Contacts of the helix formed by residues 140 - 155 (chain B) in PDB entry 5DIR
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 ASN 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ASP* 3.9 1.1 - - - -
27B LYS* 3.1 20.6 - - - +
112B ASN* 3.3 11.5 + - - -
122B VAL* 3.4 3.4 - - - +
123B VAL 2.7 23.7 + - - +
124B ASP* 3.0 9.9 + - - -
125B PHE* 3.5 22.7 - - + -
126B ILE* 3.9 11.2 - - - -
139B PHE* 1.3 79.3 - - - +
141B LEU* 1.3 62.5 + - - +
142B ALA* 3.2 4.7 + - - +
143B ASP* 2.8 39.9 + - - +
144B SER* 2.8 27.2 + - - -
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Residues in contact with LEU 141 (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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19B VAL* 5.7 1.3 - - + +
22B LEU* 4.0 16.2 - - + +
23B ASP* 3.8 16.5 + - + +
26B SER* 3.4 23.8 - - - +
125B PHE* 3.9 9.3 - - + -
126B ILE* 4.5 10.5 - - + -
140B ASN* 1.3 74.5 - - - +
142B ALA* 1.3 55.8 + - - +
144B SER* 3.0 16.6 + - - +
145B ALA* 2.7 35.6 + - - +
204B OLC 4.5 20.8 - - + +
207B OLC 4.3 29.2 - - + -
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Residues in contact with ALA 142 (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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19B VAL* 5.2 0.9 - - - -
23B ASP* 2.9 33.1 + - + +
108B GLY* 3.4 32.0 - - - +
111B GLY* 4.5 0.2 - - - -
112B ASN* 3.5 15.7 - - - +
140B ASN* 3.2 6.3 + - - +
141B LEU* 1.3 76.1 - - - +
143B ASP* 1.3 57.4 + - - +
145B ALA* 3.3 1.4 + - - -
146B ILE* 2.9 35.4 + - - +
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Residues in contact with ASP 143 (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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112B ASN* 2.9 25.1 + - - -
139B PHE* 3.2 11.5 - - + +
140B ASN* 2.8 33.1 + - - +
142B ALA* 1.3 74.3 - - - +
144B SER* 1.3 57.9 + - - +
146B ILE* 3.4 3.0 + - - +
147B THR* 2.9 35.8 + - - -
201B OLC 3.7 22.7 - - + +
202H IIL 3.4 11.2 - - + +
203H SER* 2.3 36.3 + - - -
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Residues in contact with SER 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 4.4 1.4 - - - +
139B PHE* 3.8 18.0 - - - -
140B ASN 2.8 19.0 + - - -
141B LEU* 3.0 22.8 + - - +
143B ASP* 1.3 77.8 - - - +
145B ALA* 1.3 55.5 + - - +
147B THR* 3.9 0.3 - - - -
148B VAL* 2.9 37.5 + - - +
201B OLC 3.8 31.7 - - - +
204B OLC 6.1 1.6 - - - -
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 3.6 25.8 - - + -
104B LEU* 3.5 39.5 - - + +
108B GLY* 4.2 1.3 - - - -
141B LEU 2.7 18.3 + - - +
142B ALA 3.6 4.5 - - - +
144B SER* 1.3 70.5 - - - +
146B ILE* 1.3 61.5 + - - +
148B VAL* 4.8 2.5 - - - -
149B GLY* 3.0 24.8 + - - -
201B OLC 6.6 0.2 - - - -
204B OLC 4.9 7.1 - - + +
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Residues in contact with ILE 146 (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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105B VAL* 3.7 22.5 - - + +
108B GLY* 3.4 33.9 - - - +
109B ALA 3.6 2.7 - - - +
112B ASN* 4.3 2.0 - - - +
142B ALA 2.9 21.5 + - - +
143B ASP* 3.7 3.8 - - - +
145B ALA* 1.3 76.3 - - - +
147B THR* 1.3 57.5 + - - +
150B ALA* 3.0 30.8 + - + +
202B OLC 5.6 3.4 - - + -
201H MLE 3.5 50.0 - - + +
202H IIL 4.0 20.0 - - + +
205H 5BV 5.2 0.7 - - - +
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Residues in contact with THR 147 (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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143B ASP 2.9 20.0 + - - -
