Contacts of the helix formed by residues 69 - 73 (chain i) in PDB entry 3J7Y
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 HIS 69 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1886A G 3.6 56.8 + + - +
1887A A 5.5 2.2 - - - -
162F TYR* 4.0 11.2 + - - -
164F MET* 3.9 33.9 - - + +
60i ILE* 4.6 0.9 - - - -
68i LYS* 1.3 75.6 - - - +
70i PRO* 1.4 76.0 - - - +
71i LYS* 3.5 28.0 + - + +
72i GLU* 2.8 42.7 + - - +
73i LEU* 4.0 1.9 + - - +
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Residues in contact with PRO 70 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1886A G 3.4 25.4 - - - +
102F TRP* 4.6 6.3 - - + -
106F PHE* 3.4 28.3 - - + -
164F MET* 4.3 7.4 - - + -
170F ARG* 3.9 13.0 - - - +
59i ASN* 4.8 10.5 - - - +
60i ILE* 4.2 11.2 - - + +
61i GLY 4.1 7.0 - - - +
68i LYS 3.6 7.6 - - - +
69i HIS* 1.4 88.9 - - + +
71i LYS* 1.3 57.5 + - - +
72i GLU 3.2 0.4 - - - -
73i LEU* 3.1 35.0 + - + +
74i ILE* 4.1 1.4 + - - +
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Residues in contact with LYS 71 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1737A A 5.4 10.7 + - - -
106F PHE* 4.7 0.2 - - - -
162F TYR* 3.3 36.7 - - + +
69i HIS* 3.1 32.3 + - + +
70i PRO* 1.3 75.7 - - - +
72i GLU* 1.3 67.4 + - + +
73i LEU 3.3 0.2 - - - -
74i ILE* 3.2 30.4 - - - +
81i ARG* 4.6 14.0 + - - +
82i GLY* 4.2 18.8 + - - +
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Residues in contact with GLU 72 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67i GLU 5.1 0.2 - - - +
68i LYS* 3.3 36.6 + - - +
69i HIS* 2.8 43.2 + - - +
71i LYS* 1.3 86.1 - - + +
73i LEU* 1.3 62.2 + - - +
74i ILE 3.3 4.3 - - - +
81i ARG* 6.2 0.2 - - - -
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Residues in contact with LEU 73 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F PHE* 5.0 6.3 - - + -
107F LYS* 5.2 10.2 - - - +
56i VAL 5.2 0.9 - - - +
57i TYR* 4.3 17.7 - - + -
58i ASP* 4.5 15.7 - - + +
60i ILE* 4.1 17.0 - - + -
68i LYS* 3.7 28.5 - - + +
69i HIS 4.0 9.6 - - - +
70i PRO* 3.1 17.0 + - + +
72i GLU* 1.3 78.8 - - - +
74i ILE* 1.3 63.9 + - + +
75i ARG* 3.6 12.5 + - - +
28q ARG* 4.2 21.8 - - - +
31q PRO* 4.3 11.0 - - + -
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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