Contacts of the helix formed by residues 333 - 347 (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 PRO 333 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109R ARG* 3.7 22.7 - - - +
331R PHE 2.9 6.8 - - - +
332R TRP* 1.3 97.7 - - + +
334R GLY* 1.3 68.2 + - - +
335R TRP* 3.1 38.4 - - + +
336R LEU* 2.9 34.7 + - + +
337R ARG 3.6 0.2 + - - -
405R LEU* 4.0 25.6 - - + -
486R MET* 4.4 0.9 - - - -
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Residues in contact with GLY 334 (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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105R ASN* 5.0 4.0 + - - +
106R LEU* 5.5 5.0 - - - +
109R ARG* 5.4 0.4 - - - +
332R TRP* 3.6 7.6 + - - -
333R PRO* 1.3 72.5 - - - +
335R TRP* 1.3 63.2 + - - +
337R ARG* 2.9 37.1 + - - +
338R ASP* 3.1 9.6 + - - +
388R GLU* 3.2 26.6 + - - -
390R GLY* 6.2 0.9 - - - -
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Residues in contact with TRP 335 (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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106R LEU* 6.2 2.8 - - + +
109R ARG* 3.9 5.3 - - - +
115R ALA 3.1 18.6 + - - -
116R ASP* 3.2 30.3 - - + +
117R GLY* 3.3 17.7 - - - +
118R PRO* 3.8 23.3 - - + -
127R PHE* 3.7 29.2 - + - -
333R PRO* 3.0 35.4 - - + +
334R GLY* 1.3 77.9 - - - +
336R LEU* 1.3 90.1 + - + +
338R ASP* 3.2 10.7 + - - +
339R LEU* 2.8 35.4 + - + +
405R LEU* 5.2 1.3 - - + -
485R TYR* 3.7 27.1 - + + -
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Residues in contact with LEU 336 (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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127R PHE* 4.0 25.6 - - + -
332R TRP* 4.0 13.9 - - + +
333R PRO* 2.9 23.2 + - + +
335R TRP* 1.3 96.4 - - + +
337R ARG* 1.3 57.7 + - - +
339R LEU* 4.2 8.5 - - + -
340R ILE* 2.9 54.9 + - + +
404R LEU* 4.2 8.1 - - + -
405R LEU* 3.4 50.9 - - + +
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Residues in contact with ARG 337 (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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332R TRP* 3.8 26.2 - - + -
333R PRO 3.6 2.2 + - - -
334R GLY* 2.9 20.3 + - - +
336R LEU* 1.3 80.9 - - - +
338R ASP* 1.3 91.8 + - - +
340R ILE* 3.4 4.9 + - - +
341R CYS* 2.9 37.6 + - - -
357R PHE* 5.3 2.1 - - + -
358R GLU* 3.7 14.6 - - - +
361R LEU* 3.1 49.5 + - + -
362R LYS* 3.8 23.9 - - - +
387R LEU 4.0 0.8 + - - -
388R GLU* 2.8 40.7 + - - +
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Residues in contact with ASP 338 (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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334R GLY 3.1 6.9 + - - +
335R TRP* 3.7 9.3 - - - +
337R ARG* 1.3 112.9 + - - +
339R LEU* 1.3 59.0 + - - +
341R CYS* 3.4 6.4 + - - +
342R ASP* 2.9 29.6 + - - +
358R GLU* 4.4 8.1 - - - +
362R LYS* 3.9 10.9 + - - -
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Residues in contact with LEU 339 (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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118R PRO* 3.7 30.3 - - + -
124R ASN* 3.9 9.0 - - - +
127R PHE* 3.9 26.9 - - + -
128R ARG* 3.5 43.1 + - + +
131R VAL* 4.7 0.4 - - + -
335R TRP* 2.8 30.6 + - + +
336R LEU* 3.6 7.0 - - + +
338R ASP* 1.3 70.7 - - - +
340R ILE* 1.3 68.9 + - + +
342R ASP* 3.1 7.6 + - - +
343R GLU* 2.8 27.7 + - + -
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Residues in contact with ILE 340 (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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131R VAL* 3.8 28.2 - - + +
