Contacts of the helix formed by residues 138 - 144 (chain A) in PDB entry 1CVU
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 SER 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A THR 5.4 0.2 + - - -
134A TYR* 3.2 30.1 - - - -
136A TYR* 3.4 1.7 + - - -
137A LYS* 1.3 77.0 - - - +
139A TRP* 1.3 64.6 + - - +
140A GLU 3.6 0.5 + - - -
141A ALA* 3.0 24.4 + - - +
142A PHE* 3.1 22.0 + - - +
2330B GLN* 3.6 26.5 - - - -
2334B LEU* 4.3 12.1 - - - +
2544B TYR* 4.6 4.9 + - - -
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Residues in contact with TRP 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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138A SER* 1.3 75.3 - - - +
140A GLU* 1.3 54.0 + - - +
142A PHE* 3.7 33.0 - + + -
143A SER* 2.5 56.0 + - - -
2225B GLY* 5.6 7.2 - - - -
2228B VAL 5.1 0.2 - - - -
2229B ASP* 3.3 34.7 + - + +
2330B GLN* 3.7 5.5 + - - +
2333B LYS* 3.7 43.3 - - + +
2334B LEU* 4.0 19.7 - - + +
2337B ILE* 3.5 21.1 - - + -
2537B ASN* 3.8 24.0 - - - -
2538B PRO* 3.5 26.2 - - + -
2539B ILE* 4.6 2.0 - - + -
2544B TYR* 6.3 1.3 - + - -
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Residues in contact with GLU 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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134A TYR* 3.4 39.7 - - + +
138A SER* 3.1 0.8 - - - +
139A TRP* 1.3 77.1 - - - +
141A ALA* 1.3 65.2 + - - +
143A SER* 3.9 4.7 + - - -
144A ASN* 2.8 62.0 + - - +
147A TYR* 4.0 4.6 - - + +
2238B LEU* 4.4 21.8 - - - +
2241B GLN* 4.8 7.9 + - - +
2330B GLN* 3.7 17.3 + - - +
1D NAG 3.4 13.8 + - - +
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Residues in contact with ALA 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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128A PRO* 5.7 1.0 - - - +
129A THR 3.3 25.6 - - - +
130A TYR* 4.7 0.4 - - - +
131A ASN* 3.4 28.2 - - - +
134A TYR* 3.9 16.8 - - + -
136A TYR 4.9 0.2 - - - +
138A SER* 3.0 25.1 + - - +
140A GLU* 1.3 77.7 - - - +
142A PHE* 1.3 63.8 + - - +
144A ASN 4.2 5.5 + - - +
147A TYR* 5.6 0.7 - - - +
376A ARG* 3.9 8.7 + - - -
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Residues in contact with PHE 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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127A PRO* 4.2 11.7 - - + -
128A PRO* 4.3 9.9 - - + -
129A THR 4.5 0.8 + - - -
138A SER 3.1 14.7 + - - +
139A TRP* 3.7 37.7 - + + +
141A ALA* 1.3 78.3 - - - +
143A SER* 1.3 66.0 + - - +
145A LEU* 4.8 0.2 - - - +
374A GLN* 5.2 2.9 - - - -
376A ARG* 2.7 55.2 + - - +
2373B TYR 6.0 1.6 - - - -
2538B PRO* 3.6 39.9 - - + -
2544B TYR* 3.6 24.5 - - + +
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Residues in contact with SER 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 TRP* 2.5 51.5 + - - -
140A GLU* 3.7 6.6 + - - -
142A PHE* 1.3 84.4 - - - +
144A ASN* 1.3 61.9 + - - +
145A LEU* 3.0 20.1 + - - +
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Residues in contact with ASN 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 GLU* 2.8 34.0 + - - +
141A ALA 4.3 3.3 - - - +
142A PHE 3.5 0.8 - - - -
143A SER* 1.3 74.9 + - - +
145A LEU* 1.3 58.4 + - - +
146A SER* 3.0 23.7 + - - -
147A TYR* 3.5 26.4 + - + +
376A ARG* 4.0 8.3 + - - -
1D NAG 1.4 72.4 + - - +
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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