Contacts of the strand formed by residues 429 - 434 (chain C) in PDB entry 1OVM
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 VAL 429 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378C ILE* 3.4 22.4 - - + +
380C LEU* 3.6 27.6 - - + -
417C ALA* 4.4 7.6 - - + +
420C ALA* 5.0 0.4 - - + -
421C GLN* 3.3 54.9 - - + +
424C CYS 4.9 0.2 - - - +
427C ARG 3.4 5.0 + - - +
428C ARG* 1.3 75.7 - - - +
430C ILE* 1.3 63.2 + - - +
431C VAL* 4.0 13.0 - - + -
454C HIS 5.3 0.6 + - - -
455C PRO* 3.6 3.9 - - + +
456C ILE* 3.0 29.3 + - - +
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Residues in contact with ILE 430 (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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369C LEU* 5.3 8.3 - - + -
372C PHE* 4.0 20.2 - - + -
373C ILE* 5.7 3.8 - - + -
377C ASP* 3.9 16.6 - - + +
378C ILE 2.8 10.5 + - - +
379C ILE* 3.4 16.8 - - + -
380C LEU* 2.9 27.5 + - - +
428C ARG* 3.7 41.1 - - + +
429C VAL* 1.3 77.2 - - - +
431C VAL* 1.3 62.4 + - - +
432C LEU* 4.1 26.9 - - + -
456C ILE* 3.5 9.2 - - + -
458C LEU* 4.3 11.9 - - + -
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Residues in contact with VAL 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C LEU* 3.7 5.8 - - + +
413C THR* 4.2 29.6 - - - +
414C LEU* 4.4 11.7 - - + -
417C ALA* 3.5 25.1 - - + -
429C VAL* 4.0 12.3 - - + +
430C ILE* 1.3 74.8 - - - +
432C LEU* 1.3 60.2 + - - +
433C THR* 4.4 13.7 - - + -
448C MET* 4.8 1.8 - - + -
455C PRO* 4.5 4.9 - - + -
456C ILE 3.0 8.1 + - - +
457C ILE* 4.1 24.2 - - + +
458C LEU* 2.8 33.3 + - - +
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Residues in contact with LEU 432 (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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365C PHE* 4.2 15.7 - - + -
366C TRP* 3.8 24.7 - - + -
369C LEU* 3.4 28.0 - - + -
379C ILE* 3.8 24.9 - - + -
380C LEU 2.7 13.6 + - - +
381C ALA* 3.1 10.3 - - + -
382C ASP 3.1 23.7 + - - -
386C SER* 3.5 11.7 + - - +
390C ALA* 4.0 13.2 - - + -
393C LEU* 4.5 1.3 - - + -
413C THR* 4.1 1.0 + - - -
430C ILE* 4.1 14.8 - - + -
431C VAL* 1.3 71.8 - - - +
433C THR* 1.3 59.8 + - - +
458C LEU* 3.8 15.9 - - + -
460C LEU* 5.4 2.7 - - + -
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Residues in contact with THR 433 (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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382C ASP* 4.4 3.9 + - - -
386C SER* 3.4 7.4 + - - -
413C THR* 3.9 15.3 + - - -
414C LEU* 5.2 7.6 - - + +
431C VAL* 4.4 7.6 - - + -
432C LEU* 1.3 74.4 - - - +
434C GLY* 1.3 72.8 + - - +
437C ALA* 3.7 6.9 - - - +
438C ALA* 3.5 21.3 + - + +
457C ILE* 4.4 13.7 - - + -
458C LEU 3.1 11.9 + - - +
459C VAL* 3.3 16.5 - - + -
460C LEU* 2.9 23.4 + - - +
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Residues in contact with GLY 434 (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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382C ASP* 4.7 2.0 - - - +
383C GLN 5.5 1.0 + - - -
386C SER* 3.5 7.9 + - - -
433C THR* 1.3 89.5 + - - +
435C ASP* 1.3 65.6 + - - -
436C GLY 3.3 2.2 - - - -
437C ALA* 4.2 3.0 - - - +
438C ALA* 3.1 13.3 + - - +
459C VAL* 4.3 1.3 - - - +
460C LEU* 4.0 9.6 - - - -
600C TPP 3.2 27.0 + - - -
601C MG 4.1 3.1 - - - -
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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