Contacts of the strand formed by residues 297 - 302 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E VAL* 3.7 38.1 - - + +
266E PRO 3.0 18.0 + - - +
267E GLY* 3.8 1.3 - - - -
268E VAL* 2.8 24.3 + - - +
296E TRP* 1.3 73.9 - - - +
298E LEU* 1.3 64.0 + - - +
299E THR* 3.8 7.6 - - + -
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Residues in contact with LEU 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E VAL* 4.3 6.3 - - + -
257E LEU* 3.9 13.9 - - + -
268E VAL* 3.6 17.7 - - + -
270E PHE* 4.0 11.7 - - + -
284E LEU* 3.3 4.3 - - - +
287E ILE* 3.4 25.8 - - + -
288E ASN* 2.8 36.4 + - - +
294E ARG* 3.5 39.9 - - + +
296E TRP* 3.4 33.3 + - + +
297E ALA* 1.3 76.5 - - - +
299E THR* 1.3 63.8 + - - +
339E ALA 4.2 1.5 + - - +
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Residues in contact with THR 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E VAL* 4.3 19.9 - - + +
25E ALA 5.0 0.7 - - - +
26E PRO* 6.2 0.2 - - + -
27E GLY 5.5 1.6 - - - +
28E LYS 3.0 30.0 + - - +
29E GLY* 3.5 1.9 - - - -
268E VAL 3.2 10.2 + - - -
269E THR* 4.5 9.2 - - - +
270E PHE* 3.1 31.1 + - - +
284E LEU* 3.8 9.4 - - - +
297E ALA* 3.8 6.5 - - + -
298E LEU* 1.3 80.7 - - - +
300E PHE* 1.3 84.0 + - - +
339E ALA* 3.8 22.0 - - + +
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Residues in contact with PHE 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LYS 4.1 1.6 - - - -
29E GLY* 3.2 26.2 - - - -
30E ILE* 2.8 53.7 + - - +
73E CYS 3.5 13.9 - - - -
74E ILE* 4.2 7.2 - - + -
269E THR* 3.9 5.6 - - - -
270E PHE 3.6 4.0 - - - -
284E LEU* 3.7 9.6 - - + -
299E THR* 1.3 94.5 + - - +
301E SER* 1.3 57.3 + - - +
302E TYR* 3.3 39.7 - + + -
306E LEU* 3.8 16.6 - - + -
332E ALA 4.4 5.4 - - - -
335E ASN* 3.5 43.3 - - + -
336E GLY* 3.9 3.6 - - - -
339E ALA* 4.4 1.1 - - + -
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Residues in contact with SER 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ILE* 3.4 28.0 - - - +
32E ALA* 4.4 1.6 - - - +
78E ILE* 3.7 5.2 - - - +
186E ILE* 4.9 0.3 - - - +
230E LYS* 3.3 37.6 + - - +
269E THR* 3.2 34.0 + - - -
270E PHE 2.7 13.7 + - - +
271E LEU* 3.8 4.7 - - - -
272E SER 4.3 0.2 + - - -
300E PHE* 1.3 70.5 - - - +
302E TYR* 1.3 61.4 + - - +
303E GLY 4.1 0.2 + - - -
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Residues in contact with TYR 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ILE 3.3 7.5 + - - +
31E LEU* 4.2 0.3 - - - +
32E ALA* 2.9 27.5 + - - -
233E MET* 3.2 16.4 - - + +
270E PHE* 3.5 21.3 - - + -
271E LEU 4.1 0.7 - - - -
272E SER* 3.5 21.3 - - - -
280E ALA* 3.1 41.1 + - + -
284E LEU* 3.5 9.1 - - + +
300E PHE* 3.3 28.2 - + + -
301E SER* 1.3 75.1 - - - +
303E GLY* 1.3 60.5 - - - +
305E ALA* 3.4 20.4 - - + -
306E LEU* 3.7 23.2 - - + +
335E ASN* 3.5 31.6 - - - -
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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