Contacts of the helix formed by residues 137 - 150 (chain A) in PDB entry 2V40
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 PHE 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A HIS* 4.1 2.2 - - - -
135A ILE* 3.5 34.3 - - + -
136A VAL* 1.3 79.0 - - - +
138A ASP* 1.3 66.7 + - - +
139A PHE* 3.1 34.8 - + + -
140A HIS* 3.0 31.7 + + - +
141A GLN* 3.2 9.5 + - - +
179A LEU* 3.8 35.2 - - + -
191A PHE* 3.8 19.1 - + - -
195A PHE* 3.4 26.5 - + - -
198A LEU* 4.1 8.1 - - + -
216A GLU* 3.4 10.3 - - - +
220A LEU* 3.8 17.0 - - + -
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Residues in contact with ASP 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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102A HIS* 2.8 35.2 + - - -
104A PRO* 3.9 11.8 - - - +
137A PHE* 1.3 70.6 - - - +
139A PHE* 1.3 56.5 + - - +
141A GLN* 3.2 9.5 + - - +
142A ALA* 3.0 26.6 + - - +
216A GLU* 2.8 43.7 + - + +
219A LYS* 5.7 3.8 - - - +
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Residues in contact with PHE 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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137A PHE* 3.5 29.2 - + + -
138A ASP* 1.3 76.9 - - - +
140A HIS* 1.3 75.8 + + - +
142A ALA* 3.8 8.3 - - - +
143A ALA* 2.8 30.7 + - - +
195A PHE* 3.6 20.4 - + - -
198A LEU* 3.7 23.1 - - + -
199A ALA* 3.7 16.2 - - + -
202A TYR* 3.7 34.0 - + + -
209A LEU* 4.0 11.7 - - + +
210A GLU 5.9 0.4 - - - -
211A ILE* 3.6 36.8 - - + +
216A GLU* 3.8 12.3 + - - +
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Residues in contact with HIS 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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135A ILE 3.9 9.0 - - - -
136A VAL* 3.9 14.5 - - + -
137A PHE* 3.0 48.6 + + - +
139A PHE* 1.3 88.6 - + - +
141A GLN* 1.3 58.7 + - - +
143A ALA* 3.5 1.3 + - - -
144A ASP* 3.0 28.6 + - - +
165A GLY* 3.5 5.3 - - - +
168A PRO* 3.4 27.4 + - + +
169A VAL* 4.0 12.5 - - + +
172A SER* 3.0 23.8 + - - -
178A GLY* 5.7 1.6 - - - -
198A LEU* 4.1 6.7 - - + +
202A TYR* 3.5 26.1 - + - -
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Residues in contact with GLN 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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64A ASN* 4.7 3.0 + - - +
102A HIS* 3.5 46.0 + - - +
136A VAL* 3.9 3.6 - - + -
137A PHE 3.8 10.5 - - - +
138A ASP* 3.2 9.8 + - - +
140A HIS* 1.3 76.2 - - - +
142A ALA* 1.3 61.8 + - - +
144A ASP* 3.3 15.4 - - - +
145A GLY* 3.3 5.9 + - - -
163A LYS* 3.6 22.7 - - - +
164A LYS* 3.1 43.5 + - - +
165A GLY* 3.8 7.6 - - - +
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Residues in contact with ALA 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 ASP 3.0 15.5 + - - +
139A PHE* 3.8 5.6 - - - +
141A GLN* 1.3 73.4 - - - +
143A ALA* 1.3 64.3 - - - +
145A GLY* 3.2 4.2 + - - -
146A ILE* 3.2 24.2 + - + +
163A LYS* 6.2 0.4 - - - -
209A LEU* 3.7 21.1 - - + -
210A GLU 4.8 8.7 - - - +
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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 PHE 2.8 19.4 + - - +
140A HIS 3.8 3.8 - - - +
142A ALA* 1.3 71.6 - - - +
144A ASP* 1.3 59.6 + - - +
146A ILE* 3.2 5.8 + - - +
147A GLN* 2.8 41.5 + - - +
168A PRO* 4.4 1.6 - - + -
202A TYR* 3.6 31.4 - - + -
206A TYR* 4.0 11.8 - - + -
209A LEU* 3.4 10.7 - - + +
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Residues in contact with ASP 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 HIS 3.0 14.5 + - - +
141A GLN 3.3 12.6 - - - +
142A ALA 3.3 0.2 - - - -
143A ALA* 1.3 75.0 - - - +
145A GLY* 1.3 61.4 + - - +
147A GLN* 3.4 7.6 + - - +
148A GLU* 3.1 32.1 + - - +
163A LYS* 3.4 9.8 + - - -
164A LYS 3.3 9.9 + - - -
165A GLY* 2.9 28.8 + - - +
166A ILE* 3.8 4.4 + - - +
167A GLY 5.0 2.1 + - - -
168A PRO* 3.9 17.8 - - + +
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Residues in contact with GLY 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 GLN 3.3 5.0 + - - -
142A ALA 3.2 6.9 + - - -
144A ASP* 1.3 78.4 - - - +
146A ILE* 1.3 55.5 + - - +
148A GLU* 3.3 7.3 + - - +
149A GLN* 3.0 37.1 + - - +
163A LYS* 3.7 33.9 - - - +
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Residues in contact with ILE 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 ALA* 3.2 8.1 + - + +
143A ALA* 3.7 7.2 - - - +
145A GLY* 1.3 71.1 - - - +
147A GLN* 1.3 60.7 + - - +
149A GLN* 3.1 22.6 + - - +
150A GLN* 2.8 38.8 + - + +
206A TYR* 3.6 29.4 - - + -
208A THR* 4.0 15.9 - - - +
209A LEU* 3.4 54.7 - - + +
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Residues in contact with GLN 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 24.6 + - - +
144A ASP* 3.7 7.6 - - - +
146A ILE* 1.3 72.0 - - - +
148A GLU* 1.3 58.5 + - + +
150A GLN* 2.9 38.0 + - - +
167A GLY* 5.4 0.5 - - - -
168A PRO* 3.6 31.8 - - - +
202A TYR* 4.8 4.4 + - - -
206A TYR* 2.8 39.3 + - + +
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Residues in contact with GLU 148 (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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144A ASP* 3.1 25.4 + - - +
145A GLY* 3.5 11.4 - - - +
147A GLN* 1.3 78.2 - - + +
149A GLN* 1.3 65.2 + - - +
150A GLN 3.9 4.0 - - - -
163A LYS* 6.0 3.4 - - + -
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Residues in contact with GLN 149 (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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145A GLY* 3.0 23.1 + - - +
146A ILE* 3.2 26.1 - - - +
148A GLU* 1.3 78.4 - - - +
150A GLN* 1.3 59.1 + - + +
163A LYS* 4.7 13.1 - - - +
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Residues in contact with GLN 150 (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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146A ILE* 2.8 34.7 + - + +
147A GLN* 2.9 31.2 - - - +
148A GLU 3.9 4.9 - - - -
149A GLN* 1.3 77.4 - - + +
206A TYR* 3.9 23.3 + - - -
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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