Contacts of the helix formed by residues 74 - 87 (chain B) in PDB entry 6O81
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 ALA 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B VAL 3.8 12.8 - - - +
67B LEU* 3.9 17.0 - - - +
68B LEU 3.3 10.1 - - - -
69B PRO* 4.3 1.6 - - - +
73B VAL* 1.3 81.2 - - - +
75B LEU* 1.3 64.3 + - - +
76B ILE 3.2 2.0 - - - +
77B ASP* 3.2 15.4 + - - +
78B TYR* 3.3 11.6 + - - -
105B HIS* 3.5 32.5 - - + +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ARG 4.3 10.1 - - - +
66B VAL* 3.5 8.4 + - - +
68B LEU* 3.2 32.1 - - + +
70B LEU* 3.8 23.3 - - + -
74B ALA* 1.3 71.4 - - - +
76B ILE* 1.3 56.9 + - - +
77B ASP 3.3 0.2 - - - -
78B TYR* 3.6 8.2 - - - +
79B THR* 2.7 38.2 + - - -
153B GLY 3.9 11.7 - - - +
154B ASP* 3.7 27.6 - - + +
156B ILE* 3.7 25.3 - - + +
300B VAL* 3.8 26.0 - - + -
306B TYR* 5.0 4.7 - - + -
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.8 27.1 - - + -
49B ALA* 3.9 15.7 - - + -
66B VAL* 3.2 29.7 + - + +
67B LEU* 4.4 6.5 - - + -
74B ALA 3.2 0.8 - - - -
75B LEU* 1.3 75.9 - - - +
77B ASP* 1.3 64.0 + - - +
79B THR* 3.4 2.0 + - - -
80B LEU* 2.9 48.2 + - + +
93B VAL* 5.1 2.5 - - + -
102B ILE* 4.6 5.2 - - + -
105B HIS* 4.5 11.7 - - + +
106B LEU* 4.5 21.3 - - + -
153B GLY 3.7 15.5 - - - +
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Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 3.8 14.7 - - + +
74B ALA 3.2 16.7 + - - +
76B ILE* 1.3 81.1 - - - +
78B TYR* 1.3 57.2 + - - +
80B LEU* 4.5 0.6 - - - +
81B GLU* 2.9 30.8 + - - +
105B HIS* 3.6 30.3 + - - -
106B LEU* 5.5 0.7 - - - +
109B SER* 4.1 10.8 - - - -
111B TRP* 3.3 37.2 - - + -
327B PHE* 4.2 4.7 - - + -
328B THR* 5.1 8.6 + - - +
333B GLN* 5.8 1.7 + - - -
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.7 23.8 - - + -
71B ALA* 4.2 15.1 + - - +
73B VAL* 3.4 31.1 - - + +
74B ALA 3.3 21.1 + - - -
75B LEU* 3.6 7.6 - - - +
76B ILE 3.3 0.4 - - - -
77B ASP* 1.3 79.7 - - - +
79B THR* 1.3 56.9 + - - +
81B GLU 3.4 0.5 + - - -
82B PHE* 2.9 28.1 + - - +
155B VAL 4.5 1.6 - - - -
156B ILE* 3.6 24.5 - - + -
157B SER 5.5 0.2 + - - -
313B VAL* 3.5 33.6 - - + +
318B VAL* 6.4 0.2 - - + -
321B LEU* 3.6 35.3 - - + +
323B PRO* 4.6 6.4 - - - +
327B PHE* 3.5 27.7 - + - -
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.8 18.2 - - + -
75B LEU 2.7 23.2 + - - -
76B ILE* 3.9 3.8 - - - -
78B TYR* 1.3 75.5 - - - +
80B LEU* 1.3 58.3 + - - +
82B PHE* 3.3 9.6 + - + +
83B LEU* 2.9 28.6 + - + +
151B VAL* 3.8 17.5 - - + -
152B TYR 3.5 22.2 - - - +
153B GLY 3.7 6.5 + - - -
155B VAL 2.9 31.2 + - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.1 20.2 - - + -
76B ILE* 2.9 36.9 + - + +
79B THR* 1.3 72.8 - - - +
81B GLU* 1.3 61.2 + - - +
83B LEU* 3.2 13.2 + - + +
84B THR* 2.9 32.6 + - - +
91B THR* 4.4 9.4 - - + +
93B VAL* 5.1 7.2 - - + -
106B LEU* 5.2 9.9 - - + -
109B SER* 5.2 2.0 - - - +
111B TRP* 3.5 47.1 - - + +
118B ASN* 4.8 2.0 - - - +
120B VAL* 4.4 20.9 - - + -
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASP 2.9 19.2 + - - +
