Contacts of the helix formed by residues 140 - 155 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LYS* 3.1 21.0 - - - +
112A ASN* 3.3 11.5 + - - -
122A VAL* 3.4 4.9 - - - +
123A VAL 2.9 24.3 + - - +
124A ASP* 3.2 9.4 + - - -
125A PHE* 3.6 22.0 - - + -
126A ILE* 3.9 12.8 - - - -
139A PHE* 1.3 82.3 - - - +
141A LEU* 1.3 63.0 + - - +
142A ALA* 3.1 5.8 + - - +
143A ASP* 2.8 35.1 + - - -
144A SER* 3.0 22.3 + - - -
203E SER* 3.5 1.4 + - - -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 5.6 0.4 - - - -
22A LEU* 4.0 7.9 - - + +
23A ASP* 3.8 14.8 + - + +
26A SER* 3.5 17.7 - - - +
125A PHE* 3.6 27.5 - - + -
126A ILE* 4.1 8.7 - - + -
140A ASN* 1.3 75.5 - - - +
142A ALA* 1.3 55.9 + - - +
144A SER* 3.0 9.7 + - - +
145A ALA* 2.8 35.4 + - - +
202A OLC 3.5 54.7 - - + -
203A OLC 6.3 0.9 - - + -
204A OLC 4.1 17.4 - - + +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 5.1 1.6 - - - -
23A ASP* 2.9 31.4 + - + +
108A GLY* 3.3 26.7 - - - +
111A GLY* 4.6 0.7 - - - -
112A ASN* 3.4 20.9 - - - +
140A ASN* 3.1 7.2 + - - +
141A LEU* 1.3 75.7 - - - +
143A ASP* 1.3 57.1 + - - +
145A ALA* 3.3 2.6 + - - -
146A ILE* 2.9 34.8 + - - +
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Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASN* 3.0 24.8 + - - -
139A PHE* 3.1 24.3 - - + +
140A ASN* 2.8 20.5 + - - +
142A ALA* 1.3 71.5 - - - +
144A SER* 1.3 53.7 + - - +
146A ILE* 3.3 2.1 + - - +
147A THR* 2.7 40.3 + - - -
201A OLC 3.3 27.7 - - - +
202E IIL 3.4 10.5 - - - -
203E SER* 2.4 33.8 + - - -
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 4.6 2.1 - - - +
139A PHE* 3.3 19.8 - - - -
140A ASN 3.0 14.6 + - - -
141A LEU* 3.0 14.7 + - - +
143A ASP* 1.3 75.8 - - - +
145A ALA* 1.3 59.8 + - - +
147A THR* 3.9 0.6 - - - -
148A VAL* 2.8 37.1 + - - +
201A OLC 3.8 32.9 - - - +
204A OLC 6.5 0.2 - - - -
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 3.6 31.0 - - + -
104A LEU* 3.4 39.6 - - + +
108A GLY 4.3 0.4 - - - +
141A LEU 2.8 16.1 + - - +
142A ALA 3.6 4.7 - - - +
144A SER* 1.3 73.8 - - - +
146A ILE* 1.3 53.9 + - - +
148A VAL* 4.1 2.4 - - - +
149A GLY* 2.8 29.1 + - - -
201A OLC 6.1 2.7 - - - -
204A OLC 5.0 4.9 - - + +
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Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL* 3.7 23.1 - - + +
108A GLY* 3.4 33.7 - - - +
109A ALA 3.6 2.0 - - - +
112A ASN* 4.3 1.8 - - - +
142A ALA 2.9 18.7 + - - +
143A ASP 3.5 6.1 - - - +
145A ALA* 1.3 76.4 - - - +
147A THR* 1.3 53.5 + - - +
149A GLY* 3.3 1.2 + - - -
150A ALA* 2.6 42.7 + - + +
201E MLE 3.7 46.4 - - + +
202E IIL 3.9 23.6 - - + -
205E 5BV 5.6 0.7 - - - +
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Residues in contact with THR 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ASP 2.7 17.8 + - - -
