Contacts of the helix formed by residues 82 - 93 (chain C) in PDB entry 3O9Z
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 LEU 82 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLU* 3.8 27.6 - - + +
55B GLU* 3.7 31.0 - - - +
56B ALA* 5.7 0.2 - - + -
78C SER* 3.6 11.2 - - - +
79C PRO* 2.9 19.3 + - + +
81C HIS* 1.3 99.5 - - + +
83C HIS* 1.3 66.9 + - - +
84C TYR 3.4 0.9 - - - -
85C PRO* 3.3 13.2 - - + +
86C GLN* 3.0 28.6 + - - +
311C NAD 3.6 35.9 - - + +
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Residues in contact with HIS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ILE* 3.7 14.4 - - + +
78C SER* 2.8 36.1 + - - -
79C PRO 3.3 7.9 + - - -
80C ASN* 3.0 18.6 + - - +
82C LEU* 1.3 77.4 - - - +
84C TYR* 1.3 65.3 + - - +
86C GLN* 3.7 0.5 - - - +
87C ILE* 2.8 29.0 + - + +
99C SER* 3.2 9.4 + - - +
100C GLU* 3.1 27.7 + - + +
101C LYS 3.5 4.0 - - - -
102C PRO 2.7 22.1 + - - -
103C LEU 3.1 17.0 - - - +
104C VAL* 4.6 0.9 - - - -
311C NAD 2.8 20.5 + - - -
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Residues in contact with TYR 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA* 4.9 6.3 - - + -
80C ASN 4.5 1.0 + - - -
81C HIS 4.3 1.9 + - - +
83C HIS* 1.3 78.3 - - - +
85C PRO* 1.4 70.6 - - + +
87C ILE* 3.2 4.2 + - - +
88C ARG* 2.8 68.1 + - - +
104C VAL* 3.7 13.8 - - + +
105C LEU 5.6 0.2 - - - +
109C GLU* 3.5 61.0 - - + +
112C ARG* 2.9 46.3 + - + +
113C LEU* 3.8 20.6 - - + -
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Residues in contact with PRO 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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55B GLU* 3.5 40.8 - - + +
56B ALA* 3.9 15.5 - - + +
59B ALA* 4.5 6.9 - - + +
81C HIS 3.3 13.7 - - - +
82C LEU* 3.3 24.7 - - + +
84C TYR* 1.4 103.8 - - + +
86C GLN* 1.3 55.8 + - - -
88C ARG* 3.4 8.8 + - + +
89C MET* 3.0 24.8 + - - +
92C ARG* 4.7 2.9 + - - -
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU* 2.8 37.7 + - + +
7C THR* 2.8 22.1 + - - +
32C LEU* 3.9 8.7 - - - +
74C LEU* 3.5 12.5 - - + +
76C ILE* 3.6 17.4 - - + +
78C SER* 2.8 26.7 + - - -
82C LEU* 3.0 18.3 + - + +
83C HIS 3.9 0.2 - - - +
85C PRO* 1.3 75.2 - - - +
87C ILE* 1.3 61.1 + - - +
89C MET* 3.2 12.8 + - + +
90C ALA 3.0 22.3 + - - -
311C NAD 3.1 25.3 + - - -
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Residues in contact with ILE 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ILE* 3.5 19.7 - - + -
83C HIS 2.8 23.9 + - - +
84C TYR 3.6 3.4 - - - +
86C GLN* 1.3 71.7 - - - +
88C ARG* 1.3 65.8 + - - +
90C ALA* 3.2 6.7 + - - +
91C LEU* 3.0 23.6 + - + +
97C ALA* 4.1 10.8 - - + -
99C SER* 4.1 9.2 - - - -
103C LEU* 3.6 41.7 - - + +
104C VAL* 4.0 1.1 - - + -
113C LEU* 3.7 20.6 - - + -
124C VAL* 3.5 35.9 - - + -
