Contacts of the helix formed by residues 133 - 140 (chain A) in PDB entry 4OMC
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 ASN 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A LEU 4.0 1.1 + - - -
131A ASP* 2.7 27.8 + - - +
132A LEU* 1.3 73.8 - - - +
134A VAL* 1.3 62.2 + - - +
135A LYS 3.5 2.2 - - - +
136A ALA* 3.2 30.9 + - - +
430A ASP* 2.9 31.7 + - - +
432A GLY* 3.1 23.0 + - - -
433A ALA 4.3 0.6 - - - +
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Residues in contact with VAL 134 (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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124A LEU* 3.3 32.7 + - + +
132A LEU* 3.9 24.2 - - + +
133A ASN* 1.3 73.9 - - - +
135A LYS* 1.3 67.0 + - - +
136A ALA 3.1 2.0 - - - -
137A ALA* 2.9 12.6 + - - +
138A TRP* 3.0 46.7 + - + +
215A VAL* 4.1 25.8 - - + +
377A ILE* 4.5 3.4 - - + -
380A LEU* 4.3 4.0 - - + -
431A ALA* 3.7 13.5 - - + -
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Residues in contact with LYS 135 (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 TYR* 4.4 16.4 - - + -
112A GLU* 2.7 45.0 + - + +
118A PHE* 5.4 0.2 - - + -
124A LEU 3.9 3.4 + - - -
125A SER* 3.7 29.4 - - - +
133A ASN 3.5 0.6 - - - -
134A VAL* 1.3 78.7 - - - +
136A ALA* 1.3 52.4 + - - +
138A TRP* 3.0 24.5 + - + +
139A ALA* 2.8 35.7 + - + +
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Residues in contact with ALA 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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133A ASN* 3.2 39.4 + - - +
134A VAL 3.1 0.4 - - - -
135A LYS* 1.3 77.9 - - - +
137A ALA* 1.3 60.0 + - - +
139A ALA* 3.6 7.7 + - - +
140A GLN* 3.2 32.8 + - - +
432A GLY* 4.1 5.6 - - - -
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Residues in contact with ALA 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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133A ASN 3.8 1.2 + - - -
134A VAL 2.9 10.9 + - - +
136A ALA* 1.3 77.6 - - - +
138A TRP* 1.3 65.7 + - - +
140A GLN* 3.1 10.1 + - - +
141A GLY 3.3 0.3 + - - -
142A TYR* 3.1 21.7 + - - +
380A LEU* 3.8 24.2 - - + -
431A ALA* 4.0 15.7 - - + +
432A GLY* 4.1 0.4 - - - -
435A VAL* 3.8 29.2 - - + -
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Residues in contact with TRP 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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110A TYR* 3.3 47.4 - + + +
113A PRO* 3.5 19.5 - - + -
118A PHE* 3.7 29.6 - + - -
124A LEU* 4.4 8.5 - - + -
125A SER* 5.6 0.2 - - - -
134A VAL* 3.0 32.8 + - + +
135A LYS* 3.4 24.0 - - + +
137A ALA* 1.3 76.1 - - - +
139A ALA* 1.3 54.5 + - - +
141A GLY* 2.7 26.3 + - - -
142A TYR 3.3 21.3 + - - -
143A THR* 4.4 7.9 - - + +
213A VAL* 3.9 13.0 - - + -
214A GLY 3.9 15.9 - - - -
215A VAL* 2.9 21.9 + - - -
217A TYR* 3.5 23.2 - + - +
380A LEU* 4.6 2.0 - - + -
415C GLY 5.0 1.4 - - - +
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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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109A VAL* 6.1 0.9 - - - +
110A TYR* 4.0 29.6 - - + +
135A LYS* 2.8 17.8 + - + +
136A ALA* 3.8 9.4 - - - +
138A TRP* 1.3 78.8 - - - +
140A GLN* 1.3 60.4 + - + +
141A GLY* 3.2 1.6 + - - -
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Residues in contact with GLN 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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136A ALA* 3.2 19.6 + - - +
137A ALA 3.1 9.4 + - - +
139A ALA* 1.3 75.9 - - + +
141A GLY* 1.3 58.3 + - - +
142A TYR* 3.6 23.6 + - + -
432A GLY* 3.2 28.5 + - - -
435A VAL* 3.5 12.9 - - - +
436A ALA* 3.8 12.7 - - - +
439A GLN* 3.7 19.9 + - - +
509C MET* 5.0 0.3 - - - +
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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