Contacts of the strand formed by residues 297 - 302 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24G VAL* 3.7 37.5 - - + +
266G PRO 3.0 17.6 + - - +
267G GLY* 3.8 1.8 - - - -
268G VAL* 2.8 24.4 + - - +
296G TRP* 1.3 74.8 - - - +
298G LEU* 1.3 63.5 + - - +
299G THR* 3.8 7.9 - - + -
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Residues in contact with LEU 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G VAL* 4.3 5.8 - - + -
257G LEU* 3.9 14.1 - - + -
268G VAL* 3.6 17.9 - - + -
270G PHE* 4.0 10.3 - - + -
284G LEU* 3.3 4.8 - - - +
287G ILE* 3.4 25.4 - - + -
288G ASN* 2.8 35.2 + - - +
294G ARG* 3.5 40.4 - - + +
296G TRP* 3.4 32.9 + - + +
297G ALA* 1.3 77.4 - - - +
299G THR* 1.3 63.1 + - - +
339G ALA 4.2 1.0 + - - +
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Residues in contact with THR 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 4.3 20.4 - - + +
25G ALA 5.0 0.7 - - - +
26G PRO* 6.2 0.2 - - + -
27G GLY 5.5 0.9 - - - +
28G LYS 3.0 30.4 + - - +
29G GLY* 3.5 2.1 - - - -
268G VAL 3.2 9.6 + - - -
269G THR* 4.2 8.7 - - - +
270G PHE* 3.1 31.5 + - - +
284G LEU* 3.8 8.7 - - - +
297G ALA* 3.8 6.0 - - + -
298G LEU* 1.3 82.1 - - - +
300G PHE* 1.3 83.9 + - - -
339G ALA* 3.8 22.2 - - + +
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Residues in contact with PHE 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G LYS 4.1 2.0 - - - -
29G GLY* 3.2 25.3 - - - -
30G ILE* 2.8 52.6 + - - +
73G CYS 3.5 14.4 - - - -
74G ILE* 4.2 7.0 - - + -
269G THR* 3.9 5.7 - - - -
270G PHE 3.6 4.7 - - - -
284G LEU* 3.7 10.3 - - + -
299G THR* 1.3 93.3 + - - +
301G SER* 1.3 58.2 + - - +
302G TYR* 3.3 38.8 - + + -
306G LEU* 3.8 17.7 - - + -
332G ALA 4.4 5.2 - - - -
335G ASN* 3.5 42.0 - - + -
336G GLY* 3.9 3.6 - - - -
339G ALA* 4.4 1.3 - - + -
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Residues in contact with SER 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ILE* 3.4 27.6 - - - +
32G ALA* 4.5 1.5 - - - +
78G ILE* 3.7 5.5 - - - +
186G ILE* 4.9 0.2 - - - +
230G LYS* 3.3 39.0 + - - +
269G THR* 3.2 33.3 + - - -
270G PHE 2.7 13.7 + - - +
271G LEU* 3.8 4.7 - - - -
272G SER 4.3 0.3 + - - -
300G PHE* 1.3 70.8 - - - +
302G TYR* 1.3 60.8 + - - +
303G GLY 4.1 0.5 + - - -
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Residues in contact with TYR 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ILE 3.3 8.2 + - - +
31G LEU* 4.2 0.7 - - - +
32G ALA* 2.9 27.0 + - - -
233G MET* 3.2 16.6 - - + +
270G PHE* 3.5 22.4 - - + -
271G LEU 4.1 0.7 - - - -
272G SER* 3.5 22.4 - - - -
280G ALA* 3.1 40.7 + - + -
284G LEU* 3.5 9.6 - - + +
300G PHE* 3.3 28.9 - + + -
301G SER* 1.3 75.5 - - - +
303G GLY* 1.3 62.4 + - - +
305G ALA* 3.4 20.0 - - + -
306G LEU* 3.7 23.2 - - + +
335G 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