Contacts of the helix formed by residues 133 - 147 (chain A) in PDB entry 2YXD
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 VAL 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A THR* 3.0 12.4 + - - +
132A ILE* 1.3 94.5 - - + +
134A LEU* 1.3 67.0 + - - +
135A GLU* 3.3 23.6 - - + +
136A ASN* 3.2 20.3 + - - +
137A ALA* 3.0 24.2 + - - +
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Residues in contact with LEU 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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132A ILE 4.0 1.8 + - - -
133A VAL* 1.3 75.4 - - - +
135A GLU* 1.4 75.3 + - + +
137A ALA* 3.3 7.3 + - - +
138A ALA* 2.9 32.6 + - + +
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Residues in contact with GLU 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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133A VAL* 3.3 19.5 - - + +
134A LEU* 1.4 90.9 - - + +
136A ASN* 1.3 63.1 + - - +
138A ALA* 3.4 7.9 + - - +
139A LYS* 2.9 40.1 + - + +
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Residues in contact with ASN 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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109A THR* 5.4 4.7 - - - +
112A ILE* 3.8 16.9 - - - +
131A THR* 3.5 19.4 + - - +
133A VAL* 3.2 17.7 + - - +
134A LEU 3.2 0.6 - - - -
135A GLU* 1.3 77.7 - - - +
137A ALA* 1.3 57.9 + - - +
138A ALA 3.2 0.2 - - - -
139A LYS* 3.2 33.1 - - - +
140A ILE* 2.8 51.6 + - + +
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Residues in contact with ALA 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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131A THR* 3.5 18.6 - - + +
133A VAL 3.0 13.2 + - - +
134A LEU* 3.4 12.8 - - - +
136A ASN* 1.3 77.9 - - - +
138A ALA* 1.3 63.7 + - - +
140A ILE* 4.1 0.3 - - - +
141A ILE* 3.2 32.4 + - + +
177A THR* 4.1 22.7 - - + +
179A ILE* 4.3 5.8 - - - -
170B PHE* 5.8 3.4 - - + -
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Residues in contact with ALA 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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134A LEU* 2.9 21.0 + - + +
135A GLU* 3.5 10.3 - - - +
137A ALA* 1.3 76.5 - - - +
139A LYS* 1.3 61.3 + - - +
141A ILE* 4.2 3.9 - - - +
142A ASN* 2.8 35.7 + - - +
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Residues in contact with LYS 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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112A ILE* 4.4 9.6 - - + -
113A GLU* 2.7 34.9 + - + +
116A ILE* 5.6 1.3 - - + -
135A GLU* 2.9 32.5 + - - +
136A ASN* 3.2 30.0 + - - +
138A ALA* 1.3 69.1 - - - +
140A ILE* 1.3 58.6 + - - +
142A ASN* 3.2 3.1 + - - +
143A GLU* 2.6 46.2 + - + +
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Residues in contact with ILE 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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112A ILE* 3.9 28.5 - - + -
116A ILE* 4.0 10.3 - - + -
129A ALA* 4.2 15.9 - - + -
130A ASN 5.4 0.7 - - - +
131A THR* 4.0 20.6 - - + -
136A ASN* 2.8 36.7 + - + +
139A LYS* 1.3 74.4 - - + +
141A ILE* 1.3 58.3 + - - +
143A GLU* 3.7 0.2 - - - +
144A PHE* 2.8 65.3 + - + -
179A ILE* 3.8 25.1 - - + -
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Residues in contact with ILE 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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137A ALA* 3.2 22.3 + - + +
138A ALA* 4.2 3.6 - - - +
139A LYS 3.2 0.6 - - - -
140A ILE* 1.3 79.5 - - - +
142A ASN* 1.3 58.5 + - - +
144A PHE* 4.0 1.6 - - - +
145A GLU* 3.0 34.7 + - - +
151A VAL* 4.1 14.5 - - + +
153A ALA* 3.9 22.7 - - + -
177A THR* 5.1 1.8 - - + -
179A ILE* 4.0 24.0 - - + -
161B ALA* 4.3 12.6 - - + -
168B HIS* 3.5 41.1 - - + +
170B PHE* 4.5 13.0 - - + -
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Residues in contact with ASN 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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138A ALA* 2.8 32.7 + - - +
139A LYS* 3.2 2.6 + - - +
141A ILE* 1.3 76.8 - - - +
143A GLU* 1.3 61.1 + - - +
145A GLU* 4.0 6.3 - - - +
146A SER* 2.7 35.6 + - - +
167B GLY* 5.7 2.3 - - - -
168B HIS* 3.6 26.0 + - - -
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Residues in contact with GLU 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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113A GLU* 5.4 10.5 - - - +
116A ILE* 3.5 37.2 - - + -
139A LYS* 2.6 29.0 + - + +
140A ILE 3.7 3.1 - - - +
142A ASN* 1.3 72.6 - - - +
144A PHE* 1.3 63.4 + - - +
146A SER* 3.4 6.4 - - - -
147A ARG* 2.7 64.2 + - - +
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Residues in contact with PHE 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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106A ILE* 4.6 4.9 - - + -
116A ILE* 3.5 35.9 - - + -
119A LEU* 5.5 0.2 - - + -
127A ILE* 3.5 45.8 - - + -
129A ALA* 4.6 4.3 - - + -
140A ILE* 2.8 50.0 + - + +
143A GLU* 1.3 73.7 - - - +
145A GLU* 1.4 63.6 + - - +
147A ARG* 3.1 4.2 + - - -
149A TYR* 3.0 40.7 + + + -
151A VAL* 3.6 16.4 - - + -
179A ILE* 4.0 15.5 - - + -
181A ALA* 3.4 25.6 - - + -
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Residues in contact with GLU 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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141A ILE* 3.0 23.3 + - - +
142A ASN* 4.0 7.3 - - - +
144A PHE* 1.4 74.1 - - - +
146A SER* 1.3 61.7 + - - +
148A GLY* 3.1 13.7 + - - -
149A TYR 3.8 11.4 + - - +
151A VAL* 3.4 27.6 + - + +
163B LYS* 3.3 36.6 + - - +
168B HIS* 2.9 42.6 + - - -
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Residues in contact with SER 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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142A ASN* 2.7 20.1 + - - +
143A GLU* 3.4 10.2 - - - -
145A GLU* 1.3 76.0 - - - +
147A ARG* 1.3 63.2 + - - +
148A GLY* 3.2 3.2 + - - -
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Residues in contact with ARG 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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113A GLU 5.2 0.8 + - - -
116A ILE* 4.0 10.3 - - - +
117A GLU* 3.7 32.6 + - - +
120A ASP* 2.7 48.9 + - - +
121A LYS* 4.2 14.5 - - - +
143A GLU* 2.7 52.2 + - - +
144A PHE 3.1 1.3 + - - -
146A SER* 1.3 79.1 - - - +
148A GLY* 1.3 60.5 + - - +
149A TYR* 3.3 18.4 - - + -
183A ARG* 3.3 20.6 + - - -
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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