78B TYR 3.7 3.8 - - - +
80B LEU* 1.3 72.1 - - - +
82B PHE* 1.3 60.7 + - - +
84B THR* 3.1 14.1 + - - -
85B ALA* 2.9 28.8 + - - +
110B LYS* 3.3 24.6 + - - -
111B TRP* 3.5 9.7 - - + -
321B LEU* 3.9 19.0 - - + +
327B PHE* 3.5 41.7 - - + +
20C GLU* 4.3 5.7 - - - +
24C ARG* 4.1 20.6 + - - +
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TYR 2.9 17.3 + - - +
79B THR* 3.5 17.3 - - + +
80B LEU 3.3 0.2 - - - -
81B GLU* 1.3 77.1 - - - +
83B LEU* 1.3 64.9 + - + +
85B ALA* 3.7 6.0 - - + +
86B THR* 2.5 48.4 + - + -
149B LEU* 5.1 0.7 - - + -
151B VAL* 4.7 5.4 - - + -
155B VAL* 5.2 2.7 - - + -
157B SER* 3.3 49.6 - - - +
158B ASN* 3.9 3.4 - - - +
159B ILE* 3.2 28.3 - - + -
161B ILE* 5.0 7.4 - - + -
249B ILE* 3.6 44.6 - - + -
321B LEU* 4.4 3.9 - - + +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA* 4.2 6.1 - - + -
47B LEU* 3.8 28.9 - - + -
79B THR 2.9 16.5 + - - +
80B LEU* 3.2 10.5 + - + +
82B PHE* 1.3 89.2 - - + +
84B THR* 1.3 57.0 + - - +
86B THR* 3.2 5.5 + - - +
87B GLY 3.1 21.7 + - - -
88B VAL* 3.3 37.5 - - + +
91B THR* 3.8 23.8 - - + -
118B ASN* 4.3 3.1 - - - +
149B LEU* 3.8 31.9 - - + -
151B VAL* 4.3 7.9 - - + -
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU 2.9 14.7 + - - +
81B GLU* 3.1 24.9 + - - -
83B LEU* 1.3 73.8 - - - +
85B ALA* 1.3 57.8 + - - +
86B THR 3.5 0.2 + - - -
87B GLY* 3.6 10.3 + - - +
88B VAL* 5.0 2.0 - - - +
110B LYS* 5.6 0.9 + - - -
111B TRP* 3.4 25.1 + - + +
116B SER* 5.6 0.4 - - - +
117B LEU* 4.5 10.3 - - + +
118B ASN* 3.6 28.3 - - + +
24C ARG* 2.6 44.6 + - - +
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Residues in contact with ALA 85 (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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81B GLU* 2.9 20.5 + - - +
82B PHE* 3.8 8.5 - - + +
84B THR* 1.3 75.1 + - - +
86B THR* 1.3 64.8 + - - +
158B ASN* 6.0 5.6 - - - +
159B ILE 5.6 1.1 - - - -
160B ASN* 4.2 10.6 - - - +
320B PRO* 6.4 2.5 - - + -
321B LEU* 5.1 9.2 - - + -
24C ARG* 4.0 26.0 + - + +
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 4.7 9.3 - - + +
82B PHE* 2.5 41.2 + - - -
83B LEU* 3.2 11.7 + - - -
85B ALA* 1.3 79.0 - - - +
87B GLY* 1.3 58.0 + - - +
88B VAL* 4.6 8.1 - - + -
149B LEU* 4.5 9.6 - - + -
159B ILE 4.0 4.1 + - - +
160B ASN* 3.5 16.5 - - - +
161B ILE* 3.7 38.6 - - + +
162B THR* 4.3 11.0 - - + +
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Residues in contact with GLY 87 (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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43B LEU* 4.1 12.9 - - - +
83B LEU 3.1 3.4 + - - -
84B THR 3.6 9.1 + - - -
85B ALA 3.5 1.6 - - - -
86B THR* 1.3 78.9 - - - +
88B VAL* 1.3 66.2 + - - +
89B GLN* 3.1 17.9 + - - +
117B LEU* 6.4 1.6 - - - -
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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
------------------------------------------------------------
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