Contacts of the strand formed by residues 297 - 302 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C VAL* 3.7 38.4 - - + +
266C PRO 3.0 17.8 + - - +
267C GLY* 3.8 1.8 - - - -
268C VAL* 2.8 24.8 + - - +
296C TRP* 1.3 74.1 - - - +
298C LEU* 1.3 62.2 + - - +
299C THR* 3.8 7.2 - - + -
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Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C VAL* 4.3 5.6 - - + -
257C LEU* 3.9 13.7 - - + -
268C VAL* 3.6 17.3 - - + -
270C PHE* 4.0 11.0 - - + -
284C LEU* 3.3 4.6 - - - +
287C ILE* 3.4 25.1 - - + -
288C ASN* 2.8 35.4 + - - +
294C ARG* 3.5 39.5 - - + +
296C TRP* 3.4 34.6 + - + +
297C ALA* 1.3 77.1 - - - +
299C THR* 1.3 62.9 + - - +
339C ALA 4.2 1.3 + - - +
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Residues in contact with THR 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 4.3 20.4 - - + +
25C ALA 5.0 0.4 - - - +
26C PRO* 6.2 0.2 - - + -
27C GLY 5.5 1.3 - - - +
28C LYS 3.0 30.6 + - - +
29C GLY* 3.5 2.1 - - - -
268C VAL 3.2 10.6 + - - -
269C THR* 4.5 9.0 - - - +
270C PHE* 3.1 31.2 + - - +
284C LEU* 3.8 8.6 - - - +
297C ALA* 3.8 6.0 - - + -
298C LEU* 1.3 80.5 - - - +
300C PHE* 1.3 84.6 + - - +
339C ALA* 3.8 21.5 - - + +
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Residues in contact with PHE 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LYS 4.1 1.8 - - - -
29C GLY* 3.2 25.1 - - - -
30C ILE* 2.8 53.9 + - - +
73C CYS 3.5 13.9 - - - -
74C ILE* 4.2 7.0 - - + -
269C THR* 3.9 5.7 - - - -
270C PHE 3.6 5.2 - - - -
284C LEU* 3.7 9.4 - - + -
299C THR* 1.3 93.2 + - - +
301C SER* 1.3 57.3 + - - +
302C TYR* 3.3 39.7 - + + -
306C LEU* 3.8 17.9 - - + -
332C ALA 4.4 5.4 - - - -
335C ASN* 3.5 42.0 - - + -
336C GLY* 3.9 3.8 - - - -
339C ALA* 4.4 1.1 - - + -
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Residues in contact with SER 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ILE* 3.4 28.7 - - - +
32C ALA* 4.5 1.9 - - - +
78C ILE* 3.7 5.5 - - - +
186C ILE* 4.9 0.3 - - - +
230C LYS* 3.3 37.7 + - - +
269C THR* 3.2 34.0 + - - -
270C PHE 2.7 14.1 + - - +
271C LEU* 3.8 4.3 - - - -
272C SER 4.3 0.2 + - - -
300C PHE* 1.3 71.4 - - - +
302C TYR* 1.3 61.1 + - - +
303C GLY 4.1 0.7 + - - -
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Residues in contact with TYR 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ILE 3.3 8.0 + - - +
31C LEU* 4.2 0.5 - - - +
32C ALA* 2.9 27.0 + - - +
233C MET* 3.2 16.7 - - + +
270C PHE* 3.5 22.4 - - + -
271C LEU 4.1 0.7 - - - -
272C SER* 3.5 21.8 - - - -
280C ALA* 3.1 40.9 + - + -
284C LEU* 3.5 9.8 - - + +
300C PHE* 3.3 29.8 - + + -
301C SER* 1.3 75.9 - - - +
303C GLY* 1.3 60.3 + - - +
305C ALA* 3.4 20.6 - - + -
306C LEU* 3.7 23.2 - - + +
335C ASN* 3.5 31.0 - - - -
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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