Contacts of the helix formed by residues 159 - 171 (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 TRP 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LEU* 3.8 12.8 - - + -
110A ALA* 3.9 11.7 - - + -
111A ALA* 3.8 31.9 - - + -
114A LEU* 3.6 19.5 - - + -
116A LYS* 3.3 28.9 - - + +
121A ALA* 3.7 36.8 - - + -
124A GLU* 2.9 24.0 + - - +
125A VAL* 3.4 17.9 - - + -
155A VAL* 4.4 4.5 - - + -
156A PRO* 3.1 38.1 + - + +
157A ASP 3.0 1.0 + - - -
158A GLU* 1.3 82.8 - - + +
160A LEU* 1.3 66.5 + - - +
161A PRO 3.4 0.4 - - - -
162A VAL* 3.3 3.4 + - + +
163A LEU* 2.9 43.1 + - + +
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Residues in contact with LEU 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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148A ILE* 3.7 29.8 - - + +
149A GLU* 5.4 1.3 - - + -
151A LEU* 3.8 21.3 - - + -
152A LYS* 4.0 39.5 - - + +
155A VAL* 3.7 28.7 - - + +
157A ASP* 2.9 33.8 + - - +
159A TRP* 1.3 77.6 - - - +
161A PRO* 1.3 59.3 - - + +
163A LEU* 4.6 1.6 - - + -
164A LYS* 2.7 33.4 + - - +
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Residues in contact with PRO 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP 3.4 9.4 - - - +
158A GLU* 3.4 18.6 - - - +
160A LEU* 1.3 89.8 - - + +
162A VAL* 1.3 59.8 + - + +
164A LYS* 3.4 12.1 - - + +
165A GLU* 3.3 20.8 + - - +
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Residues in contact with VAL 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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110A ALA* 3.7 32.3 - - + +
113A LYS* 3.8 26.0 - - + -
114A LEU* 3.6 37.7 - - + -
158A GLU 4.0 5.6 - - - +
159A TRP* 3.6 13.7 - - + +
161A PRO* 1.3 74.0 - - + +
163A LEU* 1.3 67.2 + - - +
164A LYS 3.0 1.1 - - - -
165A GLU* 3.2 7.5 + - - +
166A ILE* 3.1 23.3 + - + +
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Residues in contact with LEU 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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106A LEU 5.3 0.9 - - - +
107A LEU* 4.5 11.4 - - + -
110A ALA* 3.7 25.1 - - + -
125A VAL* 4.1 21.1 - - + -
140A PHE* 4.6 17.9 - - + -
148A ILE* 3.9 13.5 - - + -
151A LEU* 4.2 20.2 - - + -
155A VAL* 4.9 4.7 - - + -
159A TRP* 2.9 43.1 + - + +
160A LEU* 4.0 1.1 - - + +
162A VAL* 1.3 77.3 - - - +
164A LYS* 1.3 56.5 + - - +
166A ILE* 3.8 5.3 - - + -
167A VAL* 2.9 38.2 + - + +
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Residues in contact with LYS 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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148A ILE* 3.7 35.2 - - + +
149A GLU* 5.7 2.5 - - - -
160A LEU 2.7 23.8 + - - +
161A PRO* 3.4 11.7 - - + +
162A VAL 3.0 0.4 - - - -
163A LEU* 1.3 73.4 - - - +
165A GLU* 1.3 63.9 + - - +
167A VAL* 5.0 1.8 - - - -
168A GLU* 2.7 72.7 + - + +
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Residues in contact with GLU 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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113A LYS* 3.2 25.8 + - - -
161A PRO 3.3 9.8 + - - +
162A VAL* 3.2 10.1 + - - +
164A LYS* 1.3 80.1 - - - +
