Contacts of the strand formed by residues 411 - 415 (chain C) in PDB entry 1OHV
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 PHE 411 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C ILE* 3.5 37.0 - - + -
269C SER* 3.2 23.1 - - - -
273C ASP* 3.8 5.1 - - - +
275C HIS* 4.0 5.1 + + - -
301C GLN* 3.7 21.5 - - + -
302C THR* 3.8 17.9 - - + -
306C SER* 3.5 21.7 + - - +
307C THR* 4.2 15.0 - - + -
407C GLY* 3.2 3.8 - - - -
408C ARG 2.9 30.1 + - - +
409C GLY 3.2 0.2 - - - -
410C THR* 1.3 73.9 + - - +
412C CYS* 1.3 59.1 + - - +
446C PHE 4.0 5.2 - - - -
447C ARG* 3.2 41.7 - - - +
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Residues in contact with CYS 412 (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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273C ASP* 3.6 4.7 - - - +
384C GLY 4.1 7.4 - - - -
387C LEU* 4.0 23.3 - - + -
388C LEU* 4.0 15.3 - - - -
391C LEU* 4.2 8.1 - - + -
406C ARG 3.2 7.9 - - - +
407C GLY* 3.9 11.7 - - - -
409C GLY 3.3 24.9 - - - -
410C THR 2.9 13.6 + - - +
411C PHE* 1.3 74.1 - - - +
413C SER* 1.3 66.5 - - - +
445C ARG* 3.5 0.5 - - - -
446C PHE* 2.8 32.8 + - + +
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Residues in contact with SER 413 (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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273C ASP* 3.2 34.6 + - - +
275C HIS* 4.7 0.7 + - - -
391C LEU* 4.8 2.3 - - - +
405C VAL* 3.5 2.6 - - - +
406C ARG* 2.8 54.3 + - - +
412C CYS* 1.3 78.8 - - - +
414C PHE* 1.3 69.2 + - - +
443C SER* 5.2 1.3 - - - -
444C ILE 3.1 16.6 - - - -
445C ARG* 4.0 2.0 - - - +
446C PHE* 4.2 5.3 - - - -
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Residues in contact with PHE 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C LEU* 3.9 24.5 - - + -
402C ILE* 3.3 28.9 - - + -
403C SER 3.7 10.1 - - - +
404C ARG 4.0 0.7 - - - -
405C VAL* 3.7 16.8 - - + -
406C ARG* 3.6 7.9 - - - +
413C SER* 1.3 79.9 - - - +
415C ASP* 1.3 77.0 + - - +
416C THR* 3.9 6.1 - - + -
425C LEU* 5.1 0.2 - - + -
436C LEU* 5.7 0.2 - - + -
443C SER* 3.3 3.8 - - - -
444C ILE* 2.9 67.3 + - + +
446C PHE* 3.7 24.9 - + - -
464C PHE* 3.8 22.2 - + - -
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Residues in contact with ASP 415 (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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222C ARG* 4.3 4.9 + - - -
401C PHE 3.4 4.9 - - - +
403C SER* 2.8 49.0 + - - +
404C ARG* 2.8 35.9 + - + -
406C ARG* 3.1 12.7 + - - -
414C PHE* 1.3 79.0 - - - +
416C THR* 1.3 68.4 + - - +
442C LYS* 3.7 19.6 + - - +
443C SER* 2.5 29.2 + - - -
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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