Contacts of the helix formed by residues 106 - 120 (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 ASP 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ARG* 3.6 39.7 - - + +
103B THR 4.0 1.2 - - - +
104B ALA* 3.6 3.2 - - - +
105B GLY* 1.3 81.7 + - - +
107B GLU* 1.3 62.9 + - - +
108B ALA* 4.0 10.3 - - - +
109B GLY* 2.9 26.0 + - - -
110B THR* 2.9 24.3 + - - -
134B GLN* 3.1 8.3 + - - -
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Residues in contact with GLU 107 (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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140A PRO* 3.7 21.7 - - + +
141A ILE* 4.2 9.7 - - + +
144A ARG* 3.0 43.5 + - - +
106B ASP* 1.3 71.0 - - - +
108B ALA* 1.3 61.4 + - - +
110B THR* 3.0 8.3 + - - -
111B ILE* 2.9 33.2 + - - +
133B GLN* 2.9 39.1 + - - +
134B GLN* 4.7 4.5 - - - +
137B SER* 3.6 34.5 - - - +
138B ALA* 5.0 0.2 - - - +
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Residues in contact with ALA 108 (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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115A GLN* 3.9 16.3 + - - +
141A ILE* 3.7 23.1 - - + +
106B ASP* 3.5 11.7 + - - +
107B GLU* 1.3 77.9 + - - +
109B GLY* 1.3 57.5 + - - +
111B ILE* 3.4 5.9 + - - +
112B ASN* 3.0 40.1 + - - +
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Residues in contact with GLY 109 (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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102B ASP 4.2 2.1 - - - +
103B THR* 3.2 24.2 - - - +
104B ALA* 5.1 2.2 - - - -
106B ASP* 2.9 14.7 + - - -
108B ALA* 1.3 77.3 - - - +
110B THR* 1.3 57.1 + - - +
112B ASN* 3.6 9.2 + - - +
113B ALA* 3.0 27.5 + - - +
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Residues in contact with THR 110 (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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103B THR* 3.5 13.9 + - + -
106B ASP 2.9 15.9 + - - -
107B GLU* 3.0 8.5 + - - -
109B GLY* 1.3 76.8 - - - +
111B ILE* 1.3 60.2 + - - +
113B ALA* 3.2 0.9 + - - +
114B PHE* 2.9 40.0 + - + -
129B PRO* 3.6 30.5 - - + -
134B GLN* 3.2 24.5 + - + +
138B ALA* 3.5 22.0 - - + -
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Residues in contact with ILE 111 (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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111A ILE* 3.5 37.2 - - + -
115A GLN* 6.3 0.2 - - - +
141A ILE* 3.9 18.6 - - + -
107B GLU 2.9 19.0 + - - +
108B ALA* 3.7 4.9 - - - +
110B THR* 1.3 76.3 - - - +
112B ASN* 1.3 59.8 + - - +
114B PHE* 3.4 3.2 + - - +
115B GLN* 2.9 54.0 + - - +
137B SER* 3.4 23.6 - - - +
138B ALA* 4.0 23.1 - - + +
141B ILE* 4.2 10.8 - - + -
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Residues in contact with ASN 112 (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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115A GLN* 5.5 7.5 + - - +
108B ALA* 3.0 27.7 + - - +
109B GLY* 3.8 8.6 - - - +
111B ILE* 1.3 79.6 - - - +
113B ALA* 1.3 56.7 + - - +
115B GLN* 3.3 13.9 + - - +
116B THR* 2.9 35.4 + - - +
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Residues in contact with ALA 113 (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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60B ALA* 4.3 4.5 - - + -
101B GLN* 3.7 40.5 - - + +
102B ASP 3.8 7.0 - - - +
103B THR* 3.9 11.7 - - + -
109B GLY 3.0 19.1 + - - +
110B THR 3.2 4.0 + - - +
