Contacts of the helix formed by residues 118 - 129 (chain A) in PDB entry 4Q96
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 GLY 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A TYR* 1.3 77.4 - - - +
119A GLY* 1.3 64.8 + - - -
120A GLU* 3.2 4.7 - - - -
121A PHE* 3.2 9.3 + - - +
122A ILE* 3.0 19.5 + - - +
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Residues in contact with GLY 119 (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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112A GLN* 4.7 12.1 + - - -
117A TYR 4.0 0.4 + - - -
118A GLY* 1.3 72.0 - - - -
120A GLU* 1.3 57.0 + - - +
122A ILE* 3.7 8.9 - - - +
123A GLN* 2.9 30.8 + - - +
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Residues in contact with GLU 120 (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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118A GLY* 3.2 1.5 - - - -
119A GLY* 1.3 77.2 - - - +
121A PHE* 1.3 62.8 + - - +
123A GLN* 3.5 6.9 + - - +
124A GLN* 3.1 40.3 + - - +
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Residues in contact with PHE 121 (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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117A TYR* 3.6 38.8 - + + -
118A GLY 3.2 10.6 + - - +
120A GLU* 1.3 76.6 - - - +
122A ILE* 1.3 61.7 + - - +
124A GLN* 2.9 39.6 + - - +
125A LEU* 3.0 41.7 + - + +
82B GLU* 3.3 50.0 - - + +
85B LEU* 4.0 18.4 - - + -
86B VAL* 3.8 21.1 - - + -
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Residues in contact with ILE 122 (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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108A LEU* 4.2 10.3 - - + +
111A TRP* 3.7 38.4 - - + -
112A GLN* 3.6 39.5 - - + +
117A TYR* 3.9 20.6 - - + +
118A GLY 3.0 20.3 + - - +
119A GLY* 3.7 7.4 - - - +
121A PHE* 1.3 75.3 - - - +
123A GLN* 1.3 57.1 + - - +
125A LEU* 3.3 9.9 + - + +
126A LYS* 3.0 44.3 + - + +
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Residues in contact with GLN 123 (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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112A GLN* 5.4 1.0 - - - +
119A GLY 2.9 18.2 + - - +
120A GLU* 3.6 7.6 - - - +
122A ILE* 1.3 76.5 - - - +
124A GLN* 1.3 58.3 + - + +
126A LYS* 3.8 16.7 - - - +
127A LEU* 2.9 60.2 + - + +
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Residues in contact with GLN 124 (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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120A GLU* 3.1 34.9 + - + +
121A PHE* 2.9 36.1 + - + +
123A GLN* 1.3 78.5 - - + +
125A LEU* 1.3 56.9 + - - +
127A LEU* 3.5 13.7 + - + +
128A SER* 3.1 25.8 + - - -
86B VAL* 4.3 19.4 - - + +
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Residues in contact with LEU 125 (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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108A LEU* 3.6 31.4 - - + -
111A TRP* 4.0 18.2 - - + -
121A PHE* 3.0 41.9 + - + +
122A ILE* 3.6 9.4 - - + +
124A GLN* 1.3 74.5 - - - +
126A LYS* 1.3 66.2 + - - +
128A SER* 2.5 21.6 + - - -
129A MET* 3.3 11.3 - - - +
85B LEU* 3.3 41.1 - - + +
86B VAL* 3.6 13.0 - - + +
89B PHE* 4.1 11.1 - - + +
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Residues in contact with LYS 126 (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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108A LEU* 3.7 25.1 - - + -
109A ASN* 4.2 17.4 + - - -
112A GLN* 3.2 25.2 + - - +
122A ILE* 3.0 38.4 + - + +
123A GLN* 3.4 18.1 + - - +
125A LEU* 1.3 74.6 - - - +
127A LEU* 1.3 62.0 + - - +
129A MET* 3.3 26.1 + - + +
130A GLU* 4.5 5.5 - - - +
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Residues in contact with LEU 127 (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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123A GLN* 2.9 52.6 + - + +
124A GLN* 3.5 12.1 - - + +
126A LYS* 1.3 75.8 - - - +
128A SER* 1.3 63.6 + - - +
129A MET 3.2 1.0 + - - -
130A GLU* 3.4 27.5 + - - +
131A ASP* 3.6 5.9 + - - -
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Residues in contact with SER 128 (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 GLN 3.1 13.1 + - - -
125A LEU* 2.5 25.7 + - - -
127A LEU* 1.3 71.3 - - - +
129A MET* 1.3 56.5 + - - +
130A GLU 2.9 12.4 + - - -
131A ASP* 3.2 11.7 + - - +
86B VAL* 3.8 30.0 + - - -
89B PHE* 3.5 17.7 - - - +
90B SER* 3.5 24.3 + - - +
93B ALA* 4.4 1.2 - - - +
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Residues in contact with MET 129 (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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101A LYS* 2.7 42.4 + - + +
104A LEU* 3.5 33.0 - - + -
105A GLU* 3.6 32.1 - - + +
108A LEU* 3.6 23.3 - - + -
125A LEU 3.3 14.6 - - - +
126A LYS* 3.6 12.6 - - + +
127A LEU 3.1 2.2 - - - -
128A SER* 1.3 77.4 - - - +
130A GLU* 1.3 57.2 + - - +
89B PHE* 4.2 11.2 - - + -
93B ALA* 3.7 17.9 - - + -
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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