Contacts of the helix formed by residues 67 - 88 (chain B) in PDB entry 4OTZ
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 VAL 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA* 3.5 21.5 - - + +
65B SER* 3.0 15.4 + - - +
66B ASN* 1.3 77.9 - - + +
68B ALA* 1.3 56.9 + - - +
70B LEU* 3.0 25.6 + - + +
71B GLY 3.0 9.0 + - - -
105B GLY* 3.8 16.8 - - - +
130B THR* 3.9 8.5 - - + -
131B LEU* 3.6 45.8 - - + -
134B GLN* 4.5 2.9 - - - +
256B LEU* 4.5 11.2 - - + -
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA 3.3 12.3 - - - +
63B GLN* 3.5 34.3 - - - +
64B THR* 3.6 4.9 + - - +
65B SER 3.0 17.1 + - - +
67B VAL* 1.3 73.5 - - - +
69B LEU* 1.3 64.2 + - - +
70B LEU 3.0 2.2 - - - -
71B GLY 3.6 0.2 - - - -
72B GLN* 2.9 36.3 + - + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER 4.4 0.4 + - - +
66B ASN* 3.2 19.0 + - - +
67B VAL 3.1 1.2 - - - -
68B ALA* 1.3 77.9 - - - +
70B LEU* 1.3 60.4 + - - +
72B GLN* 4.3 7.2 - - - +
73B GLU* 4.4 1.0 - - - +
257B ALA* 4.2 13.2 - - + -
258B ALA* 3.9 36.6 - - + +
284B THR* 3.1 15.5 + - - -
286B ASN* 2.9 45.7 - - + +
290B VAL* 4.8 12.3 - - + -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN 4.5 4.9 - - - +
67B VAL* 3.0 15.7 + - + +
69B LEU* 1.3 81.0 - - + +
71B GLY* 1.3 64.9 - - - +
72B GLN 3.3 0.4 - - - -
73B GLU* 3.3 19.6 + - - +
74B GLN* 3.7 10.1 + - - +
130B THR* 4.1 8.5 - - + -
131B LEU* 4.4 9.9 - - + -
256B LEU* 4.4 9.2 - - + -
257B ALA* 3.7 32.8 - - + +
281B GLY* 3.9 19.1 - - - +
284B THR* 4.5 3.6 - - + -
331B PHE* 4.0 25.8 - - + -
501B CYS* 3.8 35.2 - - + -
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Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.4 0.5 - - - +
62B ALA 3.2 22.4 - - - -
67B VAL 3.0 11.4 + - - -
68B ALA 3.3 0.6 + - - -
70B LEU* 1.3 78.7 - - - +
72B GLN* 1.3 62.1 + - - +
74B GLN* 3.0 29.1 + - - +
75B VAL* 3.0 16.0 + - - +
130B THR* 3.9 7.8 - - - +
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Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA 3.8 2.7 + - - -
63B GLN* 5.8 2.9 - - - +
68B ALA* 2.9 28.2 + - + +
69B LEU* 4.3 6.2 - - - +
71B GLY* 1.3 76.7 - - - +
73B GLU* 1.3 65.7 + - + +
75B VAL* 3.4 10.7 + - - +
76B ALA* 3.0 22.2 + - - +
286B ASN* 3.1 37.0 + - - +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU 4.4 3.8 - - - +
70B LEU 3.6 9.0 - - - +
71B GLY 3.2 0.4 - - - -
72B GLN* 1.3 80.7 - - + +
74B GLN* 1.3 61.9 + - - +
76B ALA* 3.4 4.6 + - - +
77B GLY 3.1 12.1 + - - -
283B ASN 4.0 0.2 - - - +
284B THR* 3.0 30.3 + - - +
285B SER* 3.1 24.9 + - - -
286B ASN* 4.3 6.7 + - - +
320B TYR* 5.3 3.1 - - - +
329B PRO* 3.4 30.8 - - + +
331B PHE* 3.5 25.8 - - + +
332B SER* 2.8 30.4 + - - +
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.5 19.5 - - + +
70B LEU 3.8 10.3 - - - +
71B GLY* 3.0 9.3 + - - +
73B GLU* 1.3 73.9 - - - +
75B VAL* 1.3 65.9 + - - +
77B GLY 3.2 1.2 + - - -
78B ALA* 2.9 20.8 + - - +
130B THR* 2.7 44.2 + - - +
152B PRO* 3.6 15.9 - - + +
153B SER* 3.1 32.7 + - - -
331B PHE* 3.8 21.2 - - + +
335B ALA* 3.1 21.6 - - + +
501B CYS* 5.8 0.2 - - - -
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.8 18.6 - - + -
63B GLN* 3.9 38.4 - - + +
71B GLY 3.0 18.9 + - - +
72B GLN* 3.6 11.0 - - - +
74B GLN* 1.3 76.0 - - - +
76B ALA* 1.3 63.0 + - - +
78B ALA* 3.3 2.3 + - - +
79B LYS* 3.0 52.7 + - + +
100B PHE* 3.8 15.0 - - + -
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN 3.0 14.0 + - - +
73B GLU* 3.5 11.7 - - - +
75B VAL* 1.3 78.9 - - - +
77B GLY* 1.3 61.5 + - - +
79B LYS* 3.4 6.8 + - - +
80B ILE* 3.1 30.5 + - - +
320B TYR* 4.4 5.6 - - + +
324B TYR* 3.5 35.5 + - + +
332B SER* 4.4 5.4 - - - +
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU 3.1 8.9 + - - -
74B GLN 3.2 2.2 + - - -
76B ALA* 1.3 75.1 - - - +
78B ALA* 1.3 60.3 + - - +
80B ILE* 3.4 7.0 + - - +
81B ALA* 3.0 28.1 + - - +
