Contacts of the strand formed by residues 319 - 325 (chain R) in PDB entry 1HI0
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 LEU 319 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317R TRP* 3.6 4.0 - - - +
318R SER* 1.3 82.5 - - - +
320R CYS* 1.3 70.8 + - - +
321R VAL* 4.2 8.1 - - + -
457R LEU 4.4 0.2 - - - -
458R GLY* 3.3 5.4 - - - -
459R TRP* 3.0 45.0 + - + -
465R LEU* 4.0 14.6 - - + -
468R GLY* 3.6 33.4 - - - +
469R HIS* 3.6 30.5 - - + +
472R PHE* 3.7 27.4 - - + -
509R PRO* 3.8 5.4 - - + -
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Residues in contact with CYS 320 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314R VAL* 4.0 3.1 - - + -
317R TRP* 3.7 26.5 - - + -
319R LEU* 1.3 83.3 - - - +
321R VAL* 1.3 64.9 + - - +
322R ALA 4.0 1.6 + - - -
456R MET* 3.8 21.3 - - - -
457R LEU 3.4 3.4 - - - -
472R PHE* 4.3 8.1 - - - -
501R LEU* 3.6 26.9 - - - -
503R TYR* 3.5 16.6 + - - +
509R PRO* 3.6 23.1 - - + +
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Residues in contact with VAL 321 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319R LEU* 4.2 4.9 - - + -
320R CYS* 1.3 76.2 - - - +
322R ALA* 1.3 66.8 + - - +
323R THR* 3.5 10.8 + - + -
456R MET* 3.4 4.1 - - - -
457R LEU* 2.7 43.1 + - + +
459R TRP* 3.4 30.7 - - + -
471R LEU* 5.9 0.9 - - + -
472R PHE* 3.7 41.5 - - + +
475R LEU* 3.5 30.1 - - + -
490R TYR* 5.2 1.8 - - + -
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Residues in contact with ALA 322 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320R CYS 4.0 2.4 + - - -
321R VAL* 1.3 71.7 - - - +
323R THR* 1.3 61.4 + - - +
455R ALA 3.9 6.5 - - - +
456R MET* 3.5 27.3 - - + +
472R PHE* 5.9 1.4 - - - -
490R TYR* 3.3 9.8 - - - +
491R GLU* 2.8 34.2 + - + +
494R GLY* 3.6 24.2 - - - -
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Residues in contact with THR 323 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321R VAL* 3.5 11.2 + - + +
322R ALA* 1.3 76.0 - - - +
324R ASP* 1.3 65.1 + - - +
410R TYR* 3.4 32.6 + - + -
413R MET* 4.6 1.6 - - + -
453R ASP 4.5 4.7 - - - +
454R ASP* 4.6 0.2 - - - +
455R ALA* 3.4 20.6 + - - +
457R LEU* 3.4 35.7 - - + -
475R LEU* 5.2 4.3 - - + -
488R ILE* 4.1 11.0 - - + -
489R SER 3.4 7.2 - - - +
490R TYR* 4.5 0.2 - - - +
491R GLU* 3.8 13.0 - - - +
665R MN 3.9 6.9 + - - -
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Residues in contact with ASP 324 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323R THR* 1.3 80.9 - - - +
325R VAL* 1.3 73.5 + - - +
326R SER* 4.2 0.4 + - - -
453R ASP* 4.6 3.3 - - - -
487R LYS 3.7 0.9 - - - +
488R ILE* 3.6 4.4 - - - -
489R SER* 2.7 46.1 + - - +
490R TYR 4.0 2.9 - - - +
491R GLU* 3.8 26.3 - - + +
668R MG 3.9 13.2 - - - -
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Residues in contact with VAL 325 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324R ASP* 1.3 80.9 + - - +
326R SER* 1.3 71.3 + - - +
327R ASP 3.7 0.3 + - - -
328R HIS* 4.1 6.2 + - + -
331R PHE* 6.1 0.2 - - + -
406R MET* 3.2 29.8 - - + -
410R TYR* 3.2 16.8 - - + +
453R ASP* 3.6 22.9 + - + +
486R MET* 4.1 31.6 - - + -
487R LYS 3.7 12.3 - - - +
488R ILE* 3.9 5.6 - - + -
667R GTP 4.0 1.0 + - - -
668R MG 2.9 25.5 - - - -
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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