Contacts of the helix formed by residues 70 - 76 (chain r) 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 CYS 70 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68r GLY 3.5 1.4 + - - -
69r GLN* 1.3 78.9 - - - +
71r PRO* 1.3 72.6 - - + +
72r ILE* 4.1 5.2 - - - +
73r CYS* 2.3 33.0 - - - +
74r ARG* 2.7 42.2 + - - +
106r GLY 3.5 6.5 - - - +
107r LEU* 4.0 2.9 - - + -
108r CYS* 3.5 21.3 - - + +
200r ZN 2.1 40.8 - - - -
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Residues in contact with PRO 71 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K LEU* 3.6 34.6 - - + +
170K TRP* 3.8 13.7 - - + -
70r CYS* 1.3 84.0 - - - +
72r ILE* 1.3 56.5 + - - +
74r ARG* 3.8 12.8 - - - +
75r TRP* 2.7 32.7 - - - -
92r PHE* 3.9 8.7 - - + -
105r THR 3.5 17.0 - - - +
106r GLY 3.2 17.5 - - - +
107r LEU* 3.4 24.7 - - + -
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Residues in contact with ILE 72 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K LEU* 5.1 0.4 - - + -
70r CYS* 3.3 2.7 - - - -
71r PRO* 1.3 75.5 - - - +
73r CYS* 1.3 66.9 + - - +
74r ARG 3.4 0.2 + - - -
75r TRP 3.6 1.2 + - - -
76r ASN 3.3 16.5 + - - -
77r LEU* 3.3 47.0 + - + +
78r LYS* 4.1 0.7 - - - +
81r TYR* 3.6 9.0 - - + -
88r LEU* 5.1 2.5 - - + -
92r PHE* 4.4 11.2 - - + -
107r LEU* 4.1 7.9 - - + -
111r GLU* 2.9 60.6 - - + +
115r ILE* 2.9 33.2 - - + -
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Residues in contact with CYS 73 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I CYS* 3.1 43.1 - - - -
65r ASN* 3.1 11.4 - - - +
68r GLY* 4.0 6.1 - - - -
69r GLN 3.9 11.2 - - - -
70r CYS* 2.3 42.3 - - - +
72r ILE* 1.3 80.1 - - - +
74r ARG* 1.3 63.5 + - - +
76r ASN* 3.5 9.4 + - - +
78r LYS* 4.0 18.3 - - - -
200r ZN 2.6 9.6 - - - -
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Residues in contact with ARG 74 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K LEU 3.5 10.7 + - - -
170K TRP* 5.2 3.4 - - - +
59r GLU* 2.8 29.2 + - - -
63r PRO* 4.2 17.6 - - + +
64r PRO* 4.6 0.9 - - - -
65r ASN* 2.6 56.0 + - - +
66r PRO* 5.1 3.8 - - - -
67r SER 5.2 1.1 - - - +
68r GLY* 4.0 29.2 + - - +
69r GLN 4.7 2.0 + - - -
70r CYS* 2.7 30.4 + - - +
71r PRO* 3.8 23.2 - - - +
72r ILE 3.3 0.2 - - - -
73r CYS* 1.3 76.5 - - - +
75r TRP* 1.3 69.2 + - + +
105r THR 5.6 0.6 + - - -
106r GLY 5.5 0.2 + - - -
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Residues in contact with TRP 75 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K PRO* 3.9 12.3 - - + -
169K LEU* 3.1 31.7 + - + +
50S TYR* 2.7 28.7 - + - +
52S PRO* 4.3 15.7 - - + -
59r GLU* 4.0 5.8 - - - -
60r SER* 2.7 41.5 - - - -
61r PRO* 5.1 1.1 - - + -
62r ASN 4.3 7.6 - - - -
63r PRO* 4.0 29.6 - - + +
64r PRO* 3.2 30.4 - - + +
71r PRO 2.7 29.6 + - - +
72r ILE 3.6 0.4 + - - -
73r CYS 3.4 0.4 - - - -
74r ARG* 1.3 79.2 - - + +
76r ASN* 1.3 80.0 + - - +
77r LEU* 4.0 21.8 - - + -
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Residues in contact with ASN 76 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S GLY* 3.9 12.1 - - - +
50S TYR 3.4 25.7 + - - +
51S VAL* 3.3 25.8 - - + +
64r PRO* 4.0 7.1 - - - +
65r ASN* 3.5 15.7 - - - +
72r ILE 3.3 4.2 + - - -
73r CYS 3.5 8.5 + - - +
74r ARG 3.4 9.0 - - - +
75r TRP* 1.3 92.4 + - - +
77r LEU* 1.3 65.2 + - - +
78r LYS* 3.6 14.0 + - - +
80r LYS* 4.2 8.8 - - - +
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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
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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