Contacts of the strand formed by residues 353 - 357 (chain B) in PDB entry 1OFD
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 ARG 353 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B PRO* 5.7 3.4 - - + -
352B ALA* 1.3 78.6 - - - +
354B TYR* 1.3 61.2 + - - +
364B LEU* 3.3 3.2 - - - +
365B GLY 2.8 34.7 + - - +
366B SER 4.9 3.6 - - - +
367B GLU 4.8 1.9 - - - +
368B ALA* 3.5 45.8 - - + +
382B GLY 3.6 14.6 - - - -
383B ARG* 4.3 7.6 - - + +
1328B GLU* 4.2 7.9 + - - +
1329B ALA 2.5 31.0 + - - -
1330B ASN* 3.4 12.7 + - - +
1331B ASP* 4.7 2.2 + - - -
1358B VAL* 3.9 23.5 + - - +
1359B ILE* 4.2 8.7 - - - +
1360B ILE 3.3 5.1 - - - -
1361B GLY* 3.0 31.1 - - - +
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Residues in contact with TYR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ARG* 1.3 76.9 - - - +
355B CYS* 1.3 64.0 + - - +
356B ILE* 4.0 16.4 - - + -
362B ILE* 4.7 3.8 - - + -
363B VAL 3.2 13.5 - - - +
364B LEU* 3.9 22.2 - - + -
368B ALA* 6.5 0.2 - - - -
380B GLU* 2.9 37.4 + - + -
381B LYS* 3.5 4.9 - - - +
382B GLY* 2.8 44.7 + - - +
383B ARG* 3.3 34.3 + - - -
384B LEU* 4.4 8.7 - - + -
390B ILE* 3.6 30.1 - - + -
401B LYS* 3.8 13.2 - - - +
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Residues in contact with CYS 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B TYR* 1.3 77.5 - - - +
356B ILE* 1.3 66.8 + - - +
361B TYR 3.9 0.5 - - - +
362B ILE* 3.4 4.0 - - - +
363B VAL* 2.9 34.9 + - + +
373B LEU* 3.9 20.4 - - + +
378B ILE* 3.5 47.3 - - - -
380B GLU 3.4 5.6 - - - -
381B LYS* 4.1 10.5 - - + -
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Residues in contact with ILE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B TYR* 4.0 17.5 - - + -
355B CYS* 1.3 80.1 - - - +
357B THR* 1.3 75.7 + - - +
360B ASP* 4.2 6.5 - - - +
361B TYR 3.3 6.1 - - - +
362B ILE* 3.8 22.0 - - + -
378B ILE* 3.8 2.6 - - - +
379B VAL* 2.9 30.9 + - + +
380B GLU* 3.0 40.4 + - + +
399B ILE* 3.7 40.2 - - + -
401B LYS* 4.2 4.0 - - - -
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Residues in contact with THR 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B ILE* 1.3 84.2 - - - +
358B LYS* 1.3 59.9 + - - +
359B ASP* 3.0 18.1 + - - +
360B ASP* 3.0 18.2 + - - +
361B TYR* 2.9 38.9 + - + +
373B LEU* 4.2 29.8 - - + -
377B ASP* 3.1 28.7 - - - +
378B ILE* 5.0 2.0 - - + -
379B VAL* 4.0 6.9 - - - +
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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
------------------------------------------------------------
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