Contacts of the helix formed by residues 259 - 265 (chain I) in PDB entry 5D0K
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 ASN 259 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258I GLN* 1.3 74.7 - - + +
260I THR* 1.3 69.9 + - - +
261I ILE 3.2 0.7 - - - -
262I GLU* 3.7 14.8 - - + +
263I ARG* 3.1 24.6 + - - +
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Residues in contact with THR 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258I GLN 3.3 4.7 + - - +
259I ASN* 1.3 79.9 + - - +
261I ILE* 1.3 68.3 + - + +
263I ARG* 3.2 12.9 + - - +
264I PHE* 3.3 27.9 + - + +
329I LYS* 5.2 13.0 - - - -
338I ILE* 4.8 8.5 - - + +
339I GLU* 3.3 26.9 - - + +
91J SER* 5.6 3.5 - - - -
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Residues in contact with ILE 261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258I GLN* 3.0 41.5 + - - +
260I THR* 1.3 82.8 - - - +
262I GLU* 1.3 60.6 + - - +
263I ARG 3.2 0.5 + - - -
264I PHE 3.3 0.2 + - - -
265I THR* 2.8 32.4 + - + +
308I ARG* 3.4 39.7 - - - +
322I ASP* 4.1 10.3 - - - +
325I LEU* 3.5 48.9 - - + +
326I ALA* 4.6 2.7 - - + +
329I LYS* 5.9 3.4 - - - -
338I ILE* 4.6 12.8 - - + -
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Residues in contact with GLU 262 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258I GLN* 3.1 34.1 + - + +
259I ASN* 4.0 15.5 - - + +
260I THR 3.3 0.4 - - - -
261I ILE* 1.3 76.2 - - - +
263I ARG* 1.3 59.3 + - - +
265I THR* 3.4 14.5 - - - +
267I PRO* 3.5 19.3 - - - +
308I ARG* 3.1 29.2 + - - +
318I GLN* 5.0 3.8 + - - -
73K LEU* 5.7 0.2 - - - +
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Residues in contact with ARG 263 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259I ASN 3.1 17.3 + - - +
260I THR* 3.9 4.5 - - - +
261I ILE 3.1 1.0 - - - -
262I GLU* 1.3 77.8 - - - +
264I PHE* 1.3 88.5 + - + +
265I THR 3.6 0.2 - - - -
341I GLN* 6.0 1.2 - - - +
90J ARG* 2.9 56.5 - - - +
91J SER* 5.1 2.4 + - - -
117J ASP* 3.3 24.2 + - - -
73K LEU* 3.5 22.8 - - - +
75K GLY* 5.3 3.6 - - - -
76K GLY* 4.9 11.3 - - - -
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Residues in contact with PHE 264 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260I THR* 3.3 25.6 + - + +
261I ILE 4.4 0.9 - - - +
263I ARG* 1.3 114.1 - - + +
265I THR* 1.3 62.3 - - + +
311I PRO* 3.5 18.4 - - - +
338I ILE* 3.4 32.5 - - + +
339I GLU* 3.7 34.8 - - + -
341I GLN* 3.6 33.4 - - + -
90J ARG* 5.5 0.4 - - - -
91J SER* 3.6 28.0 - - - -
71K LEU* 4.0 3.5 - - - +
73K LEU* 4.0 12.3 - - + +
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Residues in contact with THR 265 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261I ILE* 2.8 19.0 + - + +
262I GLU 3.4 14.9 - - - +
263I ARG 3.6 0.6 - - - -
264I PHE* 1.3 87.2 - - + +
266I PHE* 1.3 60.7 + - - +
267I PRO* 3.5 6.5 - - - +
308I ARG* 2.7 37.5 + - - -
309I ARG 3.0 18.4 - - - +
310I LEU* 4.0 20.9 - - + -
311I PRO* 4.3 3.4 - - + -
325I LEU* 4.9 1.3 - - + -
338I ILE* 4.7 11.9 - - + -
71K LEU* 3.7 5.8 - - - -
73K LEU* 4.0 8.0 - - - +
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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