K LEU* 3.3 4.1 - - - +
287K ILE* 3.4 25.8 - - + -
288K ASN* 2.8 35.8 + - - +
294K ARG* 3.5 39.7 - - + +
296K TRP* 3.4 34.5 + - + +
297K ALA* 1.3 77.2 - - - +
299K THR* 1.3 64.2 + - - +
339K ALA 4.2 1.5 + - - +
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Residues in contact with THR 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K VAL* 4.3 20.2 - - + +
25K ALA 5.0 0.7 - - - +
26K PRO* 6.2 0.2 - - + -
27K GLY 5.5 1.3 - - - +
28K LYS 3.0 30.2 + - - +
29K GLY* 3.5 2.1 - - - -
268K VAL 3.2 10.0 + - - -
269K THR* 4.5 9.2 - - - +
270K PHE* 3.1 31.2 + - - +
284K LEU* 3.8 9.4 - - - +
297K ALA* 3.8 6.0 - - + -
298K LEU* 1.3 81.1 - - - +
300K PHE* 1.3 83.2 + - - +
339K ALA* 3.8 22.7 - - + +
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Residues in contact with PHE 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K LYS 4.1 1.6 - - - -
29K GLY* 3.2 25.6 - - - -
30K ILE* 2.8 53.3 + - - +
73K CYS 3.5 14.1 - - - -
74K ILE* 4.2 7.2 - - + -
269K THR* 3.9 5.3 - - - -
270K PHE 3.6 4.5 - - - +
284K LEU* 3.7 10.3 - - + -
299K THR* 1.3 95.1 + - - +
301K SER* 1.3 58.2 + - - +
302K TYR* 3.3 38.8 - + + -
306K LEU* 3.8 17.0 - - + -
332K ALA 4.4 5.2 - - - -
335K ASN* 3.5 43.7 - - + -
336K GLY* 3.9 3.4 - - - -
339K ALA* 4.4 1.3 - - + -
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Residues in contact with SER 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ILE* 3.4 28.5 - - - +
32K ALA* 4.4 1.2 - - - +
78K ILE* 3.7 5.2 - - - +
186K ILE* 4.9 0.3 - - - +
230K LYS* 3.3 38.0 + - - +
269K THR* 3.2 33.9 + - - -
270K PHE 2.7 13.3 + - - +
271K LEU* 3.8 4.9 - - - -
272K SER 4.3 0.2 + - - -
300K PHE* 1.3 70.8 - - - +
302K TYR* 1.3 60.6 + - - +
303K GLY 4.1 0.5 + - - -
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Residues in contact with TYR 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ILE 3.3 7.7 + - - +
31K LEU* 4.2 0.3 - - - +
32K ALA* 2.9 27.0 + - - -
233K MET* 3.2 16.6 - - + +
270K PHE* 3.5 22.4 - - + -
271K LEU 4.1 0.7 - - - -
272K SER* 3.5 21.8 - - - -
280K ALA* 3.1 41.1 + - + -
284K LEU* 3.5 9.3 - - + +
300K PHE* 3.3 27.5 - + + -
301K SER* 1.3 75.6 - - - +
303K GLY* 1.3 61.4 - - - +
305K ALA* 3.4 20.6 - - + -
306K LEU* 3.7 23.1 - - + +
335K ASN* 3.5 31.9 - - - -
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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