Contacts of the helix formed by residues 124 - 130 (chain D) in PDB entry 1OVM
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 ARG 124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A GLU* 3.4 26.5 + - - +
108D GLN* 4.6 9.0 + - - -
122D GLU* 3.7 1.8 - - - +
123D PHE* 1.3 87.2 - - + +
125D HIS* 1.3 66.0 + - - +
126D PHE 3.4 2.0 - - - -
127D TYR* 3.3 17.4 + - + +
128D HIS* 3.0 51.3 + - + +
139D VAL* 3.9 44.7 - - - +
166D MET* 4.9 3.1 - - - -
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Residues in contact with HIS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C TYR* 6.2 0.4 - + - -
132C PRO* 4.2 26.0 + - + +
118D LEU* 3.3 25.5 - - + +
120D ASP* 2.8 31.2 + - - -
122D GLU* 3.5 27.8 + - + +
123D PHE 3.5 2.0 - - - -
124D ARG* 1.3 79.4 - - - +
126D PHE* 1.3 76.6 + - + +
128D HIS* 3.2 7.5 + - - +
129D MET* 2.9 32.3 + - - +
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Residues in contact with PHE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ILE* 5.1 1.3 - - + -
407C TRP* 3.7 25.6 - + - -
75D PHE* 3.6 35.7 - + + -
76D GLY* 3.6 14.4 - - - -
79D GLU* 3.4 39.9 - - + +
80D LEU* 4.0 18.4 - - + -
83D MET* 4.9 2.3 - - - +
116D HIS 3.6 3.1 - - - -
117D THR* 4.5 3.6 - - - -
118D LEU* 3.7 30.3 - - + -
122D GLU 5.6 3.1 - - - -
123D PHE 5.2 0.2 + - - -
125D HIS* 1.3 83.9 - - + +
127D TYR* 1.3 66.2 + - - +
129D MET* 3.2 23.5 + - - +
130D SER* 3.1 23.9 + - - -
164D TYR* 4.8 0.2 - - - +
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Residues in contact with TYR 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D PHE* 6.2 0.6 - - - -
123D PHE 5.0 2.6 + - - +
124D ARG* 3.3 27.0 + - - +
125D HIS 3.2 0.2 - - - -
126D PHE* 1.3 78.0 - - - +
128D HIS* 1.3 87.0 + + - +
130D SER* 3.3 7.4 + - - -
131D GLU 3.6 0.5 + - - -
137D GLN* 3.2 62.0 + - + +
138D ALA* 3.7 28.3 - - - -
139D VAL* 3.6 31.4 + - + +
164D TYR* 3.5 32.4 + + + +
166D MET* 4.9 5.4 - - + -
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Residues in contact with HIS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A HIS* 6.2 3.6 - + - -
132C PRO* 6.5 1.3 - - + -
124D ARG* 3.0 44.6 + - + +
125D HIS* 3.7 6.4 - - - +
127D TYR* 1.3 95.6 - + - +
129D MET* 1.3 63.2 + - + +
130D SER 3.1 2.0 - - - -
131D GLU* 3.2 23.0 + - + +
132D PRO* 3.8 4.3 - - - +
137D GLN* 5.3 2.0 - - - -
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Residues in contact with MET 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C MET* 3.6 24.5 - - - -
129C MET* 3.3 61.4 - - + +
132C PRO* 4.1 24.2 - - + -
133C ILE* 4.1 18.2 - - + -
80D LEU* 3.8 18.2 - - + -
83D MET* 4.4 8.1 - - + -
125D HIS 2.9 20.6 + - - +
126D PHE* 3.2 28.7 + - - +
128D HIS* 1.3 76.2 - - - +
130D SER* 1.3 57.5 + - - +
132D PRO* 3.4 9.5 - - - +
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Residues in contact with SER 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D MET* 3.4 22.4 - - - +
86D ILE* 5.1 1.4 - - - +
98D HIS* 5.0 3.3 + - - -
126D PHE 3.1 14.6 + - - -
127D TYR 3.6 6.5 - - - -
128D HIS 3.1 1.0 - - - -
129D MET* 1.3 78.4 - - - +
131D GLU* 1.3 61.0 + - - +
132D PRO* 3.4 1.8 - - - -
133D ILE* 3.3 20.3 + - - +
134D THR* 3.0 21.4 + - - +
137D GLN* 4.0 1.6 - - - -
164D TYR* 3.3 31.9 - - - -
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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