Contacts of the helix formed by residues 291 - 297 (chain f) in PDB entry 5T0J
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 ILE 291 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288f ALA 3.7 1.1 + - - +
290f GLY* 1.3 74.3 - - - +
292f VAL* 1.3 68.2 + - - +
294f SER* 3.3 29.0 - - - +
295f GLY 4.0 2.3 + - - -
321f GLY* 3.6 11.8 - - - +
324f PHE* 3.5 23.6 - - + -
328f LEU* 5.8 0.2 - - + -
651f ILE* 3.6 31.0 - - + +
655f SER* 6.1 0.9 - - - -
692f ASP* 3.5 41.6 + - - +
693f VAL* 3.3 32.8 - - - +
694f VAL 5.2 1.6 - - - +
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Residues in contact with VAL 292 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274f LEU* 3.8 25.1 - - + -
288f ALA 3.2 20.4 - - - +
289f CYS* 3.5 14.6 - - - +
290f GLY 3.2 0.8 - - - -
291f ILE* 1.3 82.4 - - - +
293f ASN* 1.3 65.1 + - + +
294f SER 3.1 0.5 + - - -
295f GLY 3.8 0.7 + - - -
296f VAL* 3.2 27.4 + - + +
647f VAL* 3.7 22.7 - - + -
650f ILE* 3.8 20.9 - - + +
651f ILE* 3.8 12.5 - - + +
655f SER* 5.4 2.3 - - - -
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Residues in contact with ASN 293 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274f LEU* 4.9 9.0 - - + +
289f CYS 4.7 0.6 + - - +
290f GLY 4.0 2.2 + - - -
291f ILE 3.6 0.2 - - - -
292f VAL* 1.3 78.5 - - + +
294f SER* 1.3 66.8 + - - +
295f GLY 3.6 0.4 - - - -
296f VAL* 4.1 8.0 - - - +
297f ARG* 3.0 35.2 + - - +
303f ALA* 2.8 52.5 + - - +
304f LEU* 3.6 3.0 - - - +
307f LEU* 3.3 30.3 - - + +
325f GLY* 5.3 0.5 - - - +
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Residues in contact with SER 294 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290f GLY 3.4 2.4 + - - -
291f ILE* 3.3 31.1 - - - +
292f VAL 3.1 1.0 - - - -
293f ASN* 1.3 81.2 - - - +
295f GLY* 1.3 53.5 + - - +
297f ARG 4.0 1.9 - - - +
298f ASN* 2.3 30.7 + - - -
307f LEU* 4.8 0.4 - - - +
321f GLY 2.6 28.8 + - - -
324f PHE* 4.4 0.2 - - - -
325f GLY* 3.4 24.9 + - - +
328f LEU* 3.9 13.2 - - - +
329f ALA 4.7 1.0 + - - -
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Residues in contact with GLY 295 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291f ILE 4.0 2.2 + - - -
292f VAL 3.8 3.2 + - - -
294f SER* 1.3 79.0 - - - +
296f VAL* 1.3 67.3 + - - +
298f ASN* 3.3 16.6 + - - +
328f LEU* 4.0 10.5 - - - +
655f SER* 4.7 15.1 - - - -
657f TYR* 3.5 15.9 - - - +
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Residues in contact with VAL 296 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268f THR* 4.5 12.8 - - + -
269f GLN 4.9 5.6 - - - +
270f ILE* 4.3 4.9 - - + -
274f LEU* 4.2 20.9 - - + -
292f VAL* 3.2 28.5 + - + +
293f ASN* 4.3 6.3 - - - +
294f SER 3.4 0.6 - - - -
295f GLY* 1.3 80.6 - - - +
297f ARG* 1.3 80.6 + - + +
298f ASN 3.1 11.6 - - - +
650f ILE 5.9 0.4 - - - +
654f LYS* 3.6 25.6 - - + +
655f SER* 4.0 8.9 - - - +
657f TYR* 3.1 21.1 - - - -
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Residues in contact with ARG 297 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263f VAL* 5.6 5.1 - - - +
267f LEU* 4.8 10.1 - - - +
268f THR* 4.3 8.3 + - - +
270f ILE* 3.7 47.5 - - + +
293f ASN* 3.0 32.7 + - - +
294f SER 4.0 0.7 - - - +
296f VAL* 1.3 94.4 + - + +
298f ASN* 1.3 70.6 + - - +
299f GLU* 4.0 1.8 + - - +
300f CYS* 3.4 40.8 - - - +
304f LEU* 5.2 1.4 - - - +
325f GLY 5.1 1.2 - - - +
329f ALA* 4.1 5.4 - - - +
657f TYR* 3.1 28.2 + - - -
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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