316B PHE* 4.6 4.3 - - - -
332B SER* 3.4 30.0 - - - -
336B PHE* 3.8 12.0 - - - +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE* 4.4 11.0 - - + -
61B LEU* 5.2 0.4 - - + -
74B GLN 2.9 16.5 + - - +
75B VAL* 3.7 4.7 - - - +
77B GLY* 1.3 77.7 - - - +
79B LYS* 1.3 56.5 + - - +
81B ALA* 3.2 3.2 + - - +
82B GLU 2.9 23.9 + - - -
98B LEU* 3.3 24.6 - - + +
100B PHE* 4.3 13.2 - - + -
127B VAL* 6.1 1.3 - - + -
335B ALA* 4.0 7.5 - - + +
339B VAL* 4.2 17.3 - - + -
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLN* 5.5 3.2 - - - +
75B VAL* 3.0 40.9 + - + +
76B ALA* 3.8 7.0 - - - +
78B ALA* 1.3 76.0 - - - +
80B ILE* 1.3 61.5 + - + +
82B GLU* 3.3 11.8 + - - +
83B LYS* 3.2 21.8 + - - +
100B PHE* 3.7 27.4 - - + -
324B TYR* 5.9 2.0 - - - +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA 3.1 18.5 + - - +
77B GLY* 3.7 4.9 - - - +
79B LYS* 1.3 76.6 - - + +
81B ALA* 1.3 57.6 + - - +
83B LYS* 3.5 5.0 + - - +
84B TYR* 3.0 29.2 + - + +
316B PHE* 3.9 24.7 - - + +
319B ALA* 3.8 26.7 - - + +
320B TYR* 3.6 46.7 - - + +
323B GLN* 4.5 12.3 - - - +
324B TYR* 4.3 9.0 - - + +
336B PHE* 4.2 5.4 - - + -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLY 3.0 15.1 + - - +
78B ALA 3.4 8.7 - - - +
80B ILE* 1.3 74.9 - - - +
82B GLU* 1.3 64.8 + - - +
84B TYR 3.2 0.2 + - - -
85B PHE* 2.9 34.9 + - + +
336B PHE* 3.5 30.5 - - + +
339B VAL* 3.7 28.7 - - + -
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA 2.9 6.7 + - - -
79B LYS* 3.3 14.4 + - - +
81B ALA* 1.3 74.7 - - - +
83B LYS* 1.3 62.6 + - - +
85B PHE* 4.2 0.3 - - - +
86B ASN* 3.0 44.8 + - - +
96B ILE* 3.9 15.3 - - + +
97B LYS* 3.6 15.2 - - - +
98B LEU* 2.9 57.4 + - + +
100B PHE* 4.6 6.8 - - - -
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Residues in contact with LYS 83 (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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79B LYS 3.2 13.2 + - - +
80B ILE* 4.0 5.2 - - - +
82B GLU* 1.3 79.0 - - - +
84B TYR* 1.3 58.5 + - - +
86B ASN* 4.8 2.7 - - - -
87B ASP* 2.8 66.8 + - - +
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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 ILE* 3.0 21.8 + - + +
81B ALA 3.7 2.2 - - - +
83B LYS* 1.3 79.4 - - - +
85B PHE* 1.3 100.7 + + - +
87B ASP* 3.5 6.8 + - - +
88B LYS* 3.4 58.2 + - + +
312B ILE* 4.0 24.6 - - + +
315B ALA* 3.9 30.3 - - + +
316B PHE* 6.0 0.4 - - - -
336B PHE* 3.9 15.5 - + + -
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Residues in contact with PHE 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 ALA* 2.9 33.2 + - + +
82B GLU 4.5 0.9 - - - +
84B TYR* 1.3 97.7 - + - +
86B ASN* 1.3 63.1 + - - +
88B LYS* 3.2 14.4 + - + +
89B GLY 3.4 0.7 + - - -
90B GLY* 2.9 23.7 + - - +
96B ILE* 4.9 4.0 - - + -
312B ILE* 4.2 2.5 - - + -
336B PHE* 3.8 23.3 - + - -
339B VAL* 4.4 1.8 - - + -
340B GLN* 3.4 49.8 - - + -
343B VAL* 3.9 41.7 - - + -
344B GLU* 4.3 11.9 - - + -
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Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 3.0 34.2 + - - +
83B LYS* 4.2 3.4 - - - +
85B PHE* 1.3 73.0 - - - +
87B ASP* 1.3 62.6 + - - +
88B LYS 3.0 5.2 - - - -
89B GLY* 3.0 14.6 + - - -
90B GLY* 3.7 7.7 + - - +
95B PRO* 3.4 15.2 - - + +
96B ILE* 2.9 51.7 + - - +
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS* 2.8 60.4 + - - +
84B TYR* 3.7 6.8 - - - +
85B PHE 3.3 0.2 - - - -
86B ASN* 1.3 77.2 - - - +
88B LYS* 1.3 65.4 + - + +
89B GLY 3.3 1.1 + - - -
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Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TYR* 3.4 54.9 + - + +
85B PHE* 3.2 11.9 + - + +
86B ASN 3.0 1.4 - - - -
87B ASP* 1.3 84.9 + - - +
89B GLY* 1.3 56.9 + - - +
90B GLY 3.5 4.3 - - - +
347B LYS* 6.0 0.3 + - - -
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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