Contacts of the helix formed by residues 82 - 93 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B SER* 3.6 13.0 - - - +
79B PRO* 2.9 19.0 + - + +
81B HIS* 1.3 102.2 - - + +
83B HIS* 1.3 63.9 + - - +
84B TYR 3.4 0.9 - - - -
85B PRO* 3.4 12.1 - - + +
86B GLN* 3.0 28.1 + - - +
311B NAD 3.6 36.6 - - + +
53C GLU* 3.8 27.4 - - + +
55C GLU* 3.7 31.2 - - - +
56C ALA* 5.7 0.2 - - + -
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Residues in contact with HIS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.7 12.8 - - + +
78B SER* 2.8 38.2 + - - -
79B PRO 3.3 7.7 + - - -
80B ASN* 3.0 19.6 + - - +
82B LEU* 1.3 78.6 - - - +
84B TYR* 1.3 58.4 + - - +
86B GLN* 3.7 0.5 - - - +
87B ILE* 2.8 36.3 + - - +
99B SER* 3.3 9.0 - - - +
100B GLU* 3.1 28.3 + - + +
101B LYS 3.5 3.8 - - - -
102B PRO 2.8 22.5 + - - -
103B LEU 3.1 17.9 - - - +
104B VAL* 4.7 0.7 - - - -
311B NAD 2.8 20.4 + - - -
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Residues in contact with TYR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN 4.4 1.0 + - - -
81B HIS 4.3 1.7 + - - +
83B HIS* 1.3 80.1 - - - +
85B PRO* 1.4 75.4 - - + +
87B ILE* 3.2 4.9 + - - +
88B ARG* 2.8 61.5 + - - +
104B VAL* 3.7 14.0 - - + +
109B GLU* 3.5 65.7 - - + +
112B ARG* 3.1 33.8 - - + +
113B LEU* 3.8 26.5 - - + -
59C ALA* 4.8 6.5 - - + -
63C ASP* 5.5 0.9 - - - -
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Residues in contact with PRO 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B HIS 3.4 19.1 - - - +
82B LEU* 3.4 17.7 - - + +
84B TYR* 1.4 103.5 - - + +
86B GLN* 1.3 56.1 + - - +
88B ARG* 3.4 8.2 + - + +
89B MET* 3.0 25.3 + - - +
92B ARG* 4.9 2.4 + - - -
109B GLU* 5.3 0.2 - - - +
55C GLU* 3.5 35.9 - - + +
56C ALA* 3.9 19.1 - - + +
59C ALA* 4.3 8.5 - - + -
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Residues in contact with GLN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 2.8 28.5 + - + +
32B LEU* 3.8 9.9 - - - +
74B LEU* 3.5 14.1 - - + +
76B ILE* 3.6 14.6 - - + +
78B SER* 2.8 21.4 + - - -
82B LEU* 3.0 19.3 + - + +
83B HIS 3.9 1.3 - - - +
85B PRO* 1.3 75.3 - - - +
87B ILE* 1.3 64.4 + - - +
89B MET* 3.3 11.5 + - + +
90B ALA 3.1 17.2 + - - -
311B NAD 3.1 24.9 + - - -
55C GLU* 2.8 37.3 + - + +
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.6 19.1 - - + -
83B HIS 2.8 23.5 + - - +
84B TYR 3.5 3.8 - - - +
86B GLN* 1.3 72.8 - - - +
88B ARG* 1.3 68.3 + - - +
90B ALA* 3.1 5.0 + - - +
91B LEU* 3.0 24.2 + - + +
97B ALA* 3.9 11.0 - - + -
99B SER* 4.1 4.7 - - - -
103B LEU* 3.6 41.3 - - + +
104B VAL* 4.0 1.3 - - + -
113B LEU* 3.8 26.5 - - + -
124B VAL* 3.5 32.5 - - + -
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TYR* 2.8 53.8 + - - +
85B PRO* 3.6 8.3 - - + +
87B ILE* 1.3 80.2 - - - +
89B MET* 1.3 63.9 + - - +
91B LEU* 4.0 5.5 - - - +
92B ARG* 3.1 35.0 + - - +
112B ARG* 4.8 0.6 - - - +
113B LEU* 3.8 16.2 - - + -
116B LEU* 3.5 26.5 - - + +
59C ALA* 3.4 19.4 + - + +
62C GLU* 2.7 43.9 + - - +
63C ASP* 2.7 35.9 + - - +
66C ASP* 4.7 4.2 + - - -
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Residues in contact with MET 89 (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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32B LEU* 5.4 2.2 - - - -
54B PRO* 4.1 11.4 - - + +
57B PHE* 4.1 27.6 - - - -
58B GLU* 3.4 40.8 - - + +
74B LEU* 5.1 5.8 - - + -
85B PRO 3.0 13.5 + - - +
86B GLN* 3.4 14.8 - - - +
88B ARG* 1.3 77.1 - - - +
90B ALA* 1.3 61.9 + - - +
92B ARG* 3.2 21.1 - - - +
93B LEU* 3.1 43.3 + - + +
55C GLU* 3.7 28.9 - - + -
58C GLU* 4.7 0.9 - - - +
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Residues in contact with ALA 90 (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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74B LEU* 3.7 33.0 - - + +
86B GLN 3.1 12.0 + - - +
87B ILE 3.1 8.7 + - - +
89B MET* 1.3 74.2 - - - +
91B LEU* 1.3 64.8 + - - +
93B LEU* 3.0 14.6 + - - +
94B GLY 3.3 0.2 + - - -
95B ALA* 2.9 33.3 + - + +
96B ASN 4.1 1.1 - - - +
97B ALA* 4.0 15.7 - - + -
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.0 21.7 + - + +
88B ARG* 4.0 4.0 - - - +
90B ALA* 1.3 78.2 - - - +
92B ARG* 1.3 64.3 + - - +
94B GLY* 3.0 14.4 + - - -
95B ALA 3.5 8.3 - - - +
97B ALA 4.6 3.6 - - - +
113B LEU* 4.6 6.1 - - + +
116B LEU* 4.2 13.5 - - + -
117B GLU* 4.1 16.8 - - + +
120B THR* 3.5 35.5 - - + +
122B ARG* 3.6 36.5 - - + +
123B ARG 3.8 15.0 - - - +
124B VAL* 3.9 21.5 - - + -
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Residues in contact with ARG 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 2.4 32.3 + - - +
65B ARG* 3.6 18.1 + - - +
85B PRO 4.9 2.4 + - - -
88B ARG* 3.1 22.6 + - - +
89B MET* 3.2 37.0 - - - +
91B LEU* 1.3 77.6 - - - +
93B LEU* 1.3 63.8 + - + +
94B GLY 3.3 3.5 + - - -
120B THR* 4.2 11.1 - - + +
55C GLU* 5.4 3.2 + - - +
58C GLU* 3.3 30.6 + - - +
59C ALA* 5.5 2.6 - - - +
62C GLU* 3.1 39.4 + - - +
92C ARG* 4.8 10.5 - - - +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 3.6 20.0 - - + +
61B LEU* 3.8 31.3 - - + +
62B GLU* 3.4 42.6 - - + +
65B ARG* 3.5 31.3 - - - +
70B GLY* 5.7 1.2 - - - -
71B VAL* 5.0 6.6 + - + +
74B LEU* 5.9 1.1 - - + -
89B MET* 3.1 40.4 + - + +
90B ALA* 3.0 9.6 + - - +
92B ARG* 1.3 82.1 - - + +
94B GLY* 1.4 57.1 - - - +
95B ALA* 3.3 4.9 - - + +
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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
------------------------------------------------------------
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