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Residues in contact with ARG 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA* 3.5 25.3 + - + +
62B GLU* 3.1 34.6 + - - +
63B ASP* 2.9 36.3 + - - -
66B ASP* 4.7 3.6 + - - -
84C TYR* 2.8 56.8 + - + +
85C PRO* 3.5 10.1 - - + +
86C GLN 3.2 0.4 - - - -
87C ILE* 1.3 77.7 - - - +
89C MET* 1.3 62.5 + - - +
91C LEU* 3.4 6.4 + - - +
92C ARG* 3.0 36.4 + - - +
112C ARG* 4.7 1.0 - - - +
113C LEU* 4.0 9.6 - - + -
116C LEU* 3.7 30.9 - - + +
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Residues in contact with MET 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU* 4.1 24.7 - - + +
32C LEU* 5.5 1.6 - - + -
54C PRO* 4.5 5.8 - - + +
57C PHE* 4.0 28.5 - - + -
58C GLU* 3.7 43.7 - - + +
74C LEU* 4.8 7.2 - - - -
85C PRO 3.0 12.8 + - - +
86C GLN* 3.4 13.5 - - + +
87C ILE 3.2 0.4 - - - -
88C ARG* 1.3 76.8 - - - +
90C ALA* 1.3 64.0 + - - +
92C ARG* 3.3 20.5 + - - +
93C LEU* 3.0 45.1 + - + +
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Residues in contact with ALA 90 (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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74C LEU* 3.7 30.7 - - + +
86C GLN 3.0 11.0 + - - +
87C ILE 3.2 8.7 + - - +
89C MET* 1.3 73.8 - - - +
91C LEU* 1.3 64.2 + - + +
93C LEU* 3.1 14.6 + - - +
94C GLY 3.3 0.2 + - - -
95C ALA* 2.9 27.8 + - + +
96C ASN 4.0 13.5 - - - +
97C ALA* 4.1 12.6 - - + -
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ILE* 3.0 20.5 + - + +
88C ARG* 3.8 4.3 - - - +
90C ALA* 1.3 76.8 - - + +
92C ARG* 1.3 59.6 + - - +
94C GLY* 3.0 18.4 + - - -
95C ALA 3.7 7.6 - - - +
96C ASN* 5.1 0.2 - - - -
97C ALA 5.2 1.8 - - - +
113C LEU* 4.3 11.9 - - + +
116C LEU* 3.7 30.1 - - + -
117C GLU 4.1 8.7 - - - +
120C THR* 3.6 27.8 - - + +
122C ARG* 3.7 35.4 - - + +
123C ARG 4.3 3.8 - - - +
124C VAL* 4.0 28.7 - - + -
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU* 5.4 2.8 + - - +
58B GLU* 3.0 31.3 + - - +
59B ALA* 4.9 6.5 - - - +
62B GLU* 3.5 34.0 + - - +
92B ARG* 4.8 11.1 - - - +
58C GLU* 2.7 31.3 + - - +
65C ARG* 2.9 19.3 + - - -
85C PRO 4.7 2.8 + - - -
88C ARG* 3.0 36.7 + - - +
89C MET* 3.5 24.6 - - - +
91C LEU* 1.3 77.7 - - - +
93C LEU* 1.3 58.8 + - + +
94C GLY 3.2 2.2 + - - -
120C THR* 5.0 4.7 - - + -
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLU* 4.0 11.9 - - + +
61C LEU* 3.7 34.1 - - + +
62C GLU* 3.6 40.2 - - + +
65C ARG* 3.3 32.0 - - - +
70C GLY* 5.6 1.9 - - - -
71C VAL* 5.0 7.8 + - + +
74C LEU* 5.7 2.0 - - + -
89C MET* 3.0 43.5 + - + +
90C ALA* 3.1 8.9 + - - +
92C ARG* 1.3 78.2 - - + +
94C GLY* 1.3 61.9 + - - +
95C ALA* 3.5 5.9 + - + +
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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