Contacts of the strand formed by residues 319 - 325 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317P TRP* 3.4 5.1 - - - +
318P SER* 1.3 81.6 - - - +
320P CYS* 1.3 70.1 + - - +
321P VAL* 4.2 7.6 - - + -
458P GLY* 3.3 4.9 - - - -
459P TRP* 3.0 45.9 + - + -
465P LEU* 4.0 13.9 - - + -
468P GLY* 3.6 34.3 - - - +
469P HIS* 3.6 29.8 - - + +
472P PHE* 3.7 28.5 - - + -
509P PRO* 3.8 5.8 - - + -
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Residues in contact with CYS 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314P VAL* 4.0 3.4 - - + -
317P TRP* 3.7 26.5 - - + -
319P LEU* 1.3 83.2 - - - +
321P VAL* 1.3 64.0 + - - +
322P ALA 4.0 1.4 + - - -
456P MET* 3.8 21.5 - - - -
457P LEU 3.4 3.4 - - - -
472P PHE* 4.3 7.4 - - - -
501P LEU* 3.6 27.1 - - - -
503P TYR* 3.5 15.7 + - - +
509P PRO* 3.6 23.1 - - + +
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Residues in contact with VAL 321 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319P LEU* 4.2 4.5 - - + -
320P CYS* 1.3 77.0 - - - +
322P ALA* 1.3 67.1 + - - +
323P THR* 3.5 10.3 + - + -
456P MET* 3.4 4.3 - - - -
457P LEU* 2.7 43.3 + - + +
459P TRP* 3.4 30.5 - - + -
471P LEU* 5.9 0.4 - - + -
472P PHE* 3.7 41.7 - - + +
475P LEU* 3.5 30.3 - - + -
490P TYR* 5.2 1.8 - - + -
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Residues in contact with ALA 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320P CYS* 4.0 2.6 + - - -
321P VAL* 1.3 72.1 - - - +
323P THR* 1.3 61.3 + - - +
455P ALA 3.9 5.8 - - - -
456P MET* 3.5 27.6 - - + +
472P PHE* 5.9 1.4 - - - -
490P TYR* 3.3 9.6 - - - +
491P GLU* 2.8 33.7 + - + +
494P GLY* 3.6 24.0 - - - -
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Residues in contact with THR 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321P VAL* 3.5 11.8 + - + +
322P ALA* 1.3 75.8 - - - +
324P ASP* 1.3 65.1 + - - +
410P TYR* 3.4 31.8 + - + -
413P MET* 4.6 0.9 - - + -
453P ASP 4.5 4.3 - - - +
455P ALA* 3.4 20.6 + - - +
457P LEU* 3.4 35.2 - - + -
475P LEU* 5.2 4.7 - - + -
488P ILE* 4.1 11.7 - - + -
489P SER 3.4 7.2 - - - +
490P TYR* 4.5 0.4 - - - +
491P GLU* 3.8 13.2 - - - +
665P MN 3.9 6.9 + - - -
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Residues in contact with ASP 324 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323P THR* 1.3 81.2 - - - +
325P VAL* 1.3 72.4 + - - +
326P SER* 4.2 1.0 + - - -
453P ASP* 4.6 3.1 - - - -
487P LYS 3.7 1.0 - - - +
488P ILE* 3.6 4.6 - - - -
489P SER* 2.7 46.3 + - - +
490P TYR 4.0 2.9 - - - +
491P GLU* 3.8 27.5 - - + +
492P HIS 5.5 0.2 + - - -
668P MG 3.9 12.6 - - - -
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Residues in contact with VAL 325 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324P ASP* 1.3 82.0 + - - +
326P SER* 1.3 70.9 + - - +
327P ASP 3.7 0.7 + - - -
328P HIS* 4.1 6.5 + - + -
406P MET* 3.2 29.2 - - + -
410P TYR* 3.2 17.0 - - + +
453P ASP* 3.6 23.5 + - + +
486P MET* 4.1 31.6 - - + -
487P LYS 3.7 12.6 - - - +
488P ILE* 3.9 6.5 - - + -
667P GTP 4.0 1.0 + - - -
668P MG 2.9 25.1 - - - -
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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