Contacts of the strand formed by residues 446 - 451 (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 ILE 446 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411R LEU* 3.9 23.6 - - + -
414R GLN* 3.8 27.8 - - + +
415R LEU* 4.3 6.7 - - + -
418R THR* 4.0 5.6 - - - +
419R ALA* 4.6 3.4 - - + -
422R LEU* 4.0 25.8 - - + -
435R PHE* 4.7 2.2 - - + -
439R TYR* 3.1 25.5 - - + -
444R GLU* 3.6 11.0 + - + +
445R GLU* 1.3 80.5 - - + +
447R ARG* 1.3 69.3 + - - +
458R GLY 3.5 2.9 - - - -
459R TRP* 3.4 34.3 - - + +
464R ALA* 3.9 15.0 - - + -
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Residues in contact with ARG 447 (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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300R TYR* 3.2 39.5 + - + +
313R LYS 5.0 0.2 + - - -
316R GLU* 4.2 20.8 + - - +
317R TRP* 3.6 25.5 - - + +
414R GLN* 3.4 9.2 + - - +
439R TYR* 3.9 10.5 - - - +
442R GLY* 2.9 31.6 + - - +
443R HIS* 5.1 1.8 - - - +
444R GLU 3.1 16.1 + - - +
445R GLU 4.7 1.1 - - - -
446R ILE* 1.3 82.9 - - - +
448R GLN* 1.3 61.8 + - - +
457R LEU* 3.5 0.5 - - - -
458R GLY 2.7 36.4 + - - +
460R THR* 3.7 22.0 - - + +
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Residues in contact with GLN 448 (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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300R TYR* 4.0 1.6 - - - -
301R THR* 2.7 46.3 - - + +
302R PHE* 4.1 6.9 - - - -
317R TRP* 4.5 2.5 - - - -
407R SER* 2.6 48.9 + - - +
410R TYR* 3.6 13.1 - - - +
439R TYR* 3.4 23.2 + - + +
440R TRP* 5.2 0.2 - - + -
447R ARG* 1.3 80.3 - - - +
449R ILE* 1.3 64.5 + - - +
450R SER* 2.9 27.5 + - - -
455R ALA* 5.5 0.2 - - + -
456R MET 3.2 7.2 - - - -
457R LEU* 3.6 17.5 - - + -
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Residues in contact with ILE 449 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300R TYR* 3.5 22.4 - - + +
301R THR 3.4 4.9 - - - -
304R HIS* 3.7 11.7 - - + +
310R LYS* 5.3 4.7 - - + +
313R LYS* 3.9 19.1 - - + -
314R VAL* 3.8 21.5 - - + -
317R TRP* 4.0 12.8 - - + -
448R GLN* 1.3 74.4 - - - +
450R SER* 1.3 61.3 + - - +
455R ALA* 3.1 3.6 - - - +
456R MET* 2.9 49.6 + - + +
496R PHE* 3.3 27.6 - - + -
514R PHE* 4.8 3.1 - - + -
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Residues in contact with SER 450 (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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301R THR 2.7 17.2 + - - +
302R PHE* 3.8 21.1 - - - +
304R HIS* 3.3 17.2 + - - -
403R THR* 4.9 2.3 - - - +
407R SER* 4.4 5.0 + - - -
410R TYR* 4.8 2.0 - - - -
448R GLN* 2.9 28.4 + - - -
449R ILE* 1.3 76.7 - - - +
451R LYS* 1.3 65.5 + - - +
452R SER 4.7 5.1 + - - -
454R ASP 3.3 4.9 - - - -
455R ALA* 3.2 21.3 - - - -
496R PHE* 3.6 4.3 - - - -
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Residues in contact with LYS 451 (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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295R TYR* 3.1 29.9 + - + +
302R PHE 5.3 6.3 - - - +
304R HIS* 5.6 0.4 - - + -
399R ASP* 5.1 15.7 + - - -
403R THR* 4.2 7.0 - - - +
450R SER* 1.3 78.2 - - - +
452R SER* 1.3 78.4 + - - +
453R ASP* 4.2 0.5 - - - +
454R ASP* 2.8 23.4 + - + +
497R LEU* 4.1 32.3 - - + -
630R TYR* 3.1 38.6 + - + +
631R LYS 5.3 1.6 - - - -
632R TRP 5.2 5.5 + - - -
633R THR* 6.3 0.6 - - - -
666R GTP 6.2 0.2 - - - +
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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