Contacts of the helix formed by residues 58 - 72 (chain B) in PDB entry 2OZL
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 SER 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU* 3.4 36.7 + - - +
180A ASN* 5.2 1.0 + - - -
181A MET* 4.2 12.6 - - - +
28B GLU* 4.0 1.0 + - - -
56B PRO* 3.0 17.8 + - - +
57B ILE* 1.3 72.3 - - - +
59B GLU* 1.3 65.9 + - - +
60B MET 3.5 1.8 - - - -
61B GLY 3.1 1.6 + - - -
62B PHE* 2.9 25.4 + - - -
171C ASN* 2.9 27.5 + - - +
172C GLN* 4.3 0.4 - - - +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLU* 4.2 0.4 + - - -
28B GLU* 2.6 28.4 - - - +
57B ILE* 3.9 0.2 - - - +
58B SER* 1.3 70.7 + - - +
60B MET* 1.3 64.3 + - - +
62B PHE* 3.7 18.0 - - + -
63B ALA* 3.0 28.2 + - - +
80B PHE* 4.2 11.6 - - + -
81B MET 5.5 1.6 + - - -
85B PHE* 3.4 28.2 - - + +
88B GLN* 3.3 27.5 + - + +
89B ALA* 3.6 7.9 - - + -
172C GLN* 3.4 10.2 + - - -
1330C TPP 2.7 32.3 + - - +
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Residues in contact with MET 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PRO* 4.4 0.5 - - - +
174A GLN* 3.3 36.3 - - + +
177A GLU* 3.7 10.6 + - - +
58B SER 3.5 0.4 - - - -
59B GLU* 1.3 76.9 - - - +
61B GLY* 1.3 62.7 + - - +
64B GLY* 3.1 18.9 + - - -
88B GLN* 3.2 29.5 + - + +
89B ALA* 3.5 20.5 - - - +
91B ASP* 4.4 10.5 - - + +
92B GLN* 3.7 28.1 + - - +
88D GLN* 3.6 44.0 - - + +
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PRO* 3.6 15.2 - - - +
174A GLN* 4.9 0.9 - - - -
177A GLU* 2.7 28.9 + - - -
178A ALA* 5.2 1.1 - - - -
181A MET* 3.4 15.7 - - - -
58B SER 3.1 1.7 + - - -
60B MET* 1.3 74.3 - - - +
62B PHE* 1.3 56.4 + - - +
64B GLY 3.3 1.6 + - - -
65B ILE* 3.0 30.3 + - - +
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Residues in contact with PHE 62 (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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181A MET* 3.4 20.6 - - - +
26B LEU* 3.9 15.7 - - + +
27B GLY* 4.5 3.6 - - - -
28B GLU* 3.4 29.8 - - + -
55B THR* 3.4 33.9 - - + -
56B PRO 3.8 5.8 - - - -
58B SER* 2.9 34.6 + - - -
59B GLU* 3.7 17.9 - - + -
61B GLY* 1.3 70.1 - - - -
63B ALA* 1.3 62.7 + - - +
65B ILE* 3.7 6.4 - - + +
66B ALA* 2.9 28.4 + - - +
78B CYS* 3.8 19.5 - - - -
79B GLU 3.7 24.7 - - - -
80B PHE* 4.2 11.2 - + - -
81B MET 6.1 0.2 - - - -
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Residues in contact with ALA 63 (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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59B GLU 3.0 19.2 + - - +
60B MET 3.9 0.9 - - - +
62B PHE* 1.3 78.9 - - - +
64B GLY* 1.3 57.7 + - - +
66B ALA* 3.3 3.6 + - - +
67B VAL* 3.0 33.3 + - - +
78B CYS* 4.0 12.3 - - - -
80B PHE* 4.1 17.5 - - + -
89B ALA* 3.7 20.2 - - + +
92B GLN* 4.4 8.7 - - + -
114B PHE* 4.5 6.9 - - + -
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Residues in contact with GLY 64 (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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143A PRO* 3.7 16.2 - - - -
144A LEU* 3.2 13.0 - - - +
60B MET 3.1 10.9 + - - -
63B ALA* 1.3 75.6 - - - +
65B ILE* 1.3 64.3 + - - +
67B VAL* 3.2 1.0 + - - -
68B GLY 2.9 19.2 + - - -
92B GLN* 3.6 30.5 - - - +
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Residues in contact with ILE 65 (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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143A PRO* 3.3 21.1 + - + +
146A ALA* 3.8 18.4 - - + +
147A GLY* 3.2 20.2 - - - +
150A LEU* 4.0 23.1 - - + -
178A ALA* 5.2 3.8 - - - +
181A MET* 3.6 46.0 - - + -
185A TRP* 4.2 9.9 - - + -
187A LEU* 5.1 3.4 - - + -
26B LEU* 4.7 8.3 - - + -
61B GLY 3.0 14.9 + - - +
