Contacts of the helix formed by residues 288 - 292 (chain C) in PDB entry 1FSJ
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 PRO 288 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286C PHE 4.7 0.4 - - - +
287C THR* 1.3 101.7 + - - +
289C LYS* 1.3 67.9 + - - +
290C ASN* 3.1 19.3 - - - +
291C GLN* 3.0 15.9 + - + -
292C GLN* 3.5 0.7 - - - +
299C TYR* 3.5 17.5 - - + +
323C THR* 5.5 1.1 - - + -
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Residues in contact with LYS 289 (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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16B LYS* 6.1 1.2 - - - +
104B ASP* 3.5 32.6 + - - +
105B LYS* 3.4 31.7 - - + +
115B ASP* 5.8 0.4 + - - -
117B ASP* 2.7 39.8 + - - +
118B ASN* 4.2 10.2 - - + +
287C THR 3.5 1.0 + - - +
288C PRO* 1.3 71.8 - - - +
290C ASN* 1.3 58.8 + - - +
291C GLN 3.0 4.7 + - - -
292C GLN* 3.2 32.5 + - - +
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Residues in contact with ASN 290 (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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104B ASP* 3.5 26.8 + - - +
106B PRO* 4.2 8.0 - - + +
109B GLN* 3.0 20.8 + - - +
288C PRO* 3.6 18.1 - - - +
289C LYS* 1.3 77.8 - - - +
291C GLN* 1.3 80.5 + - - +
532D ARG* 5.3 8.9 - - - +
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Residues in contact with GLN 291 (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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227C GLY* 3.7 17.7 + - - +
287C THR* 3.7 7.4 - - - +
288C PRO* 3.0 14.4 + - + +
290C ASN* 1.3 100.3 + - - +
292C GLN* 1.3 60.9 + - - +
323C THR* 2.7 44.3 + - + -
324C PRO* 3.4 8.7 - - - +
325C LYS* 3.1 46.3 + - - +
326C ARG 4.2 0.7 + - - -
532D ARG* 6.0 5.9 - - - +
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Residues in contact with GLN 292 (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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105B LYS* 3.3 37.1 - - - +
109B GLN* 2.8 27.9 + - - +
286C PHE* 4.5 6.6 - - - +
287C THR* 3.0 35.2 + - - +
288C PRO 3.5 4.5 - - - +
289C LYS* 3.2 26.2 + - - +
291C GLN* 1.3 79.1 - - - +
293C VAL* 1.3 62.5 + - - +
296C ARG 3.7 9.9 - - - +
297C LYS* 3.6 34.9 - - - +
324C PRO* 4.2 1.1 - - - -
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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