144B SER 3.9 2.2 - - - -
146B ILE* 1.3 75.2 - - - +
148B VAL* 1.3 67.3 + - + +
150B ALA* 3.2 5.5 + - - +
151B VAL* 3.1 30.6 + - + +
201B OLC 3.8 33.6 - - + +
202B OLC 3.6 25.2 - - + +
202H IIL 3.5 17.5 - - - +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.2 12.3 - - + -
144B SER 2.9 21.3 + - - +
145B ALA* 4.2 2.5 - - - +
147B THR* 1.3 74.4 - - + +
149B GLY* 1.3 67.1 + - - +
151B VAL* 3.0 28.4 - - + +
152B MET* 3.2 16.0 + - + +
201B OLC 3.5 73.4 - - + -
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Residues in contact with GLY 149 (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 ALA* 3.7 21.3 - - - -
104B LEU* 4.1 11.4 - - - +
105B VAL* 3.8 3.4 - - - -
145B ALA 3.0 18.0 + - - -
148B VAL* 1.3 75.7 - - - +
150B ALA* 1.3 62.9 + - - +
152B MET* 3.0 15.1 + - - +
153B LEU* 3.0 22.5 + - - +
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Residues in contact with ALA 150 (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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105B VAL* 3.7 5.7 - - + +
146B ILE* 3.0 20.9 + - + +
147B THR* 3.2 6.0 + - - +
149B GLY* 1.3 75.3 - - - +
151B VAL* 1.3 61.7 + - - +
153B LEU* 3.1 16.2 + - + +
154B ALA* 3.1 19.9 + - - +
202B OLC 3.8 26.1 - - + +
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Residues in contact with VAL 151 (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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147B THR* 3.1 22.3 + - + +
148B VAL* 3.0 27.6 - - + +
150B ALA* 1.3 75.1 - - - +
152B MET* 1.3 67.1 + - + +
154B ALA* 3.1 10.5 + - - +
155B LEU* 3.0 36.9 + - + +
202B OLC 3.7 26.7 - - + -
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Residues in contact with MET 152 (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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97B TRP* 3.4 71.1 + - + +
98B LEU* 5.8 0.4 - - - +
100B ILE* 4.1 7.2 - - + -
101B ALA* 3.6 17.9 - - + +
104B LEU* 4.0 26.7 - - - -
148B VAL* 3.3 13.7 - - + +
149B GLY 3.0 11.3 + - - +
151B VAL* 1.3 87.8 - - + +
153B LEU* 1.3 59.0 + - - +
155B LEU* 3.2 14.1 + - + +
156B ASP* 3.5 8.8 + - - +
201B OLC 4.0 30.3 - - + -
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Residues in contact with LEU 153 (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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87B TRP* 3.6 35.9 - - + -
98B LEU* 4.8 9.9 - - + -
101B ALA* 3.5 26.0 - - + +
102B LEU* 4.3 9.2 - - + -
105B VAL* 4.4 5.6 - - + -
149B GLY 3.0 33.8 + - - +
150B ALA* 3.1 12.1 + - - +
152B MET* 1.3 75.1 - - - +
154B ALA* 1.3 62.5 + - - +
156B ASP* 3.1 23.7 + - - +
202B OLC 5.5 3.4 - - - +
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Residues in contact with ALA 154 (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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150B ALA 3.1 10.3 + - - +
151B VAL* 3.1 9.1 + - - +
153B LEU* 1.3 77.1 - - - +
155B LEU* 1.3 63.6 + - + +
156B ASP 3.2 6.6 + - - +
202B OLC 3.6 61.6 - - + +
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Residues in contact with LEU 155 (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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97B TRP* 4.8 20.1 + - + +
151B VAL* 3.0 30.3 + - + +
152B MET* 3.7 12.1 - - + +
153B LEU 3.1 0.8 - - - -
154B ALA* 1.3 80.0 - - + +
156B ASP* 1.3 62.7 + - - +
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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