166A ILE* 1.3 64.7 + - + +
168A GLU* 4.0 2.6 - - - -
169A ASN* 2.9 34.3 + - - +
116B GLY* 4.5 2.1 - - - -
118B TYR* 2.6 42.9 + - + +
175B PRO* 3.8 22.7 - - + +
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Residues in contact with ILE 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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106A LEU* 3.5 42.2 - - + +
109A LEU* 4.1 18.4 - - + -
110A ALA* 3.5 44.2 - - + +
113A LYS* 4.3 12.6 - - + -
162A VAL* 3.1 20.7 + - + +
163A LEU* 4.0 5.6 - - + +
165A GLU* 1.3 74.2 - - + +
167A VAL* 1.3 69.2 + - + +
169A ASN 3.2 1.2 + - - -
170A TYR* 3.1 33.4 + - + +
118B TYR* 4.9 5.2 - - - +
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Residues in contact with VAL 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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106A LEU* 6.2 0.4 - - + -
140A PHE* 4.1 32.3 - - + +
143A ALA* 4.0 10.3 - - + +
144A ALA* 3.8 30.7 - - + +
148A ILE* 4.5 10.1 - - + -
163A LEU* 2.9 28.9 + - + +
164A LYS* 4.4 2.9 - - - +
166A ILE* 1.3 75.8 - - + +
168A GLU* 1.3 71.5 + - + +
169A ASN 3.0 0.2 + - - -
171A VAL* 2.9 46.2 + - + +
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Residues in contact with GLU 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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143A ALA 5.6 1.8 - - - +
144A ALA* 5.4 9.8 - - - +
147A GLY* 5.6 5.9 - - - -
148A ILE 5.9 0.5 + - - -
164A LYS* 2.7 57.1 + - + +
165A GLU* 4.1 4.5 - - - +
167A VAL* 1.3 86.6 - - + +
169A ASN* 1.3 65.8 + - - +
170A TYR 3.7 0.2 + - - -
171A VAL 4.9 4.2 - - - +
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Residues in contact with ASN 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 GLU* 2.9 27.5 + - - +
166A ILE 3.2 2.6 + - - -
167A VAL 3.1 0.8 - - - -
168A GLU* 1.3 85.0 - - - +
170A TYR* 1.3 71.2 + - + +
171A VAL 4.0 0.2 - - - -
94B ARG* 4.7 8.8 + - - -
95B ASP* 5.0 4.5 - - - +
118B TYR* 3.4 57.9 - - + +
119B LEU 4.6 6.6 - - - +
120B GLU* 5.6 1.9 - - - +
175B PRO* 5.2 2.4 - - - +
178B ILE* 5.9 0.2 - - - +
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Residues in contact with TYR 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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102A LYS* 5.5 2.1 + - - +
106A LEU* 4.2 22.4 - - + +
109A LEU* 4.6 15.5 - - + +
137A TYR* 3.9 6.8 + - - -
166A ILE* 3.1 32.5 + - + +
167A VAL 3.1 1.4 + - - -
169A ASN* 1.3 87.4 - - + +
171A VAL* 1.3 63.6 + - - +
172A GLU* 4.0 3.4 + - - +
88B LEU* 4.3 21.4 - - + +
91B TRP* 3.7 53.2 + + + -
92B LYS* 4.5 20.3 - - + +
94B ARG* 5.4 4.2 + - - +
95B ASP* 5.0 7.6 - - - -
115B GLU* 5.8 0.2 + - - -
117B GLU 5.4 0.7 + - - -
118B TYR* 3.9 34.8 - + - -
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.0 20.6 - - + -
137A TYR* 3.4 18.2 - - + +
140A PHE* 3.7 21.5 - - + +
141A GLU* 3.9 14.8 - - + -
144A ALA* 3.4 28.1 - - + +
167A VAL* 2.9 32.9 + - + +
168A GLU* 4.9 4.0 - - - +
170A TYR* 1.3 80.2 - - - +
172A GLU* 1.3 71.5 + - - +
173A VAL* 3.9 1.0 + - - +
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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