Contacts of the helix formed by residues 119 - 128 (chain D) in PDB entry 6OY5
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 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D SER* 6.6 0.2 - - - -
113D GLY* 5.1 0.6 - - - -
117D ASP 4.3 0.4 - - - -
118D LEU* 1.3 77.6 - - - +
120D ALA* 1.3 65.1 + - - +
121D THR* 3.5 8.5 + - - -
122D GLU* 3.1 37.6 + - - +
123D LEU* 3.1 21.0 + - - +
22H G 5.2 9.6 - - - -
23H C 5.4 2.9 + - - -
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Residues in contact with ALA 120 (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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108D VAL* 6.2 4.9 - - + -
110D SER* 6.0 6.7 - - - -
119D SER* 1.3 75.7 - - - +
121D THR* 1.3 66.5 + - - +
123D LEU* 3.4 4.0 + - - +
124D GLU* 3.2 21.0 + - - +
22H G 5.5 15.0 + - - +
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Residues in contact with THR 121 (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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119D SER* 3.3 8.1 + - - -
120D ALA* 1.3 79.3 - - - +
122D GLU* 1.3 63.9 + - + +
124D GLU* 3.3 10.0 + - + +
125D GLN* 3.1 44.1 + - + +
23H C 4.2 14.2 + - - -
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Residues in contact with GLU 122 (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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117D ASP 4.4 1.6 - - - +
118D LEU* 3.4 26.7 - - + +
119D SER* 3.1 36.1 + - - +
120D ALA 3.3 0.2 - - - -
121D THR* 1.3 78.8 - - + +
123D LEU* 1.3 61.7 + - - +
125D GLN* 3.0 21.9 + - - +
126D VAL* 3.0 18.1 + - - +
152D LEU* 3.6 30.6 - - + +
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Residues in contact with LEU 123 (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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105D VAL* 4.5 12.8 - - + -
110D SER* 3.5 27.4 - - - +
112D ILE* 3.8 21.3 - - + -
113D GLY* 3.5 19.3 - - - +
118D LEU* 4.6 14.3 - - + +
119D SER 3.1 16.3 + - - +
120D ALA* 3.9 4.3 - - - +
122D GLU* 1.3 79.1 - - - +
124D GLU* 1.3 61.4 + - - +
126D VAL* 4.7 2.5 - - + +
127D LEU* 3.0 56.2 + - + +
461D ILE* 4.2 19.7 - - + -
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Residues in contact with GLU 124 (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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105D VAL* 5.8 3.2 - - - +
106D LYS* 4.5 8.4 - - - -
120D ALA 3.2 12.7 + - - +
121D THR* 3.4 13.7 - - + +
122D GLU 3.2 0.2 - - - -
123D LEU* 1.3 75.9 - - - +
125D GLN* 1.3 63.3 + - + +
127D LEU* 5.5 0.4 - - - -
128D TYR* 2.8 60.7 + - + +
130D SER* 6.3 0.4 - - - -
587D ARG* 2.3 46.0 + - - -
78F SER* 4.7 8.1 + - - -
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Residues in contact with GLN 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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121D THR* 3.1 34.6 + - + +
122D GLU* 3.0 9.4 + - - +
124D GLU* 1.3 83.6 - - + +
126D VAL* 1.3 63.2 + - + +
129D PHE 3.2 1.6 + - - -
130D SER* 2.6 52.4 + - - +
131D LYS* 3.3 36.0 + - + +
152D LEU* 3.4 25.3 - - + +
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Residues in contact with VAL 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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118D LEU* 6.2 2.2 - - + -
122D GLU* 3.0 14.7 + - + +
123D LEU* 4.3 3.1 - - - +
125D GLN* 1.3 76.7 - - + +
127D LEU* 1.3 60.6 + - - +
129D PHE* 3.5 7.3 + - - -
131D LYS 3.8 13.5 - - - +
133D ILE* 3.8 31.6 - - + -
152D LEU* 3.7 26.5 - - + -
456D MET* 3.8 3.4 - - - -
457D GLY 2.6 44.2 + - - +
460D ALA* 4.5 0.9 - - + -
461D ILE* 3.9 23.6 - - + -
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Residues in contact with LEU 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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100D ALA* 3.9 17.7 - - + -
105D VAL* 3.6 38.1 - - + -
112D ILE* 5.7 1.3 - - + -
123D LEU* 3.0 42.6 + - + +
126D VAL* 1.3 76.5 - - - +
128D TYR* 1.3 73.0 + - + +
129D PHE* 3.3 22.6 - - - -
457D GLY* 4.0 3.2 - - - -
458D ALA* 3.7 31.4 + - + +
461D ILE* 4.0 15.0 - - + -
575D GLN* 4.5 14.2 - - + +
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Residues in contact with TYR 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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102D ILE* 4.6 3.3 - - - +
105D VAL* 5.3 9.1 - - + +
106D LYS* 5.8 0.3 - - - +
124D GLU* 2.8 43.8 + - + +
125D GLN* 3.8 0.7 - - - -
127D LEU* 1.3 90.3 - - + +
129D PHE* 1.3 72.3 + - - +
130D SER* 3.4 4.8 + - - -
572D ARG* 3.5 17.0 + - + +
575D GLN* 3.8 23.9 + - + +
576D GLU* 3.9 21.5 - - + -
579D ASP* 2.2 30.7 + - - -
587D ARG* 3.1 52.0 - - - +
83F GLN* 3.4 14.0 + - - +
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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