144A SER 3.9 2.7 - - - -
146A ILE* 1.3 74.9 - - - +
148A VAL* 1.3 57.5 + - + +
150A ALA* 3.2 6.7 + - + +
151A VAL* 2.9 46.0 + - + +
201A OLC 2.3 50.2 + - + +
202E IIL 3.7 11.1 - - - +
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 3.8 17.0 - - + -
144A SER 2.8 22.7 + - - +
145A ALA* 4.1 2.2 - - - +
147A THR* 1.3 72.0 - - + +
149A GLY* 1.3 63.9 + - - +
151A VAL* 3.4 5.9 + - - +
152A MET* 3.0 41.0 + - + +
201A OLC 3.5 61.0 - - + -
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Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ALA* 3.6 19.2 - - - +
104A LEU* 3.9 10.0 - - - +
105A VAL* 3.5 15.5 - - - -
145A ALA 2.8 20.4 + - - -
146A ILE 3.5 1.1 - - - -
148A VAL* 1.3 78.4 - - - +
150A ALA* 1.3 59.5 + - - +
152A MET* 3.3 4.8 + - - +
153A LEU* 3.1 20.3 + - - +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL* 3.6 6.4 - - + +
146A ILE* 2.6 26.0 + - + +
147A THR* 3.2 7.4 + - - +
149A GLY* 1.3 72.3 - - - +
151A VAL* 1.3 58.3 + - + +
153A LEU* 3.3 11.6 + - - +
154A ALA* 2.9 27.1 + - - +
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A THR* 2.9 30.7 + - + +
148A VAL* 3.9 6.7 - - - +
150A ALA* 1.3 74.5 - - + +
152A MET* 1.3 61.5 + - + +
154A ALA* 3.1 7.7 + - + +
155A LEU* 2.9 51.0 + - + +
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Residues in contact with MET 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TRP* 2.7 82.9 + - + +
100A ILE* 4.0 19.5 - - + -
101A ALA* 3.6 10.1 - - + +
104A LEU* 3.9 24.5 - - - -
148A VAL* 3.0 30.6 + - + +
149A GLY 3.6 5.2 - - - +
150A ALA 3.3 0.2 - - - -
151A VAL* 1.3 78.8 - - + +
153A LEU* 1.3 60.5 + - - +
155A LEU* 3.5 1.6 + - + -
156A ASP* 3.4 9.9 + - - +
201A OLC 5.8 3.1 - - + -
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 5.6 2.5 - - + -
87A TRP* 3.9 39.3 - - + -
97A TRP* 6.0 0.4 - - + -
98A LEU* 4.8 15.3 - - + -
101A ALA* 4.1 16.2 - - + -
102A LEU* 4.4 14.6 - - + -
105A VAL* 4.9 9.9 - - + -
149A GLY 3.1 16.1 + - - +
150A ALA* 3.4 13.2 - - - +
151A VAL 3.2 0.2 - - - -
152A MET* 1.3 77.2 - - - +
154A ALA* 1.3 59.0 + - - +
156A ASP* 3.1 26.3 + - + +
157A MET* 4.0 4.0 + - - +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA 2.9 16.4 + - - +
151A VAL* 3.1 10.9 + - + +
153A LEU* 1.3 76.9 - - - +
155A LEU* 1.3 63.0 + - + +
156A ASP 3.1 0.7 - - - -
157A MET* 3.3 40.5 - - + +
158A PHE 5.9 0.2 - - - -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TRP* 4.8 15.2 - - + -
151A VAL* 2.9 38.3 + - + +
152A MET* 3.9 6.7 - - - +
153A LEU 3.2 0.2 - - - -
154A ALA* 1.3 81.2 - - + +
156A ASP* 1.3 60.3 + - - +
157A MET 3.3 1.6 - - - -
158A PHE* 3.5 23.9 + - - +
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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