Contacts of the helix formed by residues 47 - 52 (chain Q) in PDB entry 3H1J
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 ALA 47 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Q VAL* 1.3 77.7 - - - +
48Q PHE* 1.3 55.0 + - - +
49Q ARG* 3.0 18.8 - - + +
50Q ASN* 2.7 46.9 + - - +
51Q LEU 3.8 1.4 + - - -
87Q ILE 4.1 0.4 - - - +
88Q SER 4.0 8.1 - - - +
89Q ASP 3.0 25.8 - - - +
90Q TYR* 3.8 12.1 - - + +
91Q PHE* 3.8 6.8 - - - -
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Residues in contact with PHE 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q PHE* 5.3 4.9 - + - -
34Q LYS* 5.5 2.9 - - - -
47Q ALA* 1.3 73.0 - - - +
49Q ARG* 1.3 62.1 + - - +
51Q LEU* 3.3 25.2 + - + +
61Q ALA* 3.5 25.0 - - - +
64Q LEU* 3.3 35.7 - - + -
65Q ALA* 3.4 24.2 - - + -
68Q VAL* 4.0 13.7 - - + -
85Q GLY* 6.4 0.2 - - - -
86Q LYS 4.4 3.1 - - - -
87Q ILE* 3.9 13.0 - - - +
89Q ASP* 3.4 18.3 + - + -
90Q TYR 3.7 16.2 - - - -
91Q PHE* 3.6 33.0 - + - -
92Q PRO* 4.0 14.8 - - + -
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Residues in contact with ARG 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P ARG 5.5 0.4 + - - -
73P ASN* 3.0 23.4 + - - -
47Q ALA* 3.0 13.4 + - + +
48Q PHE* 1.3 77.1 - - - +
50Q ASN* 1.3 84.9 + - - +
52Q ILE* 3.0 35.6 + - + +
87Q ILE* 2.9 33.8 + - + +
88Q SER* 4.4 15.1 + - - +
90Q TYR* 3.1 25.1 + - - -
66R ALA* 3.5 38.7 + - - +
67R ASP* 3.3 13.9 + - - +
69R LEU* 5.9 4.2 - - - +
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Residues in contact with ASN 50 (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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72P ARG* 5.3 7.2 - - - +
73P ASN* 5.4 0.9 + - - +
45Q TYR 4.3 4.2 + - - -
46Q VAL* 3.6 21.5 - - + +
47Q ALA* 2.7 44.7 + - - +
49Q ARG* 1.3 99.6 + - - +
51Q LEU* 1.3 57.8 + - - +
52Q ILE 3.8 2.1 - - - +
54Q VAL* 3.4 21.0 - - - +
90Q TYR* 5.1 1.0 - - - -
192Q TRP* 3.5 15.0 - - + -
196Q PRO* 5.8 5.3 - - + +
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Residues in contact with LEU 51 (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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30Q PHE* 3.8 40.6 - - + -
48Q PHE* 3.5 20.6 - - + +
49Q ARG 3.1 0.4 - - - -
50Q ASN* 1.3 76.4 - - - +
52Q ILE* 1.3 66.7 + - - +
53Q GLY 3.3 0.2 + - - -
54Q VAL* 2.8 17.1 + - - +
55Q THR* 3.0 31.5 + - + +
56Q HIS* 3.3 24.8 + - + +
61Q ALA* 4.7 2.9 - - + -
64Q LEU* 3.9 16.6 - - + -
91Q PHE* 4.1 19.3 - - + -
189Q PHE* 4.7 3.1 - - + -
192Q TRP* 4.4 18.2 - - + -
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Residues in contact with ILE 52 (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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48Q PHE 3.8 1.1 - - - +
49Q ARG* 3.0 29.3 + - + +
50Q ASN 3.8 2.4 - - - +
51Q LEU* 1.3 79.5 - - - +
53Q GLY* 1.3 63.1 + - - +
54Q VAL* 3.0 10.0 + - - +
56Q HIS 3.3 7.6 - - - -
58Q GLU* 3.9 37.2 - - + +
61Q ALA* 3.4 26.9 - - + +
87Q ILE* 3.9 23.6 - - + -
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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