Contacts of the helix formed by residues 140 - 155 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C LYS* 3.2 21.0 - - - +
112C ASN* 3.3 13.1 + - - -
122C VAL* 3.5 2.2 - - - +
123C VAL 2.8 23.9 + - - +
124C ASP* 3.1 9.6 + - - -
125C PHE* 3.6 20.4 - - + -
126C ILE* 4.0 11.9 - - - -
139C PHE* 1.3 79.2 - - - +
141C LEU* 1.3 62.7 + - - +
142C ALA* 3.1 5.0 + - - +
143C ASP* 2.8 36.6 + - - -
144C SER* 2.9 26.0 + - - -
203F SER* 3.5 3.6 + - - -
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 5.2 3.1 - - + +
22C LEU* 3.6 22.0 - - + +
23C ASP* 3.7 14.5 + - + +
26C SER* 3.3 27.8 - - - +
125C PHE* 3.5 20.4 - - + -
126C ILE* 4.7 6.1 - - + -
140C ASN* 1.3 75.3 - - - +
142C ALA* 1.3 56.7 + - - +
144C SER* 2.9 9.6 + - - +
145C ALA* 2.7 36.4 + - - +
204C OLC 3.8 30.5 - - + -
301F OLC 4.4 16.8 - - + +
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 5.1 0.7 - - - -
23C ASP* 2.9 29.1 + - - +
108C GLY* 3.3 34.0 - - - +
111C GLY* 4.6 0.4 - - - -
112C ASN* 3.3 22.7 - - - +
140C ASN* 3.1 1.7 + - - +
141C LEU* 1.3 73.8 - - - +
143C ASP* 1.3 58.8 + - - +
145C ALA* 3.3 1.5 + - - -
146C ILE* 2.9 35.0 + - - +
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Residues in contact with ASP 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ASN* 3.0 14.0 + - - -
139C PHE* 3.2 28.0 - - + +
140C ASN* 2.8 23.9 + - - +
142C ALA* 1.3 72.1 - - - +
144C SER* 1.3 53.4 + - - +
146C ILE* 3.3 7.1 + - - +
147C THR* 2.7 39.8 + - - -
202F IIL 3.3 8.1 - - + +
203F SER* 2.4 48.2 + - - -
301F OLC 3.5 17.4 - - + +
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Residues in contact with SER 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ILE* 4.5 3.5 - - - +
139C PHE* 3.7 17.5 - - - -
140C ASN 2.9 14.8 + - - -
141C LEU* 2.9 13.5 + - - +
143C ASP* 1.3 79.1 - - - +
145C ALA* 1.3 56.5 + - - +
147C THR* 3.3 0.7 + - - -
148C VAL* 2.8 37.3 + - - +
301F OLC 3.7 45.7 - - - +
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 3.6 22.7 - - + -
104C LEU* 3.3 36.8 - - + +
141C LEU 2.7 18.6 + - - +
142C ALA 3.7 4.0 - - - +
144C SER* 1.3 72.3 - - - +
146C ILE* 1.3 56.8 + - - +
148C VAL* 4.1 1.1 - - - +
149C GLY* 2.9 25.6 + - - -
301F OLC 4.1 19.9 - - + +
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Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C VAL* 3.9 22.6 - - + +
108C GLY* 3.6 31.0 - - - +
112C ASN* 4.2 3.4 - - - +
142C ALA 2.9 24.8 + - - +
143C ASP* 3.5 3.8 - - - +
145C ALA* 1.3 75.1 - - - +
147C THR* 1.3 58.0 + - - +
149C GLY* 3.8 0.7 - - - -
150C ALA* 2.8 29.7 + - + +
201F MLE 3.7 30.1 - - + -
202F IIL 3.9 29.6 - - + +
302F OLC 3.9 22.7 - - + -
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Residues in contact with THR 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ASP 2.7 25.7 + - - -
144C SER 3.7 3.6 - - - -
146C ILE* 1.3 75.4 - - - +
148C VAL* 1.3 64.3 + - - +
150C ALA* 3.3 5.7 + - - +
151C VAL* 3.1 37.1 + - + +
202F IIL 4.1 6.1 - - - +
