Contacts of the helix formed by residues 141 - 150 (chain A) in PDB entry 2DVW
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 THR 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A HIS* 3.6 7.8 - - - -
132A PRO 4.5 8.1 - - - -
133A ASP* 4.0 6.7 - - - +
134A ALA 3.5 17.5 - - - +
135A LYS* 4.0 1.8 - - + -
140A ALA* 1.3 77.4 - - - +
142A ALA* 1.3 66.0 + - - +
143A MET* 3.2 11.9 + - - +
144A HIS* 2.8 41.4 + - + +
145A ARG* 3.4 6.4 + - - +
164A SER 5.3 2.6 + - - +
167A ILE* 3.8 44.6 - - + -
175A PRO* 4.4 0.9 - - - +
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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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110A LEU* 3.9 29.2 - - + +
111A HIS* 3.6 18.9 + - + +
114A ALA* 3.9 22.3 - - + +
132A PRO 4.6 6.4 + - - +
134A ALA 4.4 1.4 + - - -
141A THR* 1.3 72.9 - - - +
143A MET* 1.3 63.1 + - - +
145A ARG* 3.1 7.4 + - - +
146A ALA* 3.1 21.7 + - - +
158A LEU* 3.8 13.9 - - + -
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Residues in contact with MET 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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132A PRO 5.3 1.0 + - - -
141A THR* 3.1 9.7 + - - +
142A ALA* 1.3 81.5 - - - +
144A HIS* 1.3 60.1 + - - +
146A ALA* 4.5 0.7 - - - +
147A ALA* 3.0 30.2 + - + +
155A VAL* 4.9 7.9 - - + -
158A LEU* 3.6 18.4 - - + +
159A LEU* 3.6 20.2 - - + -
163A ALA* 3.2 33.4 - - + +
164A SER 3.2 23.3 - - - +
165A THR* 4.0 8.3 - - + -
175A PRO* 3.9 20.4 - - + -
191A LEU* 3.6 28.7 - - + -
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Residues in contact with HIS 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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139A ASP 4.2 2.4 + - - -
140A ALA* 3.8 12.3 - - + -
141A THR* 2.8 50.6 + - - +
143A MET* 1.3 75.4 - - - +
145A ARG* 1.3 65.2 + - + +
148A ALA* 3.0 28.3 + - - +
167A ILE* 3.1 30.1 + - - +
169A ASP* 3.9 15.2 + - + +
173A ASN 2.9 30.1 + - - -
174A THR 3.7 0.2 - - - -
175A PRO* 3.6 22.2 - - + +
178A LEU* 3.4 27.9 - - + +
338B ARG* 4.9 2.0 - - - +
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Residues in contact with ARG 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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105A ASN* 4.6 0.6 - - - +
107A CYS* 3.8 6.2 - - - -
111A HIS* 3.6 39.7 - - - +
112A TYR* 5.4 0.6 - - - -
115A SER* 3.9 21.1 - - - +
136A ASP* 3.4 25.4 + - - -
140A ALA* 3.9 17.2 - - - +
141A THR 3.4 2.5 + - - +
142A ALA 3.1 8.2 + - - +
144A HIS* 1.3 81.7 - - - +
146A ALA* 1.3 62.8 + - - +
148A ALA* 3.8 2.8 - - - +
149A LYS* 3.1 32.5 + - - +
338B ARG* 4.9 2.8 - - - +
359B ASP* 4.6 3.4 + - - -
361B GLU* 3.8 27.4 + - + +
362B ASP* 2.7 41.8 + - - +
365B ALA* 4.0 15.4 - - - +
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Residues in contact with ALA 146 (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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114A ALA* 4.2 4.2 + - + +
142A ALA 3.1 14.5 + - - +
143A MET 4.1 2.5 - - - +
145A ARG* 1.3 77.2 - - - +
147A ALA* 1.3 62.3 + - - +
149A LYS 3.9 0.2 - - - -
150A GLY 3.2 3.8 + - - -
151A ASN* 2.9 41.5 + - + +
154A MET* 3.8 28.5 - - + -
155A VAL* 3.9 17.0 - - + +
158A LEU* 4.3 7.0 - - + -
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Residues in contact with ALA 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 MET* 3.0 19.4 + - + +
144A HIS 4.1 1.3 - - - +
146A ALA* 1.3 74.6 - - - +
148A ALA* 1.3 67.3 + - - +
150A GLY* 3.3 4.3 + - - -
155A VAL* 3.9 12.5 - - + +
175A PRO* 3.6 30.7 - - + +
178A LEU* 4.9 0.2 - - + -
179A ALA* 3.9 8.1 - - + -
184A ARG* 3.3 24.1 - - - +
187A GLU* 4.3 4.6 - - + +
191A LEU* 4.2 12.8 - - + -
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Residues in contact with ALA 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 HIS 3.0 19.8 + - - +
145A ARG 3.8 3.1 - - - +
147A ALA* 1.3 77.6 - - - +
149A LYS* 1.3 56.9 + - - +
178A LEU* 4.0 22.6 - - + +
182A GLU* 3.1 30.7 - - - +
184A ARG* 2.8 20.6 + - - -
338B ARG* 3.7 22.4 - - - +
342B ARG* 4.0 3.8 - - - +
361B GLU* 4.3 0.4 - - - +
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Residues in contact with LYS 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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115A SER* 2.8 49.2 + - - +
116A LYS* 4.3 6.3 - - - +
145A ARG 3.1 18.0 + - - +
147A ALA 3.3 0.2 - - - -
148A ALA* 1.3 75.8 - - - +
150A GLY* 1.3 62.4 + - - +
151A ASN* 3.8 15.8 - - - +
184A ARG* 3.6 17.5 + - - +
342B ARG* 3.7 30.1 - - - +
359B ASP* 4.0 9.5 + - - -
361B GLU* 3.5 21.6 + - + +
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Residues in contact with GLY 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 ALA 3.2 4.0 + - - -
147A ALA 3.3 5.8 + - - -
148A ALA 3.3 1.4 + - - -
149A LYS* 1.3 79.0 - - - +
151A ASN* 1.3 59.8 + - - +
152A LEU* 3.2 3.1 + - - +
184A ARG* 3.6 19.5 - - - -
187A GLU* 3.0 27.9 - - - +
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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