62B PHE* 3.7 6.5 - - - +
63B ALA 3.3 0.2 - - - -
64B GLY* 1.3 75.4 - - - +
66B ALA* 1.3 64.5 + - - +
68B GLY 3.2 0.7 + - - -
69B ALA* 2.9 20.6 + - - +
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Residues in contact with ALA 66 (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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24B PHE* 5.3 0.9 - - - -
26B LEU* 4.0 23.1 - - + -
62B PHE 2.9 14.7 + - - +
63B ALA 3.4 9.6 - - - +
64B GLY 3.2 0.2 - - - -
65B ILE* 1.3 79.3 - - - +
67B VAL* 1.3 62.3 + - - +
69B ALA* 3.2 4.4 + - - +
70B ALA 3.0 17.5 + - - -
76B PRO* 3.2 19.9 - - + +
78B CYS* 4.1 8.3 - - + -
112B ILE* 3.5 18.8 - - + -
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 3.5 24.0 - - + -
63B ALA 3.0 17.4 + - - +
64B GLY* 3.2 3.1 + - - +
66B ALA* 1.3 74.0 - - - +
68B GLY* 1.3 62.5 - - - +
70B ALA* 3.2 5.8 + - - +
71B MET* 2.9 30.7 + - + +
92B GLN* 4.1 15.9 - - - +
96B SER* 3.8 24.9 - - - +
97B ALA* 4.1 4.5 - - + -
110B VAL* 4.0 11.7 - - + -
112B ILE* 3.9 16.4 - - + -
114B PHE* 4.0 13.0 - - + -
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Residues in contact with GLY 68 (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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144A LEU* 3.5 31.1 - - - +
147A GLY 3.8 6.3 - - - -
148A ILE* 3.7 7.3 - - - +
64B GLY 2.9 13.3 + - - -
65B ILE 3.7 2.5 - - - -
67B VAL* 1.3 77.0 - - - +
69B ALA* 1.3 60.0 + - - +
71B MET* 3.2 9.1 + - - +
72B ALA* 3.0 23.2 + - - +
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Residues in contact with ALA 69 (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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147A GLY* 3.5 17.8 + - - +
150A LEU* 4.7 5.4 - - + -
151A ALA* 4.4 1.3 - - - +
24B PHE* 4.0 30.5 - - + -
65B ILE 2.9 12.9 + - - +
66B ALA* 3.2 9.8 + - - +
68B GLY* 1.3 76.1 - - - +
70B ALA* 1.3 60.4 + - - +
72B ALA* 3.2 11.0 + - - +
73B GLY 3.3 0.9 + - - -
74B LEU* 3.0 33.9 + - + +
76B PRO* 4.7 0.2 - - + -
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Residues in contact with ALA 70 (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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66B ALA 3.0 12.2 + - - +
67B VAL 3.2 8.9 + - - +
69B ALA* 1.3 74.9 - - - +
71B MET* 1.3 64.0 + - - +
73B GLY* 3.0 12.1 + - - -
74B LEU 3.3 13.5 - - - +
76B PRO* 3.7 7.8 - - + +
109B PRO 4.3 0.5 - - - +
110B VAL* 4.0 18.4 - - + -
111B PRO* 3.6 40.8 - - - +
112B ILE* 4.1 2.0 - - + -
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Residues in contact with MET 71 (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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127A TYR* 5.6 4.0 - - + -
132A TYR* 3.9 32.1 - - + +
135A ASN* 5.5 2.5 - - - +
144A LEU* 4.4 20.9 - - + -
148A ILE* 5.4 1.8 - - + -
67B VAL* 2.9 30.1 + - + +
68B GLY* 3.2 11.2 + - - +
70B ALA* 1.3 76.0 - - - +
72B ALA* 1.3 59.3 + - - +
73B GLY 3.2 1.1 + - - -
96B SER* 3.3 26.9 - - - +
100B THR* 3.7 22.7 - - + +
108B GLN* 3.1 45.2 + - + +
109B PRO 4.1 2.0 + - - -
110B VAL* 4.4 9.2 - - + +
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Residues in contact with ALA 72 (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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84A HIS* 5.9 2.7 - - + -
132A TYR* 4.5 10.5 - - - +
148A ILE* 4.2 19.1 - - + -
151A ALA* 3.5 31.4 - - + +
155A ASN* 4.9 4.7 + - - -
68B GLY 3.0 15.0 + - - +
69B ALA 3.6 2.2 - - - +
70B ALA 3.1 0.6 - - - -
71B MET* 1.3 79.2 - - - +
73B GLY* 1.3 56.2 + - - +
74B LEU* 3.7 3.0 - - - +
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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