135R PHE* 5.1 5.6 - - + -
332R TRP* 4.6 1.3 - - + -
336R LEU* 2.9 51.4 + - + +
337R ARG* 3.6 4.0 - - - +
339R LEU* 1.3 76.8 - - + +
341R CYS* 1.3 63.0 + - - +
343R GLU* 3.3 2.1 + - - +
344R LEU* 2.9 41.0 + - + +
357R PHE* 4.4 13.9 - - + -
401R MET* 3.9 26.5 - - + -
404R LEU* 3.9 22.0 - - + -
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Residues in contact with CYS 341 (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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337R ARG* 2.9 22.3 + - - +
338R ASP* 3.6 7.6 - - - +
340R ILE* 1.3 77.8 - - - +
342R ASP* 1.3 63.0 + - - +
344R LEU* 3.2 5.8 + - - +
345R LEU* 3.0 31.0 + - + +
354R VAL* 3.5 21.8 - - + +
357R PHE* 4.0 15.7 - - - -
358R GLU* 3.5 44.6 - - + +
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Residues in contact with ASP 342 (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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128R ARG* 2.9 32.9 + - - +
338R ASP 2.9 14.2 + - - +
339R LEU* 3.5 7.9 - - - +
341R CYS* 1.3 76.3 - - - +
343R GLU* 1.3 62.1 + - - +
345R LEU* 3.1 16.7 + - - +
346R ASN* 3.0 32.1 + - - +
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Residues in contact with GLU 343 (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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128R ARG* 2.6 70.5 + - + +
131R VAL* 3.9 17.5 - - + -
132R ARG* 2.2 42.7 + - + +
339R LEU 2.8 19.2 + - - +
340R ILE 3.8 3.8 - - - +
342R ASP* 1.3 74.5 - - - +
344R LEU* 1.3 57.7 + - - +
346R ASN* 3.2 12.0 + - - +
347R MET* 2.8 33.1 + - + +
429R MET* 4.0 4.3 - - - +
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Residues in contact with LEU 344 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131R VAL* 3.9 11.0 - - + -
135R PHE* 3.6 41.1 - - + -
340R ILE* 2.9 34.5 + - + +
341R CYS* 3.5 8.5 - - - +
343R GLU* 1.3 73.5 - - - +
345R LEU* 1.3 67.3 + - - +
347R MET* 3.3 4.9 + - - -
348R GLY 3.2 5.0 + - - -
349R TYR* 3.0 53.9 + - + +
353R TRP* 4.1 23.6 - - + -
354R VAL* 4.3 7.6 - - + -
357R PHE* 4.9 6.5 - - + -
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Residues in contact with LEU 345 (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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341R CYS* 3.0 22.1 + - + +
342R ASP* 3.4 17.5 - - - +
344R LEU* 1.3 75.6 - - - +
346R ASN* 1.3 57.8 + - - +
348R GLY* 2.7 27.4 + - - -
349R TYR 3.8 9.5 + - - +
351R PRO* 3.8 27.4 - - + -
354R VAL* 3.7 26.9 - - + -
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Residues in contact with ASN 346 (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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128R ARG* 3.7 2.2 - - - +
132R ARG* 4.0 15.4 + - - +
342R ASP* 3.0 36.8 + - - +
343R GLU* 3.2 26.0 + - - +
345R LEU* 1.3 77.8 - - - +
347R MET* 1.3 59.3 + - - +
348R GLY* 2.8 7.6 + - - -
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Residues in contact with MET 347 (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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131R VAL* 3.8 22.2 - - - +
132R ARG* 3.3 65.4 + - + +
135R PHE* 3.6 34.5 - - + +
136R SER* 4.2 7.0 - - - +
343R GLU 2.8 21.5 + - - +
344R LEU* 3.6 11.9 - - - +
345R LEU 3.3 0.2 - - - -
346R ASN* 1.3 70.3 - - - +
348R GLY* 1.3 58.5 + - - +
349R TYR* 4.1 8.1 - - + -
663R PRO* 3.2 20.9 - - + +
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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