Contacts of the helix formed by residues 28 - 32 (chain X) in PDB entry 3HI6
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 THR 28 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H SER* 3.2 43.5 + - - +
76H LYS* 3.9 4.5 - - - +
27X PHE* 1.3 62.9 - - - +
29X PHE* 1.3 63.8 + - - +
30X SER* 3.2 13.0 - - - +
31X ARG* 2.9 42.2 + - + +
32X TYR* 3.2 13.9 - - - -
221X SO4 2.4 40.6 + - - -
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Residues in contact with PHE 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H SER 4.6 0.2 + - - -
4X LEU* 5.1 0.7 - - + -
22X CYS 5.1 0.9 - - - -
24X ALA* 3.4 29.8 - - + -
27X PHE* 2.8 20.3 + + - +
28X THR* 1.3 70.9 - - - +
30X SER* 1.3 58.6 + - - +
31X ARG 3.1 1.9 + - - -
32X TYR* 3.1 11.8 + - - +
34X MET* 3.6 38.1 - - + -
72X ARG* 2.9 31.8 + - + -
73X ASP 4.3 1.3 - - - -
74X ASN* 3.2 23.3 - - - -
77X ASN* 3.5 49.8 - - + +
78X THR 3.6 26.2 - - - -
79X LEU* 4.1 9.6 - - + -
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Residues in contact with SER 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B GLU* 3.2 15.7 - - - +
28X THR* 3.8 14.9 - - - +
29X PHE* 1.3 78.0 - - - +
31X ARG* 1.3 59.8 + - - +
32X TYR 3.4 0.4 - - - -
53X PRO* 3.2 22.7 - - - +
72X ARG* 4.0 1.1 - - - +
74X ASN* 3.7 37.7 - - - -
77X ASN* 4.8 1.7 + - - -
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Residues in contact with ARG 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B GLU* 3.6 41.1 + - - +
242B ALA 2.9 26.3 + - - -
243B THR 4.7 4.8 + - - -
244B ASP 5.3 1.6 + - - -
269B GLU* 4.3 15.8 + - + +
273B THR* 4.5 6.5 + - - -
28X THR* 2.9 36.8 + - + +
30X SER* 1.3 78.5 + - - +
32X TYR* 1.3 58.6 + - + +
53X PRO* 3.4 15.8 - - - +
102X PHE* 3.6 42.3 - - + +
103X TRP* 4.4 2.4 - - - -
221X SO4 5.0 2.3 + - - -
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Residues in contact with TYR 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B THR* 5.8 2.3 - - - +
27X PHE* 3.6 26.0 - + + -
28X THR 3.2 21.5 - - - -
29X PHE 3.1 6.4 + - - +
30X SER 3.4 0.4 - - - -
31X ARG* 1.3 80.2 - - - +
33X VAL* 1.3 66.9 + - - +
34X MET* 3.8 11.3 - - - +
53X PRO* 3.7 4.4 - - - +
72X ARG* 2.9 30.1 + - - -
98X SER* 4.1 8.7 - - - -
99X SER 3.1 28.7 - - - -
101X ASP* 4.8 2.2 - - - -
102X PHE* 3.5 33.1 - + - -
108X ASP* 4.4 16.0 + - - -
109X ILE* 6.4 0.2 - - + -
221X SO4 2.7 34.4 + - - -
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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