Contacts of the helix formed by residues 135 - 147 (chain A) in PDB entry 3AEV
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 GLU 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLU* 4.0 27.7 - - + +
99A ARG* 2.8 54.2 + - - +
100A ALA* 5.0 3.0 + - + +
130A GLU* 4.9 3.1 - - - -
133A TRP* 3.0 10.3 + - - +
134A GLY* 1.3 79.5 - - - +
136A VAL* 1.3 67.6 + - - +
137A TYR* 3.7 6.1 - - + +
138A ALA* 2.9 34.3 + - + +
139A ALA 3.3 4.7 + - - -
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Residues in contact with VAL 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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103A ALA* 3.8 14.8 - - + -
125A VAL* 5.8 0.9 - - + -
126A TRP* 3.6 57.2 - - + +
129A LEU* 4.2 11.2 - - + -
130A GLU* 3.8 27.9 + - + +
134A GLY 4.3 0.4 - - - -
135A GLU* 1.3 70.8 - - - +
137A TYR* 1.3 63.7 + - - +
139A ALA* 2.9 18.0 + - - +
140A PHE* 3.1 31.8 + - + -
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Residues in contact with TYR 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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99A ARG* 3.4 63.3 - - + +
100A ALA* 5.5 1.4 - - - +
102A LYS* 3.8 38.6 + - + +
103A ALA* 3.9 16.5 - - + +
106A LEU* 4.3 14.1 - - + -
135A GLU* 3.3 11.1 - - + +
136A VAL* 1.3 77.8 - - - +
138A ALA* 1.3 56.0 + - - +
140A PHE* 3.3 10.2 + + - +
141A GLU* 2.8 48.8 + - + +
170A TYR 3.9 5.2 + - - -
171A VAL* 3.4 28.8 - - + +
172A GLU 4.6 2.6 + - - -
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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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99A ARG* 4.3 2.7 - - - +
133A TRP* 4.1 19.7 - - + +
135A GLU* 2.9 31.3 + - + +
137A TYR* 1.3 73.7 - - - +
139A ALA* 1.3 68.1 + - - +
141A GLU* 2.8 14.0 + - - +
142A ASP* 2.8 25.1 + - - +
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Residues in contact with ALA 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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129A LEU* 3.7 31.0 - - + -
133A TRP* 3.8 35.9 - - + -
135A GLU 3.3 3.2 + - - -
136A VAL 2.9 11.5 + - - +
138A ALA* 1.3 76.5 - - - +
140A PHE* 1.3 66.5 + - - +
142A ASP* 3.0 7.4 + - - +
143A ALA* 2.9 20.6 + - - +
151A LEU* 4.1 8.9 - - + +
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Residues in contact with PHE 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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103A ALA* 3.9 38.4 - - + -
106A LEU* 4.1 24.0 - - + -
107A LEU* 4.8 10.1 - - + -
125A VAL* 4.8 4.9 - - + -
129A LEU* 4.0 21.5 - - + -
136A VAL* 3.1 20.9 + - + -
137A TYR* 3.5 11.2 - + + +
139A ALA* 1.3 82.2 - - + +
141A GLU* 1.3 62.2 + - - +
143A ALA* 3.1 6.6 + - + +
144A ALA* 3.0 23.2 + - - +
151A LEU* 4.8 5.6 - - + -
163A LEU* 4.6 26.7 - - + -
167A VAL* 4.1 18.7 - - + +
171A VAL* 3.7 19.6 - - + +
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Residues in contact with GLU 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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99A ARG* 2.9 42.1 + - - -
137A TYR* 2.8 35.7 + - + +
138A ALA* 2.8 11.4 + - - +
140A PHE* 1.3 72.5 - - - +
142A ASP* 1.3 64.5 + - - +
144A ALA* 3.2 4.7 + - - +
145A LYS* 3.1 21.7 + - - +
171A VAL* 3.9 13.7 - - + -
172A GLU 4.2 6.2 - - - +
174A PRO* 3.8 36.3 - - + +
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Residues in contact with ASP 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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133A TRP* 2.8 31.9 + - - +
138A ALA 2.8 10.5 + - - +
139A ALA 3.4 7.9 - - - +
141A GLU* 1.3 77.7 - - - +
143A ALA* 1.3 57.8 + - - +
145A LYS* 3.1 16.0 + - - +
146A ASP* 2.9 39.8 + - - +
150A VAL* 4.0 14.8 - - + +
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Residues in contact with ALA 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 ALA 2.9 13.2 + - - +
140A PHE* 3.1 10.3 + - - +
142A ASP* 1.3 75.9 - - - +
144A ALA* 1.3 57.7 + - - +
147A GLY* 2.8 38.7 + - - -
148A ILE* 3.8 30.2 + - + -
150A VAL* 3.7 12.0 - - + +
151A LEU* 4.4 6.7 - - + -
167A VAL* 4.0 11.0 - - + +
168A GLU* 5.6 2.6 - - - +
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Residues in contact with ALA 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 PHE 3.0 12.2 + - - +
141A GLU* 3.5 9.0 - - - +
142A ASP 3.2 0.2 - - - -
143A ALA* 1.3 79.3 - - - +
145A LYS* 1.3 58.9 + - - +
147A GLY 4.8 0.5 + - - -
167A VAL* 3.8 13.8 - - + +
168A GLU* 5.4 8.3 - - - +
171A VAL* 3.4 32.1 - - + +
172A GLU 4.5 1.8 - - - +
173A VAL* 3.7 18.5 - - + +
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Residues in contact with LYS 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 GLU 3.1 13.7 + - - +
142A ASP* 3.1 16.1 + - - +
144A ALA* 1.3 78.3 - - - +
146A ASP* 1.3 88.5 + - - +
173A VAL* 4.3 24.5 - - + -
174A PRO* 5.1 8.1 - - + -
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Residues in contact with ASP 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASP* 2.9 17.7 + - - +
145A LYS* 1.3 108.3 - - - +
147A GLY* 1.3 59.9 + - - +
149A GLU* 4.5 3.5 - - - +
150A VAL* 3.9 19.5 - - + +
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Residues in contact with GLY 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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143A ALA 2.8 21.1 + - - +
144A ALA 4.6 0.6 + - - -
145A LYS 3.8 1.0 - - - -
146A ASP* 1.3 75.9 - - - +
148A ILE* 1.3 66.9 + - - -
149A GLU* 3.0 13.0 + - - -
150A VAL* 3.1 20.8 + - - +
168A GLU* 5.6 5.4 - - - -
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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