Contacts of the helix formed by residues 333 - 347 (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 PRO 333 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109P ARG* 3.7 22.9 - - - +
331P PHE 2.9 7.7 - - - +
332P TRP* 1.3 98.0 - - + +
334P GLY* 1.3 66.7 + - - +
335P TRP* 3.1 37.0 - - + +
336P LEU* 2.9 34.5 + - + +
337P ARG 3.6 0.2 + - - -
405P LEU* 4.0 26.7 - - + -
485P TYR* 6.5 0.2 - - + -
486P MET* 4.4 0.9 - - - -
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Residues in contact with GLY 334 (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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105P ASN* 5.0 4.2 + - - -
106P LEU* 5.5 4.2 - - - +
109P ARG* 5.4 0.8 - - - +
332P TRP* 3.6 7.6 + - - -
333P PRO* 1.3 72.7 - - - +
335P TRP* 1.3 63.2 + - - +
337P ARG* 2.9 38.2 + - - +
338P ASP* 3.1 10.4 + - - +
388P GLU* 3.2 25.7 + - - -
390P GLY* 6.2 0.9 - - - -
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Residues in contact with TRP 335 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106P LEU* 6.2 2.2 - - + +
109P ARG* 3.9 5.1 - - - +
115P ALA 3.1 18.8 + - - -
116P ASP* 3.2 30.1 - - + +
117P GLY* 3.3 17.4 - - - +
118P PRO* 3.8 24.9 - - + -
127P PHE* 3.7 29.2 - + - -
333P PRO* 3.0 35.1 - - + +
334P GLY* 1.3 78.1 - - - +
336P LEU* 1.3 91.6 + - + +
338P ASP* 3.2 11.1 + - - +
339P LEU* 2.8 34.9 + - + +
405P LEU* 5.2 1.6 - - + -
485P TYR* 3.7 26.9 - + + -
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Residues in contact with LEU 336 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P PHE* 4.0 25.6 - - + -
332P TRP* 4.0 14.1 - - + +
333P PRO* 2.9 22.2 + - + +
335P TRP* 1.3 96.3 - - + +
337P ARG* 1.3 56.9 + - - +
339P LEU* 4.2 7.9 - - + -
340P ILE* 2.9 56.3 + - + +
404P LEU* 4.2 7.6 - - + -
405P LEU* 3.4 50.9 - - + +
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Residues in contact with ARG 337 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332P TRP* 3.8 26.2 - - + -
333P PRO 3.6 2.0 + - - -
334P GLY* 2.9 20.6 + - - +
336P LEU* 1.3 79.7 - - - +
338P ASP* 1.3 91.6 + - - +
340P ILE* 3.4 5.5 + - - +
341P CYS* 2.9 37.8 + - - -
357P PHE* 5.3 1.5 - - - -
358P GLU* 3.7 15.3 - - - +
361P LEU* 3.1 49.8 + - + -
362P LYS* 3.8 24.6 - - - +
387P LEU 4.0 1.0 + - - -
388P GLU* 2.8 39.4 + - - +
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Residues in contact with ASP 338 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334P GLY 3.1 6.9 + - - +
335P TRP* 3.2 8.8 + - - +
337P ARG* 1.3 112.2 + - - +
339P LEU* 1.3 59.4 + - - +
341P CYS* 3.4 6.5 + - - +
342P ASP* 2.9 29.3 + - - +
358P GLU* 4.4 8.3 - - - +
362P LYS* 3.9 10.2 + - - -
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Residues in contact with LEU 339 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P PRO* 3.7 31.0 - - + -
124P ASN* 3.9 8.7 - - - +
127P PHE* 3.9 27.1 - - + -
128P ARG* 3.5 42.9 + - + +
131P VAL* 4.7 0.9 - - + -
335P TRP* 2.8 30.4 + - + +
336P LEU* 3.6 6.7 - - + +
338P ASP* 1.3 72.9 - - - +
340P ILE* 1.3 66.5 + - + +
342P ASP* 3.1 7.4 + - - +
343P GLU* 2.8 28.1 + - + -
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Residues in contact with ILE 340 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131P VAL* 3.8 28.8 - - + +
135P PHE* 5.1 5.2 - - + -
332P TRP* 4.6 1.3 - - + -
