Contacts of the helix formed by residues 76 - 85 (chain C) in PDB entry 1JPL
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 76 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C CYS* 3.7 25.6 - - - -
36C ILE* 4.1 13.2 - - + -
37C ASN* 3.3 26.5 + - - +
43C PRO* 6.1 0.2 - - + -
72C CYS* 2.8 37.9 + - - +
75C ASN* 1.3 76.0 - - - +
77C GLY* 1.3 66.7 + - - +
79C ARG* 4.0 11.4 - - - +
80C PHE* 3.5 26.3 + - + +
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Residues in contact with GLY 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C CYS 4.3 1.6 + - - -
73C MSE 4.6 1.6 + - - -
74C LYS 5.1 0.6 - - - -
75C ASN 3.5 3.4 + - - +
76C CYS* 1.3 77.6 - - - +
78C ARG* 1.3 66.0 + - - -
80C PHE* 3.0 6.6 + - - +
81C HIS* 2.9 40.4 + - - -
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Residues in contact with ARG 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C GLY* 1.3 69.2 - - - -
79C ARG* 1.3 65.8 + - + +
81C HIS* 2.9 27.6 + - - -
82C ASN* 2.9 42.3 + - - +
127C GLU* 2.8 34.3 + - - +
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Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 2.7 28.3 + - - +
37C ASN* 3.8 18.3 + - - +
39C GLU 2.6 23.4 + - - -
40C LEU* 3.0 17.8 + - - +
43C PRO* 3.0 36.3 - - + +
44C GLN* 4.8 0.2 + - - -
76C CYS 4.0 10.1 - - - +
78C ARG* 1.3 79.5 - - - +
80C PHE* 1.3 60.5 + - - +
82C ASN* 3.7 10.3 + - - +
83C GLU* 3.7 23.4 + - - +
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Residues in contact with PHE 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 4.1 7.2 - - + -
43C PRO* 4.1 18.4 - - + -
46C ALA* 3.9 24.7 - - + -
47C VAL* 4.0 15.5 - - + -
50C LEU* 3.8 18.6 - - + -
69C LEU* 4.1 5.8 - - + -
72C CYS* 3.3 37.9 - - + +
73C MSE 3.8 17.5 - - - -
76C CYS* 3.5 28.2 + - + -
77C GLY 3.0 8.5 + - - +
79C ARG* 1.3 77.9 - - + +
81C HIS* 1.3 65.9 + - - +
82C ASN 3.1 2.0 - - - -
83C GLU* 3.1 12.1 + - - +
84C VAL* 3.2 26.5 + - + +
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Residues in contact with HIS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C CYS 5.0 0.2 - - - -
73C MSE 2.8 59.8 + - + +
77C GLY* 2.9 36.2 + - - -
78C ARG* 2.9 22.3 + - - +
80C PHE* 1.3 73.3 - - + +
82C ASN* 1.3 57.5 + - - +
84C VAL* 3.4 2.3 + - - +
85C GLY* 2.9 26.2 + - - -
125C LEU* 4.0 28.1 - - + +
127C GLU* 5.3 3.1 - - - +
128C GLU* 3.7 17.9 - - + +
131C ILE* 5.4 0.3 - - - +
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Residues in contact with ASN 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ARG* 2.9 48.7 + - - +
79C ARG* 3.9 9.2 - - - +
81C HIS* 1.3 78.7 - - - +
83C GLU* 1.3 65.6 + - - +
85C GLY 3.5 6.2 + - - +
86C LYS* 3.3 28.3 + - - +
127C GLU* 3.9 5.4 - - - +
128C GLU* 3.3 20.3 - - - +
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Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PRO* 3.6 31.4 - - + +
44C GLN* 3.5 31.0 - - - +
47C VAL* 3.7 27.3 - - + +
79C ARG 3.7 6.1 - - - +
80C PHE 3.1 5.8 + - - +
82C ASN* 1.3 77.9 - - - +
84C VAL* 1.3 65.0 + - - +
85C GLY 3.2 0.4 + - - -
86C LYS* 3.5 38.6 + - - +
88C ARG* 4.6 7.8 + - - -
89C PHE* 3.7 11.6 - - - +
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 3.9 11.2 - - + -
69C LEU* 4.3 3.8 - - + -
73C MSE 3.8 15.9 - - + -
80C PHE* 3.2 36.4 + - + +
81C HIS 3.8 6.3 - - - +
83C GLU* 1.3 75.8 - - - +
85C GLY* 1.3 57.3 + - - +
86C LYS 2.9 8.9 + - - +
89C PHE* 3.4 32.9 - - + -
90C LEU* 2.9 28.1 - - + +
121C TRP* 3.7 28.7 - - + -
131C ILE* 4.5 3.6 - - + -
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Residues in contact with GLY 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C HIS 2.9 11.4 + - - -
82C ASN 3.9 2.4 - - - +
83C GLU 3.2 0.8 - - - -
84C VAL* 1.3 75.3 - - - +
86C LYS* 1.3 61.2 + - - +
90C LEU* 4.1 5.4 - - - -
128C GLU* 3.6 25.4 - - - +
130C LYS* 3.2 23.4 - - - +
131C ILE* 4.1 17.9 - - - +
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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