112B ASN* 1.3 75.7 - - - +
114B PHE* 1.3 62.3 - - - +
116B THR* 3.4 2.4 + - - -
117B LEU* 3.0 30.0 + - - +
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Residues in contact with PHE 114 (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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60B ALA* 3.6 28.5 - - + -
110B THR* 2.9 33.7 + - + +
111B ILE* 3.7 6.3 - - - +
113B ALA* 1.3 75.1 - - - +
115B GLN* 1.3 59.3 + - - +
117B LEU* 3.3 3.1 + - - +
118B ILE* 2.9 39.4 + - + +
126B ILE* 4.0 32.1 - - + -
128B GLY 4.3 1.3 - - - -
129B PRO* 4.0 18.2 - - + -
138B ALA* 3.5 25.4 - - + +
139B ASN* 3.3 29.8 - - - -
141B ILE* 4.7 6.1 - - + -
142B ALA* 4.2 8.3 - - + -
149B VAL* 4.2 12.1 - - + -
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Residues in contact with GLN 115 (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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108A ALA* 3.8 27.9 + - - +
111A ILE* 6.3 0.6 - - - +
112A ASN* 5.4 7.4 + - - +
111B ILE* 2.9 42.2 + - - +
112B ASN* 3.9 11.1 - - - +
114B PHE* 1.3 75.1 - - - +
116B THR* 1.3 57.3 + - - +
118B ILE* 4.6 3.6 - - + -
119B ASN* 2.9 47.6 + - - +
141B ILE* 3.9 19.5 - - + +
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Residues in contact with THR 116 (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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101B GLN* 4.0 24.3 + - - +
112B ASN* 2.9 18.9 + - - +
113B ALA 3.7 3.6 - - - -
115B GLN* 1.3 77.6 - - - +
117B LEU* 1.3 58.5 + - - +
119B ASN* 5.3 0.2 - - - -
120B LYS* 3.0 63.4 + - + +
121B ASP* 3.0 14.6 + - - +
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Residues in contact with LEU 117 (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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58B GLY* 3.9 22.0 - - - -
59B ILE 4.0 3.8 - - - +
60B ALA* 3.8 26.9 - - + -
99B ILE* 3.5 28.7 - - + +
101B GLN* 3.9 15.7 - - + -
113B ALA 3.0 21.9 + - - +
114B PHE* 3.7 4.3 - - - +
116B THR* 1.3 76.7 - - - +
118B ILE* 1.3 58.0 + - - +
121B ASP* 3.4 19.6 - - - +
122B LYS 3.1 22.5 + - - -
123B VAL* 3.1 26.2 + - + +
126B ILE* 4.4 11.9 - - + -
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Residues in contact with ILE 118 (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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114B PHE* 2.9 26.0 + - + +
115B GLN* 4.0 3.1 - - + +
117B LEU* 1.3 78.4 - - - +
119B ASN* 1.3 76.5 + - - +
122B LYS* 3.7 8.8 - - - +
123B VAL* 4.4 1.1 - - + -
126B ILE* 4.0 18.6 - - + -
141B ILE* 4.6 9.2 - - + -
142B ALA* 4.1 27.6 - - + +
145B ALA* 4.3 15.0 - - + -
147B VAL* 3.9 25.4 - - + -
364B ARG* 3.0 37.2 + - - +
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Residues in contact with ASN 119 (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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115B GLN* 2.9 36.1 + - - +
116B THR* 5.3 0.4 - - - -
118B ILE* 1.3 92.1 + - - +
120B LYS* 1.3 58.5 + - - +
122B LYS* 3.2 32.1 + - - +
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Residues in contact with LYS 120 (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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101B GLN* 5.0 5.7 + - - +
115B GLN 4.2 0.2 + - - -
116B THR* 3.0 35.2 + - + +
119B ASN* 1.3 79.9 - - - +
121B ASP* 1.3 82.7 + - - +
122B LYS* 3.3 10.5 + - - +
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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