Contacts of the helix formed by residues 140 - 153 (chain C) in PDB entry 2W8I
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 THR 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C GLU* 3.7 29.1 + - + +
85C TYR 3.9 15.5 - - - +
86C ARG* 3.4 30.5 - - - +
87C ILE* 4.4 0.7 - - - -
139C LYS* 1.3 75.0 - - - +
141C VAL* 1.3 71.0 + - - +
142C SER* 2.8 8.3 + - - -
143C GLN* 2.8 34.6 + - - +
144C VAL* 2.8 23.7 + - - +
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Residues in contact with VAL 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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85C TYR* 4.9 4.1 + - + +
87C ILE* 4.4 6.4 - - + +
140C THR* 1.3 72.5 - - - +
142C SER* 1.3 59.1 + - - +
144C VAL* 3.4 5.2 + - - +
145C ARG* 2.6 39.0 + - - +
163C VAL* 3.4 34.6 - - + +
164C SER* 3.8 8.5 - - - -
165C ILE* 3.7 33.9 - - + -
189C ASN* 6.5 0.7 - - + -
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Residues in contact with SER 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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140C THR* 2.8 7.9 + - - -
141C VAL* 1.3 81.9 - - - +
143C GLN* 1.3 64.3 + - - +
145C ARG* 3.0 32.1 + - - +
146C GLN* 2.9 37.0 + - - +
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Residues in contact with GLN 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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86C ARG* 3.4 21.2 + - - +
139C LYS* 3.4 27.6 - - + +
140C THR* 2.8 41.0 + - - +
142C SER* 1.3 74.2 - - - +
144C VAL* 1.3 65.4 + - - +
146C GLN* 3.4 12.5 + - - +
147C ASP* 3.0 22.6 + - - +
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Residues in contact with VAL 144 (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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87C ILE* 3.4 30.7 - - + -
93C LEU* 4.6 5.8 - - + -
134C VAL* 5.2 2.9 - - + -
135C GLN 4.9 0.9 - - - +
136C VAL* 3.8 27.8 - - + -
139C LYS* 4.0 14.6 - - + +
140C THR 2.8 15.2 + - - +
141C VAL* 3.5 8.5 - - - +
143C GLN* 1.3 73.6 - - - +
145C ARG* 1.3 64.4 + - - +
147C ASP* 3.0 8.8 + - - +
148C ILE* 2.9 44.5 + - + +
163C VAL* 4.3 12.8 - - + -
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Residues in contact with ARG 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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141C VAL* 2.6 24.4 + - - +
142C SER* 3.0 37.7 + - - +
144C VAL* 1.3 74.1 - - - +
146C GLN* 1.3 65.6 + - + +
148C ILE* 3.3 2.4 + - - +
149C THR* 2.9 28.8 + - - +
161C VAL* 2.9 32.3 - - - +
162C ASP* 2.5 38.6 + - - +
163C VAL* 3.9 24.2 + - + -
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Residues in contact with GLN 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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142C SER* 2.9 22.1 + - - +
143C GLN* 3.8 10.0 + - - +
145C ARG* 1.3 76.7 - - + +
147C ASP* 1.3 67.8 + - - +
149C THR* 3.6 6.4 - - - -
150C SER* 3.1 26.2 + - - -
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Residues in contact with ASP 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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134C VAL* 3.5 22.2 - - + +
135C GLN 3.8 1.4 + - - +
139C LYS* 3.0 27.8 + - - +
143C GLN 3.0 13.1 + - - +
144C VAL* 3.0 14.0 + - - +
146C GLN* 1.3 81.0 - - - +
148C ILE* 1.3 62.4 + - - +
150C SER* 3.2 16.9 + - - -
151C ARG* 3.2 27.2 + - - +
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Residues in contact with ILE 148 (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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95C VAL* 4.0 32.8 - - + -
126C ILE* 4.7 12.6 - - + -
128C TYR* 4.7 6.7 - - + -
131C ILE* 4.1 23.6 - - + +
134C VAL* 4.4 11.9 - - + -
144C VAL* 2.9 35.9 + - + +
145C ARG 4.0 3.4 - - - +
147C ASP* 1.3 74.7 - - - +
149C THR* 1.3 58.3 + - - +
151C ARG* 3.9 1.4 - - - +
152C LEU* 2.8 55.9 + - + +
161C VAL* 4.1 13.2 - - + -
163C VAL* 4.2 4.9 - - + -
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Residues in contact with THR 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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145C ARG* 2.9 23.8 + - - +
146C GLN* 3.6 8.4 - - - -
148C ILE* 1.3 74.9 - - - +
150C SER* 1.3 70.5 + - - +
152C LEU* 2.9 16.7 + - - +
153C THR* 3.1 15.2 + - - +
159C PRO* 3.5 32.2 - - + +
161C VAL* 3.6 23.0 + - - +
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Residues in contact with SER 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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146C GLN 3.1 11.9 + - - -
147C ASP* 3.2 10.9 + - - -
149C THR* 1.3 80.8 - - - +
151C ARG* 1.3 79.8 + - - +
153C THR* 3.0 25.6 + - - -
154C THR* 4.3 1.9 + - - +
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Residues in contact with ARG 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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131C ILE* 2.6 55.0 + - + +
133C LYS 2.9 27.5 + - - +
134C VAL* 3.4 27.3 - - - +
135C GLN 4.7 1.0 - - - +
147C ASP* 3.2 35.2 + - - +
148C ILE 3.9 2.2 - - - +
149C THR 3.2 0.4 - - - -
150C SER* 1.3 86.6 + - - +
152C LEU* 1.3 58.0 - - - +
153C THR 3.0 5.2 + - - -
154C THR* 3.1 25.6 - - - +
155C TYR* 4.1 0.5 - - - -
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Residues in contact with LEU 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 VAL* 4.7 7.2 - - + -
103C LEU* 5.0 3.1 - - + -
128C TYR* 4.2 17.3 - - + -
129C PRO 4.6 2.5 - - - +
130C TYR* 4.5 19.3 - - + -
131C ILE* 3.7 17.0 - - + -
148C ILE* 2.8 38.5 + - + +
149C THR* 2.9 7.1 + - - +
151C ARG* 1.3 77.1 - - - +
153C THR* 1.3 57.6 + - - +
154C THR 3.4 0.7 - - - -
155C TYR* 3.2 19.6 + - + -
156C ILE* 3.2 35.6 + - + +
159C PRO* 3.9 6.7 - - + -
161C VAL* 4.0 17.5 - - + -
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Residues in contact with THR 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C THR* 3.1 11.7 + - - +
150C SER* 3.0 22.7 + - - -
151C ARG 3.0 0.6 - - - -
152C LEU* 1.3 75.0 - - - +
154C THR* 1.3 66.3 + - - +
155C TYR 3.0 3.1 + - - -
156C ILE 3.4 14.1 + - - +
157C GLU* 5.1 1.2 - - - -
158C SER 5.6 1.6 - - - +
159C PRO* 3.7 19.2 - - + +
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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