Contacts of the helix formed by residues 67 - 72 (chain B) in PDB entry 3HN3
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 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B TRP 4.8 0.2 - - - +
66B ARG* 1.3 99.4 - - + +
68B LEU* 1.3 66.4 + - - +
69B TRP* 3.2 26.9 - - + +
70B GLU* 3.0 34.4 + - + +
71B SER* 4.2 1.2 + - - -
102B GLU* 3.4 11.2 - - - +
104B GLU* 4.2 11.7 - - - +
167B ARG* 3.9 20.2 - - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 4.2 16.8 - - - +
47B PHE 4.3 1.6 - - - +
48B ARG* 2.5 47.4 + - + +
63B TRP* 4.2 20.2 - - + +
66B ARG 3.2 4.7 + - - -
67B PRO* 1.3 70.8 - - - +
69B TRP* 1.3 56.0 + - - +
71B SER* 2.9 12.1 + - - -
74B THR* 3.9 20.6 - - + -
100B TRP* 3.8 45.1 - - + +
101B TYR 4.7 0.2 - - - -
102B GLU* 2.8 33.8 + - + +
169B THR* 5.0 3.6 - - + -
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Residues in contact with TRP 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 6.1 0.8 - - - -
67B PRO* 3.7 24.2 - - + +
68B LEU* 1.3 77.8 - - - +
70B GLU* 1.3 88.7 + - + +
72B GLY* 3.0 25.3 + - - +
74B THR* 4.1 16.7 - - + +
102B GLU* 5.6 0.7 - - - -
265E ALA 5.6 2.0 - - - -
266E GLU* 3.8 42.8 - - + -
267E ASN* 5.6 3.6 - - - -
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ARG* 3.1 57.1 + - + +
67B PRO* 3.0 22.0 + - + +
69B TRP* 1.3 116.1 - - + +
71B SER* 1.3 58.0 + - - +
72B GLY 3.3 0.9 + - - -
266E GLU* 5.6 0.7 - - - +
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ARG* 2.9 28.3 + - - -
57B ARG* 5.6 3.3 + - - -
61B GLU* 4.9 5.5 - - - +
63B TRP* 3.4 43.5 + - - +
67B PRO 4.9 0.6 + - - -
68B LEU* 2.9 10.7 + - - -
69B TRP 3.2 0.4 - - - -
70B GLU* 1.3 78.3 - - - +
72B GLY* 1.3 55.7 + - - +
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ARG* 2.8 18.5 + - - +
69B TRP* 3.0 21.6 + - - +
70B GLU 3.3 1.8 + - - -
71B SER* 1.3 79.3 - - - +
73B PRO* 1.3 75.0 - - - +
74B THR 3.6 0.7 + - - -
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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