Contacts of the strand formed by residues 319 - 325 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317Q TRP* 3.4 4.9 - - - +
318Q SER* 1.3 81.6 - - - +
320Q CYS* 1.3 71.2 + - - +
321Q VAL* 4.2 7.9 - - + -
457Q LEU 4.4 0.4 - - - -
458Q GLY* 3.3 5.0 - - - -
459Q TRP* 3.0 46.1 + - + -
465Q LEU* 4.0 13.5 - - + -
468Q GLY* 3.6 33.7 - - - +
469Q HIS* 3.6 29.4 - - + +
472Q PHE* 3.7 28.5 - - + -
509Q PRO* 3.8 6.3 - - + -
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Residues in contact with CYS 320 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314Q VAL* 4.0 3.6 - - + -
317Q TRP* 3.7 25.8 - - + -
319Q LEU* 1.3 82.8 - - - +
321Q VAL* 1.3 64.4 + - - +
322Q ALA 4.0 1.4 + - - -
456Q MET* 3.8 21.3 - - - -
457Q LEU 3.4 4.0 - - - -
472Q PHE* 4.3 7.1 - - - -
501Q LEU* 3.6 26.9 - - - -
503Q TYR* 3.5 16.6 + - - +
509Q PRO* 3.6 22.9 - - + +
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Residues in contact with VAL 321 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319Q LEU* 4.2 4.0 - - + -
320Q CYS* 1.3 77.0 - - - +
322Q ALA* 1.3 69.4 + - - +
323Q THR* 3.5 10.5 + - + -
456Q MET* 3.4 3.6 - - - -
457Q LEU* 2.7 43.1 + - + +
459Q TRP* 3.4 30.5 - - + -
471Q LEU* 5.9 0.7 - - + -
472Q PHE* 3.7 42.0 - - + +
475Q LEU* 3.5 30.7 - - + -
490Q TYR* 5.2 1.6 - - + -
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Residues in contact with ALA 322 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320Q CYS* 4.0 2.4 + - - -
321Q VAL* 1.3 73.1 - - - +
323Q THR* 1.3 63.2 + - - +
455Q ALA 3.9 6.3 - - - +
456Q MET* 3.5 27.1 - - + -
472Q PHE* 5.9 1.0 - - - -
490Q TYR* 3.3 9.2 - - - +
491Q GLU* 2.8 33.1 + - + +
494Q GLY* 3.6 23.6 - - - -
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Residues in contact with THR 323 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321Q VAL* 4.2 11.0 - - + +
322Q ALA* 1.3 76.0 - - - +
324Q ASP* 1.3 66.5 + - - +
410Q TYR* 3.4 32.2 + - + -
413Q MET* 4.6 0.9 - - + -
453Q ASP 4.5 4.5 - - - +
455Q ALA* 3.4 20.7 + - - +
457Q LEU* 3.4 35.7 - - + -
475Q LEU* 5.2 4.7 - - + -
488Q ILE* 4.1 11.0 - - + -
489Q SER 3.4 7.2 - - - +
490Q TYR* 4.5 0.4 - - - +
491Q GLU* 3.8 12.8 - - - +
665Q MN 3.9 6.6 + - - -
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Residues in contact with ASP 324 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323Q THR* 1.3 78.2 - - - +
325Q VAL* 1.3 73.7 + - - +
326Q SER* 4.2 0.6 + - - -
453Q ASP* 4.6 3.3 - - - -
487Q LYS 3.7 0.9 - - - +
488Q ILE* 3.6 5.1 - - - -
489Q SER* 2.7 46.6 + - - +
490Q TYR 4.0 2.6 - - - +
491Q GLU* 3.8 28.7 - - + +
492Q HIS 5.5 0.2 + - - -
668Q MG 3.9 13.7 - - - -
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Residues in contact with VAL 325 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324Q ASP* 1.3 80.9 + - - +
326Q SER* 1.3 72.0 + - - +
327Q ASP 3.7 0.7 + - - -
328Q HIS* 4.1 6.7 + - + -
406Q MET* 3.2 30.7 - - + -
410Q TYR* 3.2 16.4 - - + +
453Q ASP* 3.6 23.3 + - + +
486Q MET* 4.1 31.2 - - + -
487Q LYS 3.7 11.2 - - - +
488Q ILE* 3.9 6.7 - - + -
667Q GTP 4.0 0.9 + - - -
668Q 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