301F OLC 3.4 49.8 + - + +
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Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 4.0 18.4 - - + -
144C SER 2.8 22.6 + - - +
145C ALA* 4.1 3.1 - - - +
147C THR* 1.3 73.4 - - + +
149C GLY* 1.3 58.3 + - - +
151C VAL* 3.3 7.7 + - - +
152C MET* 3.0 39.8 + - + +
204C OLC 6.4 2.0 - - + -
301F OLC 3.6 42.2 - - + -
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Residues in contact with GLY 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ALA* 3.6 26.5 - - - -
104C LEU* 4.3 4.7 - - - +
105C VAL* 3.7 9.0 - - - -
145C ALA 2.9 18.5 + - - -
148C VAL* 1.3 78.0 - - - +
150C ALA* 1.3 61.0 + - - +
152C MET* 3.1 3.7 + - - +
153C LEU* 3.1 28.0 + - - +
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Residues in contact with ALA 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C VAL* 3.8 3.0 - - + +
146C ILE 2.8 19.2 + - - +
147C THR* 3.7 7.0 - - - +
148C VAL 3.3 0.2 - - - -
149C GLY* 1.3 76.4 - - - +
151C VAL* 1.3 63.7 + - + +
153C LEU* 3.5 6.2 + - - +
154C ALA* 3.3 19.8 + - - +
302F OLC 4.3 42.2 - - + +
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C THR* 3.1 24.4 + - + +
148C VAL* 3.6 9.9 - - - +
150C ALA* 1.3 79.5 - - + +
152C MET* 1.3 62.7 + - + +
154C ALA* 3.1 9.1 + - + +
155C LEU* 3.0 42.2 + - + +
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Residues in contact with MET 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C TRP* 3.0 83.0 + - + +
100C ILE* 3.7 21.8 - - + -
101C ALA* 3.5 18.2 - - + +
104C LEU* 4.1 15.7 - - - -
148C VAL* 3.0 35.5 + - + +
149C GLY 3.1 3.1 + - - +
151C VAL* 1.3 75.3 - - + +
153C LEU* 1.3 64.8 + - - +
155C LEU* 3.2 10.8 + - + +
156C ASP* 3.3 3.8 + - - +
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Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LEU* 6.1 1.3 - - + -
87C TRP* 3.6 32.1 - - + -
98C LEU* 4.5 6.3 - - + -
101C ALA* 3.5 21.8 - - + +
102C LEU* 3.8 16.2 - - + -
105C VAL* 4.6 5.6 - - + -
149C GLY 3.1 32.5 + - - +
150C ALA* 3.8 5.4 - - - +
151C VAL 3.3 0.2 - - - -
152C MET* 1.3 76.1 - - - +
154C ALA* 1.3 62.9 + - - +
156C ASP* 3.1 23.4 + - - +
157C MET* 4.2 5.9 + - - +
302F OLC 3.7 37.9 - - + +
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Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ALA 3.3 10.0 + - - +
151C VAL* 3.1 14.2 + - + +
153C LEU* 1.3 78.3 - - - +
155C LEU* 1.3 65.0 + - + +
156C ASP 3.2 1.8 + - - -
157C MET* 3.8 24.0 + - - +
158C PHE* 5.3 4.2 - - - -
79D VAL* 6.1 2.9 - - + -
302F OLC 4.6 11.8 - - + +
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Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C TRP* 4.5 23.8 + - + -
151C VAL* 3.0 38.2 + - + +
152C MET* 3.6 9.4 - - + +
153C LEU 3.1 0.8 - - - -
154C ALA* 1.3 78.4 - - + +
156C ASP* 1.3 60.8 + - - +
157C MET 3.2 2.4 + - - -
158C PHE* 3.7 45.6 + - + +
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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