Contacts of the helix formed by residues 131 - 144 (chain A) in PDB entry 2W27
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 ASP 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A PHE* 3.3 5.1 - - - -
130A GLY* 1.3 67.4 - - - -
132A ILE* 1.3 71.2 + - - +
133A GLU* 3.0 26.9 + - - +
134A GLN* 3.0 37.4 + - + +
135A LEU 3.3 4.3 + - - -
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Residues in contact with ILE 132 (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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125A GLU* 4.3 8.1 - - + +
128A PHE* 3.7 19.7 - - + -
130A GLY 3.2 5.2 + - - +
131A ASP* 1.3 73.8 + - - +
133A GLU* 1.3 83.7 + - + +
135A LEU* 3.1 14.9 + - + +
136A TYR* 2.8 27.8 + - + +
163A ARG* 3.4 46.0 - - + +
166A LEU* 5.7 4.3 - - + -
167A LEU* 4.6 18.2 - - + -
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Residues in contact with GLU 133 (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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131A ASP* 3.0 17.4 + - - +
132A ILE* 1.3 94.2 - - + +
134A GLN* 1.3 56.9 + - - +
136A TYR* 3.6 12.0 - - + +
137A HIS* 3.0 25.8 + - - +
166A LEU* 3.6 24.6 - - - +
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Residues in contact with GLN 134 (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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95A MET* 3.4 26.9 - - + +
98A HIS* 3.2 28.1 + - + +
128A PHE* 5.6 0.7 - - + -
131A ASP* 3.0 27.8 + - + +
133A GLU* 1.3 76.9 - - - +
135A LEU* 1.3 64.9 + - - +
136A TYR 3.3 0.2 - - - -
137A HIS* 3.1 14.7 - - + +
138A MET* 3.0 19.1 + - - +
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Residues in contact with LEU 135 (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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91A ALA* 3.8 24.2 - - + +
94A LEU* 6.1 1.6 - - + -
95A MET* 3.9 13.7 - - - +
123A ILE* 4.9 11.2 - - + -
125A GLU* 5.3 4.3 - - - -
128A PHE* 3.5 45.5 - - + -
131A ASP 3.3 2.8 + - - -
132A ILE* 3.1 18.0 + - + +
134A GLN* 1.3 77.4 - - - +
136A TYR* 1.3 63.5 + - - +
138A MET* 3.2 13.8 + - + +
139A LEU* 3.1 47.9 + - + +
167A LEU* 4.8 5.6 - - + -
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Residues in contact with TYR 136 (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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132A ILE* 2.8 17.9 + - + +
133A GLU* 3.6 11.9 - - - +
135A LEU* 1.3 73.4 - - - +
137A HIS* 1.3 64.7 + - - +
139A LEU* 3.7 3.8 + - + +
140A ALA* 3.4 24.2 + - + +
166A LEU* 2.2 48.4 + - + +
167A LEU* 3.1 50.5 - - + +
168A SER* 4.6 6.4 - - - -
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Residues in contact with HIS 137 (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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98A HIS* 6.1 3.1 - + - -
133A GLU 3.0 17.1 + - - +
134A GLN* 3.1 20.9 - - + +
136A TYR* 1.3 80.3 - - - +
138A MET* 1.3 66.9 + - + +
140A ALA* 3.1 22.3 - - - +
141A TYR* 3.5 4.3 + - - +
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Residues in contact with MET 138 (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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94A LEU* 3.6 33.0 - - + +
95A MET* 3.9 27.6 - - + +
98A HIS* 3.8 26.5 - - + +
99A GLY* 4.0 3.6 - - - -
134A GLN 3.0 12.5 + - - +
135A LEU* 3.6 13.9 - - - +
137A HIS* 1.3 79.3 - - + +
139A LEU* 1.3 71.8 + - + +
141A TYR* 2.9 32.1 + - + +
142A TYR* 3.2 44.6 + - + +
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Residues in contact with LEU 139 (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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94A LEU* 5.2 1.1 - - + -
121A LEU* 4.9 3.4 - - + -
123A ILE* 4.2 20.0 - - + -
135A LEU* 3.1 31.2 + - + +
136A TYR* 4.1 4.3 - - + +
138A MET* 1.3 96.5 - - + +
140A ALA* 1.3 63.3 + - - +
142A TYR* 3.1 8.8 + - + +
143A ARG* 2.9 29.6 + - - +
149A ILE* 3.7 39.4 - - + +
167A LEU* 3.3 36.8 - - + +
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Residues in contact with ALA 140 (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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136A TYR* 3.4 18.5 + - + +
137A HIS* 3.1 16.9 + - - +
139A LEU* 1.3 75.9 - - - +
141A TYR* 1.3 63.6 + - - +
143A ARG* 3.1 23.0 + - - +
144A THR* 3.1 20.4 + - + +
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Residues in contact with TYR 141 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.8 21.1 - - + -
137A HIS 3.5 3.8 + - - +
138A MET* 2.9 16.7 + - + +
140A ALA* 1.3 77.1 - - - +
142A TYR* 1.3 67.9 + + + +
144A THR* 2.3 31.7 + - - -
145A TYR* 3.4 37.9 + + - -
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Residues in contact with TYR 142 (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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94A LEU* 4.0 1.9 - - + +
98A HIS 4.9 0.7 - - - -
99A GLY* 2.6 37.5 + - - -
102A PHE* 3.5 19.6 - + - +
103A LEU* 3.5 28.9 + - + -
106A LEU* 4.9 1.1 - - + -
121A LEU* 3.5 34.1 - - + -
138A MET* 3.2 38.5 + - + +
139A LEU* 3.1 14.7 + - + +
141A TYR* 1.3 83.6 - + + +
143A ARG* 1.3 62.6 + - - +
145A TYR* 3.0 19.8 + - - +
147A ILE* 3.3 41.1 - - + +
149A ILE* 4.9 4.0 - - + -
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Residues in contact with ARG 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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139A LEU* 2.9 19.8 + - - +
140A ALA* 3.1 15.5 + - - +
142A TYR* 1.3 75.6 - - - +
144A THR* 1.3 54.6 + - + +
145A TYR 3.0 0.2 - - - -
146A GLY* 2.6 27.4 + - - -
147A ILE 3.5 19.4 + - - +
149A ILE* 4.3 14.4 - - + +
167A LEU 4.2 8.2 + - - -
168A SER* 2.5 32.0 + - - -
169A PRO* 3.3 3.4 + - - +
170A ASP* 3.0 47.7 + - - +
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Residues in contact with THR 144 (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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140A ALA* 3.1 15.4 + - + +
141A TYR* 2.3 35.0 + - - -
143A ARG* 1.3 74.1 - - + +
145A TYR* 1.3 66.5 + - - +
146A GLY 3.4 0.4 - - - -
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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