Contacts of the strand formed by residues 297 - 302 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H VAL* 3.7 38.8 - - + +
266H PRO 3.0 18.6 + - - +
267H GLY* 3.8 1.6 - - - -
268H VAL 2.8 23.9 + - - -
296H TRP* 1.3 74.2 - - - +
298H LEU* 1.3 63.5 + - - +
299H THR* 3.8 7.6 - - + -
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Residues in contact with LEU 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254H VAL* 4.3 5.6 - - + -
257H LEU* 3.9 13.7 - - + -
268H VAL* 3.6 17.5 - - + -
270H PHE* 4.0 10.8 - - + -
284H LEU* 3.3 4.4 - - - +
287H ILE* 3.4 24.7 - - + -
288H ASN* 2.8 35.2 + - - +
294H ARG* 3.5 40.4 - - + +
296H TRP* 3.4 33.8 + - + +
297H ALA* 1.3 77.3 - - - +
299H THR* 1.3 63.3 + - - +
339H ALA 4.2 1.9 + - - +
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Residues in contact with THR 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H VAL* 4.3 20.5 - - + +
25H ALA 5.0 0.7 - - - +
26H PRO* 6.2 0.4 - - + -
27H GLY 5.5 1.1 - - - +
28H LYS 3.0 29.7 + - - +
29H GLY* 3.5 1.9 - - - -
30H ILE* 5.7 0.2 - - - +
268H VAL 3.1 9.6 + - - -
269H THR* 4.2 9.1 - - - +
270H PHE* 3.1 31.8 + - - +
284H LEU* 3.8 8.8 - - - +
297H ALA* 3.8 6.7 - - + -
298H LEU* 1.3 80.9 - - - +
300H PHE* 1.3 83.1 + - - +
339H ALA* 3.8 22.7 - - + +
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Residues in contact with PHE 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H LYS 4.1 1.8 - - - -
29H GLY* 3.2 25.6 - - - -
30H ILE* 2.8 52.9 + - - +
73H CYS 3.5 13.9 - - - -
74H ILE* 4.2 7.2 - - + -
269H THR* 3.9 5.3 - - - -
270H PHE 3.6 5.2 - - - -
284H LEU* 3.7 9.4 - - + -
299H THR* 1.3 95.4 + - - +
301H SER* 1.3 58.3 + - - +
302H TYR* 3.3 38.6 - + + -
306H LEU* 3.8 17.3 - - + -
332H ALA 4.4 4.7 - - - -
335H ASN* 3.5 43.3 - - + -
336H GLY* 3.9 3.6 - - - -
339H ALA* 4.4 1.3 - - + -
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Residues in contact with SER 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ILE* 3.4 28.8 - - - +
32H ALA* 4.5 1.5 - - - +
78H ILE* 3.7 5.5 - - - +
186H ILE* 4.9 0.2 - - - +
230H LYS* 3.3 37.7 + - - +
269H THR* 3.2 33.5 + - - -
270H PHE 2.7 14.1 + - - +
271H LEU* 3.8 4.5 - - - -
272H SER 4.3 0.2 + - - -
300H PHE* 1.3 70.7 - - - +
302H TYR* 1.3 61.1 + - - +
303H GLY 4.1 0.7 + - - -
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Residues in contact with TYR 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ILE 3.3 7.5 + - - +
31H LEU* 4.2 0.5 - - - +
32H ALA* 2.9 26.2 + - - -
233H MET* 3.2 16.7 - - + +
270H PHE* 3.5 22.7 - - + -
271H LEU 4.1 0.9 - - - -
272H SER* 3.5 21.8 - - - -
280H ALA* 3.1 41.6 + - + -
284H LEU* 3.5 10.0 - - + +
300H PHE* 3.3 27.8 - + + -
301H SER* 1.3 76.6 - - - +
303H GLY* 1.3 61.6 + - - +
305H ALA* 3.4 20.4 - - + -
306H LEU* 3.7 24.2 - - + +
335H ASN* 3.5 30.5 - - - -
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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