Contacts of the strand formed by residues 297 - 302 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.7 38.8 - - + +
266A PRO 3.0 18.3 + - - +
267A GLY* 3.8 1.3 - - - -
268A VAL 2.8 24.5 + - - -
296A TRP* 1.3 73.7 - - - +
298A LEU* 1.3 64.1 + - - +
299A THR* 3.8 7.2 - - + -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A VAL* 4.3 5.6 - - + -
257A LEU* 3.9 13.5 - - + -
268A VAL* 3.6 17.9 - - + -
270A PHE* 4.0 11.7 - - + -
284A LEU* 3.3 4.6 - - - +
287A ILE* 3.4 25.1 - - + -
288A ASN* 2.8 35.7 + - - +
294A ARG* 3.5 40.6 - - + +
296A TRP* 3.4 33.6 + - + +
297A ALA* 1.3 77.4 - - - +
299A THR* 1.3 63.6 + - - +
339A ALA 4.2 1.1 + - - +
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.3 21.0 - - + +
25A ALA 5.0 0.4 - - - +
26A PRO* 6.2 0.4 - - + -
27A GLY 5.5 1.6 - - - +
28A LYS 3.0 30.1 + - - +
29A GLY* 3.5 1.9 - - - -
268A VAL 3.2 10.4 + - - -
269A THR* 4.2 9.1 - - - +
270A PHE* 3.1 31.4 + - - +
284A LEU* 3.8 8.8 - - - +
297A ALA* 3.8 5.6 - - + -
298A LEU* 1.3 81.4 - - - +
300A PHE* 1.3 83.4 + - - +
339A ALA* 3.8 21.8 - - + +
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Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS 4.1 1.8 - - - -
29A GLY* 3.2 25.1 - - - -
30A ILE* 2.8 53.6 + - - +
73A CYS 3.5 15.0 - - - -
74A ILE* 4.2 7.0 - - + -
269A THR* 3.9 5.6 - - - -
270A PHE 3.6 4.7 - - - -
284A LEU* 3.7 9.4 - - + -
299A THR* 1.3 93.6 + - - +
301A SER* 1.3 58.0 + - - +
302A TYR* 3.3 39.5 - + + -
306A LEU* 3.8 17.3 - - + -
332A ALA 4.4 4.9 - - - -
335A ASN* 3.5 43.1 - - + -
336A GLY* 3.9 3.6 - - - -
339A ALA* 4.4 0.9 - - + -
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.4 28.2 - - - +
32A ALA* 4.5 2.3 - - - +
78A ILE* 3.7 5.7 - - - +
186A ILE* 4.9 0.3 - - - +
230A LYS* 3.3 37.2 + - - +
269A THR* 3.2 34.2 + - - -
270A PHE 2.7 14.3 + - - +
271A LEU* 3.8 4.7 - - - +
272A SER 4.3 0.2 + - - -
300A PHE* 1.3 71.0 - - - +
302A TYR* 1.3 60.4 + - - +
303A GLY 4.1 0.9 + - - -
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Residues in contact with TYR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE 3.3 7.6 + - - +
31A LEU* 4.2 0.3 - - - +
32A ALA* 2.9 27.2 + - - -
233A MET* 3.2 16.9 - - + +
270A PHE* 3.5 22.0 - - + -
271A LEU 4.1 0.4 - - - -
272A SER* 3.5 22.7 - - - -
280A ALA* 3.1 40.5 + - + -
284A LEU* 3.5 9.0 - - - +
300A PHE* 3.3 29.6 - + + -
301A SER* 1.3 76.0 - - - +
303A GLY* 1.3 61.1 + - - +
305A ALA* 3.4 20.0 - - + -
306A LEU* 3.7 23.8 - - + +
335A ASN* 3.5 30.1 - - - -
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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