Contacts of the helix formed by residues 156 - 171 (chain A) in PDB entry 1O0L
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 LEU 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ALA* 4.9 2.0 - - + +
154A GLY* 2.9 33.4 + - - +
155A ALA* 1.3 76.2 - - - +
157A GLU* 1.3 66.6 + - + +
158A GLU* 3.1 30.3 - - + -
159A ALA* 3.0 24.6 + - + +
160A ARG* 3.0 11.3 + - - +
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Residues in contact with GLU 157 (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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155A ALA 3.8 0.4 + - - -
156A LEU* 1.3 74.2 - - + +
158A GLU* 1.3 63.2 + - + +
160A ARG* 3.4 12.5 + - - +
161A ARG* 2.8 74.4 + - - +
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Residues in contact with GLU 158 (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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156A LEU* 3.1 19.6 - - + +
157A GLU* 1.3 79.8 - - + +
159A ALA* 1.3 62.0 + - - +
161A ARG* 3.1 43.8 + - - +
162A LEU* 3.0 42.7 + - - +
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Residues in contact with ALA 159 (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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149A ALA 4.3 1.1 - - - +
150A LEU* 3.3 46.9 - - + +
156A LEU* 3.0 29.1 + - + +
158A GLU* 1.3 79.3 - - - +
160A ARG* 1.3 62.2 + - - +
162A LEU* 3.2 13.3 - - + +
163A ARG* 3.1 17.2 + - - +
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Residues in contact with ARG 160 (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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151A TYR* 3.5 41.5 + - + +
155A ALA* 2.7 35.7 + - + +
156A LEU 3.0 13.9 + - - +
157A GLU* 3.7 11.8 - - - +
159A ALA* 1.3 74.5 - - - +
161A ARG* 1.3 65.3 + - - +
163A ARG* 3.1 6.8 + - - +
164A GLU* 3.1 20.5 + - - +
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Residues in contact with ARG 161 (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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157A GLU* 2.8 44.9 + - - +
158A GLU* 3.1 47.9 + - - +
160A ARG* 1.3 76.5 - - - +
162A LEU* 1.3 55.8 + - - +
164A GLU* 3.3 8.8 + - - +
165A GLY* 2.8 27.7 + - - -
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Residues in contact with LEU 162 (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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93A TRP* 6.2 0.2 - - + -
150A LEU* 4.6 11.9 - - + -
158A GLU* 3.0 32.3 + - - +
159A ALA* 3.2 14.1 - - - +
160A ARG 3.1 0.2 - - - -
161A ARG* 1.3 79.7 - - - +
163A ARG* 1.3 57.8 - - - +
165A GLY* 3.4 1.1 + - - -
166A ASN* 2.8 51.5 + - - +
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Residues in contact with ARG 163 (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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48A ALA 3.5 5.7 + - - -
49A ALA* 3.4 19.8 + - - +
52A GLU* 2.6 43.4 + - - +
93A TRP* 4.8 6.5 - - + -
94A GLY* 4.6 17.7 - - - +
97A VAL* 4.5 5.9 - - - +
147A PHE* 3.3 32.6 - - - -
150A LEU* 3.8 21.9 - - + +
151A TYR* 3.3 46.7 - - + +
159A ALA 3.1 2.9 + - - +
160A ARG 3.1 9.2 + - - +
162A LEU* 1.3 78.8 - - - +
164A GLU* 1.3 58.4 + - - +
166A ASN* 3.3 7.0 + - - +
167A TRP* 3.0 35.0 + - + +
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Residues in contact with GLU 164 (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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52A GLU* 5.9 0.2 - - - +
56A ARG* 2.6 46.1 + - - +
151A TYR* 5.6 2.2 + - - +
160A ARG 3.1 12.2 + - - +
161A ARG* 3.5 12.1 - - - +
162A LEU 3.2 0.2 - - - -
163A ARG* 1.3 78.0 - - - +
165A GLY* 1.3 61.9 + - - +
167A TRP* 3.2 34.8 + - - +
168A ALA* 3.2 14.2 + - - +
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Residues in contact with GLY 165 (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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161A ARG 2.8 19.6 + - - -
162A LEU* 3.8 1.6 - - - -
164A GLU* 1.3 74.2 - - - +
166A ASN* 1.3 61.4 + - - +
168A ALA* 3.5 12.2 - - - +
169A SER* 3.2 16.1 + - - -
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Residues in contact with ASN 166 (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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92A ASN* 2.9 43.0 + - + +
93A TRP* 4.4 8.9 - - - +
94A GLY 5.2 3.4 - - - +
150A LEU* 5.7 0.2 - - - +
162A LEU* 2.8 40.3 + - - +
163A ARG* 3.4 9.6 - - - +
164A GLU 3.1 0.2 - - - -
165A GLY* 1.3 74.5 - - - +
167A TRP* 1.3 67.2 + - - +
168A ALA 3.1 2.0 + - - -
169A SER* 3.1 7.7 + - - -
170A VAL* 3.0 26.8 + - - +
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Residues in contact with TRP 167 (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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52A GLU* 6.0 2.2 - - - -
53A PHE* 5.0 7.6 - + + -
56A ARG* 3.5 33.2 - - - +
94A GLY* 3.9 20.6 - - - +
163A ARG* 3.0 30.7 + - + +
164A GLU* 3.2 38.0 + - + +
166A ASN* 1.3 76.1 - - - +
168A ALA* 1.3 70.8 + - + +
170A VAL* 3.2 11.2 - - - +
171A ARG* 2.7 70.6 + - + +
172A THR* 4.4 5.8 - - - -
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Residues in contact with ALA 168 (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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164A GLU 3.2 14.1 + - - +
165A GLY* 3.5 16.2 - - - +
166A ASN 3.1 1.0 - - - -
167A TRP* 1.3 93.3 - - + +
169A SER* 1.3 58.1 + - - +
172A THR* 2.6 27.3 + - - -
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Residues in contact with SER 169 (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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165A GLY 3.2 16.3 + - - -
166A ASN* 3.1 4.9 + - - -
168A ALA* 1.3 76.8 - - - +
170A VAL* 1.3 64.5 + - - +
172A THR* 5.3 0.2 - - - -
173A VAL* 3.3 26.1 + - - +
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Residues in contact with VAL 170 (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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89A GLY 5.4 0.7 - - - +
90A GLY* 3.9 24.2 - - - +
92A ASN* 3.7 37.0 - - + +
94A GLY* 4.6 0.2 - - - -
95A ARG* 4.4 11.2 - - + +
166A ASN* 3.0 29.4 + - - +
167A TRP* 3.2 13.5 - - + +
169A SER* 1.3 82.6 - - - +
171A ARG* 1.3 67.9 + - - +
172A THR 3.3 1.3 - - - -
173A VAL* 3.2 11.5 - - + +
174A LEU* 3.1 25.3 - - - +
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Residues in contact with ARG 171 (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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53A PHE* 3.7 26.6 - - + -
56A ARG* 4.5 23.0 + - - +
57A PHE* 3.6 34.2 - - - -
94A GLY 5.2 0.2 - - - +
95A ARG* 3.1 40.1 + - - +
167A TRP* 2.7 64.5 + - + +
170A VAL* 1.3 76.1 - - + +
172A THR* 1.3 59.6 + - - +
175A THR* 3.2 24.7 + - - -
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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