Contacts of the helix formed by residues 119 - 130 (chain B) in PDB entry 4DAJ
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 ILE 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B ILE* 3.4 13.1 + - + +
118B VAL* 1.3 99.6 - - + +
120B SER* 1.3 66.5 + - - +
121B MET 3.5 1.3 - - - -
122B ASN* 3.0 4.1 + - - +
123B LEU* 2.9 61.4 + - + +
143B TRP* 4.1 9.9 - - + -
146B ILE* 4.2 33.4 - - + -
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Residues in contact with SER 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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116B ILE* 3.2 20.0 + - - -
119B ILE* 1.3 70.6 - - - +
121B MET* 1.3 59.0 + - - +
122B ASN 2.9 5.4 - - - -
124B PHE* 2.9 34.6 + - - +
143B TRP* 3.3 17.0 + - - +
146B ILE* 4.4 7.3 - - - +
147B ASP* 3.5 48.1 + - - +
533B TYR* 3.7 5.8 - - - -
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Residues in contact with MET 121 (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 THR 5.7 0.2 - - - -
77B LEU* 4.3 2.9 - - + -
78B ALA* 3.9 21.7 - - + +
81B THR* 3.5 20.6 - - - +
116B ILE* 3.1 19.1 + - - +
117B GLY* 3.4 26.9 - - - +
119B ILE 3.5 0.6 - - - -
120B SER* 1.3 73.7 - - - +
122B ASN* 1.3 52.2 + - - +
124B PHE* 4.3 0.4 - - - -
125B THR* 2.5 28.9 + - - -
530B TRP* 3.1 48.7 - - + -
533B TYR* 3.6 36.1 - - + +
534B ILE* 4.9 0.7 - - + +
537B THR* 3.6 18.2 - - - +
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Residues in contact with ASN 122 (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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75B GLY* 5.4 5.2 - - - -
78B ALA* 4.5 12.4 - - - +
117B GLY 4.2 4.9 + - - -
118B VAL* 3.2 23.2 + - - +
119B ILE 3.0 8.4 + - - +
120B SER 2.9 1.8 - - - -
121B MET* 1.3 78.6 - - - +
123B LEU* 1.3 75.7 + - + +
124B PHE 2.9 0.9 - - - -
125B THR* 2.7 22.3 + - - -
126B THR* 2.9 13.5 + - - -
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Residues in contact with LEU 123 (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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118B VAL 5.3 0.4 - - - +
119B ILE* 2.9 37.5 + - + +
122B ASN* 1.3 83.1 - - + +
124B PHE* 1.3 64.0 + - - +
126B THR* 3.1 12.4 + - - +
127B TYR* 2.9 22.2 + - - +
133B TRP* 4.7 17.6 - - + -
135B LEU* 4.9 13.7 - - + -
139B ALA 5.3 1.1 - - - +
143B TRP* 3.7 39.5 - - + +
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Residues in contact with PHE 124 (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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120B SER 2.9 22.3 + - - +
121B MET 4.2 2.0 - - - +
122B ASN 2.9 0.4 + - - -
123B LEU* 1.3 73.5 - - - +
125B THR* 1.3 64.6 + - - +
127B TYR* 2.9 24.7 + + + +
128B ILE* 2.9 31.7 + - + +
143B TRP* 3.7 32.3 - + + -
526B ASN* 4.1 23.8 - - + -
529B TYR* 4.0 31.6 - + + -
530B TRP* 2.9 50.5 - + - -
533B TYR* 4.0 9.9 - + + -
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Residues in contact with THR 125 (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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71B ALA* 3.6 13.5 - - - +
74B THR* 3.1 34.5 + - + +
121B MET 2.5 24.6 + - - -
122B ASN* 2.7 15.7 + - - -
124B PHE* 1.3 74.6 - - - +
126B THR* 1.3 62.5 + - - +
128B ILE* 3.1 15.8 + - + +
129B ILE* 2.9 43.6 + - + +
530B TRP* 3.4 4.5 - - - -
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Residues in contact with THR 126 (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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122B ASN 2.9 10.5 + - - -
123B LEU* 3.2 15.9 - - - -
124B PHE 3.1 0.2 - - - -
125B THR* 1.3 77.7 - - - +
127B TYR* 1.3 63.5 + - - +
129B ILE* 3.2 8.4 + - - +
130B MET* 2.9 50.6 + - + +
132B ARG 5.6 0.7 - - - +
133B TRP* 6.3 3.4 - - + -
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Residues in contact with TYR 127 (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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123B LEU 2.9 11.5 + - - +
124B PHE* 2.9 20.2 + + + +
126B THR* 1.3 77.3 - - - +
128B ILE* 1.3 70.2 + - + +
131B ASN* 3.3 22.6 + - - -
132B ARG* 3.8 11.6 + - - -
133B TRP* 3.6 47.8 - + + -
143B TRP* 5.6 6.3 - + + -
218B GLY 4.2 3.1 + - - -
219B GLU* 3.3 25.8 - - - +
220B CYS* 3.4 33.7 + - + -
522B LYS* 4.0 23.6 + - - -
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Residues in contact with ILE 128 (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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67B VAL* 5.5 9.0 - - + +
74B THR* 6.0 1.6 - - + -
124B PHE* 2.9 55.6 + - + +
125B THR* 3.3 12.6 - - + +
127B TYR* 1.3 81.4 - - + +
129B ILE* 1.3 68.2 + - + +
131B ASN* 3.2 13.0 + - - +
526B ASN* 4.9 15.7 - - + +
530B TRP* 3.6 14.8 - - + +
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Residues in contact with ILE 129 (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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67B VAL* 4.9 20.0 - - + +
68B VAL* 5.9 4.7 - - + -
71B ALA* 3.7 30.5 - - + -
72B PHE* 6.1 3.1 - - + -
125B THR* 2.9 27.7 + - + +
126B THR* 3.2 6.5 + - - +
128B ILE* 1.3 77.2 - - + +
130B MET* 1.3 66.2 + - + +
131B ASN* 2.9 13.9 + - - +
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Residues in contact with MET 130 (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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126B THR* 2.9 41.5 + - + +
129B ILE* 1.3 77.6 - - + +
131B ASN* 1.3 61.6 + - - +
132B ARG* 2.8 76.2 + - + +
134B ALA* 3.5 24.5 - - + -
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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