336P LEU* 2.9 51.6 + - + +
337P ARG* 3.6 5.2 - - - +
339P LEU* 1.3 76.6 - - + +
341P CYS* 1.3 62.2 + - - +
343P GLU* 3.3 2.1 + - - +
344P LEU* 2.9 41.0 + - + +
357P PHE* 4.4 14.1 - - + -
401P MET* 3.9 27.4 - - + -
404P LEU* 3.9 21.5 - - + -
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Residues in contact with CYS 341 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337P ARG* 2.9 21.9 + - - +
338P ASP* 3.6 7.9 - - - +
340P ILE* 1.3 77.2 - - - +
342P ASP* 1.3 63.1 + - - +
344P LEU* 3.2 6.3 + - - +
345P LEU* 3.0 30.4 + - + +
354P VAL* 3.5 21.7 - - + +
357P PHE* 4.0 15.9 - - - -
358P GLU* 3.5 44.6 - - + +
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Residues in contact with ASP 342 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P ARG* 2.9 33.7 + - - +
338P ASP 2.9 14.4 + - - +
339P LEU* 3.1 8.0 + - - +
341P CYS* 1.3 75.6 - - - +
343P GLU* 1.3 62.6 + - - +
345P LEU* 3.1 17.0 + - - +
346P ASN* 3.0 33.2 + - - +
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Residues in contact with GLU 343 (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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128P ARG* 2.6 70.4 + - + +
131P VAL* 3.9 18.8 - - + -
132P ARG* 2.2 43.6 + - + +
339P LEU 2.8 19.8 + - - +
340P ILE 3.8 3.6 - - - +
342P ASP* 1.3 73.9 - - - +
344P LEU* 1.3 55.8 + - - +
346P ASN* 3.2 12.5 + - - +
347P MET* 2.8 33.8 + - + +
429P MET* 4.0 4.5 - - - +
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Residues in contact with LEU 344 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131P VAL* 3.9 11.4 - - + -
135P PHE* 3.6 41.3 - - + -
340P ILE* 2.9 35.4 + - + +
341P CYS* 3.5 8.7 - - - +
343P GLU* 1.3 73.8 - - - +
345P LEU* 1.3 66.5 + - - +
347P MET* 3.3 4.0 + - - -
348P GLY 3.2 5.5 + - - -
349P TYR* 3.0 54.4 + - + +
353P TRP* 4.1 23.8 - - + -
354P VAL* 4.3 7.4 - - + -
357P PHE* 4.9 6.5 - - + -
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Residues in contact with LEU 345 (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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341P CYS* 3.0 21.6 + - + +
342P ASP* 3.4 18.2 - - - +
344P LEU* 1.3 76.7 - - - +
346P ASN* 1.3 56.2 + - - +
348P GLY* 2.7 27.5 + - - -
349P TYR 3.8 7.8 + - - +
351P PRO* 3.8 28.0 - - + +
354P VAL* 3.7 27.4 - - + -
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Residues in contact with ASN 346 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P ARG* 3.7 2.4 - - - +
132P ARG* 4.0 15.9 + - - +
342P ASP* 3.0 36.2 + - - +
343P GLU* 3.2 26.6 + - - +
345P LEU* 1.3 79.3 - - - +
347P MET* 1.3 58.1 + - - +
348P GLY* 2.8 8.0 + - - -
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Residues in contact with MET 347 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131P VAL* 3.8 22.4 - - - +
132P ARG* 3.3 66.5 + - + +
135P PHE* 3.6 34.1 - - + +
136P SER* 4.2 7.2 - - - +
343P GLU 2.8 21.6 + - - +
344P LEU* 3.6 11.2 - - - +
345P LEU 3.3 0.4 - - - -
346P ASN* 1.3 70.2 - - - +
348P GLY* 1.3 57.8 + - - +
349P TYR* 4.1 8.3 - - + -
663P PRO* 3.2 20.8 - - + +
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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
------------------------------------------------------------
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