Contacts of the helix formed by residues 114 - 124 (chain A) in PDB entry 4II9
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ALA 3.5 4.2 + - - -
113A TYR* 1.3 86.7 - - - +
115A ASP* 1.3 60.4 + - - +
116A GLU* 3.7 7.8 + - - +
117A PHE* 3.0 27.6 + - - +
118A ASN* 2.9 31.2 + - - +
317A ILE* 4.5 2.6 - - - +
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Residues in contact with ASP 115 (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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113A TYR* 2.7 34.9 + - - -
114A SER* 1.3 73.1 - - - +
116A GLU* 1.3 65.6 + - - +
118A ASN* 3.2 1.7 + - - +
119A THR* 2.9 30.9 + - - +
131A ARG* 4.4 6.5 + - - -
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Residues in contact with GLU 116 (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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114A SER* 3.4 7.6 + - - +
115A ASP* 1.3 78.8 - - - +
117A PHE* 1.4 67.9 + - - +
119A THR* 3.4 5.5 + - - -
120A THR* 2.8 51.8 + - - -
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Residues in contact with PHE 117 (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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81A VAL* 3.5 44.2 - - + -
82A THR* 3.7 22.2 - - + -
84A VAL* 3.7 20.6 - - + -
111A VAL* 3.8 23.6 - - + -
112A ALA 4.2 11.7 - - - +
114A SER* 3.0 21.0 + - - +
116A GLU* 1.4 81.7 + - - +
118A ASN* 1.3 69.9 + - - +
120A THR* 3.3 3.0 + - - -
121A LEU* 3.0 36.8 + - + +
317A ILE* 3.8 27.8 - - + -
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Residues in contact with ASN 118 (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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113A TYR* 3.9 20.0 + - + +
114A SER 2.9 18.3 + - - +
115A ASP 3.7 3.6 - - - +
117A PHE* 1.3 77.4 - - - +
119A THR* 1.3 64.6 + - - +
121A LEU* 3.3 6.1 + - - +
122A GLN* 3.0 50.0 + - - +
128A THR* 2.7 26.8 + - - +
130A ASN* 2.9 25.4 + - - -
317A ILE* 4.0 7.8 - - + +
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Residues in contact with THR 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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115A ASP* 2.9 21.4 + - - +
116A GLU* 3.9 4.7 - - - -
118A ASN* 1.3 79.0 + - - +
120A THR* 1.4 57.3 + - - +
122A GLN* 3.2 13.6 + - + +
123A ASP* 2.8 49.9 + - - +
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Residues in contact with THR 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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84A VAL* 3.8 23.1 - - + -
116A GLU* 2.8 37.4 + - - -
117A PHE* 3.7 8.1 - - - -
119A THR* 1.4 76.6 - - - +
121A LEU* 1.3 65.2 + - - +
123A ASP* 3.1 9.0 + - - +
124A HIS* 3.0 50.6 + - + +
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Residues in contact with LEU 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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84A VAL* 4.4 6.5 - - + -
87A LEU* 3.9 26.0 - - + -
117A PHE* 3.0 46.5 + - + +
118A ASN 3.6 3.8 - - - +
120A THR* 1.3 77.8 - - - +
122A GLN* 1.3 62.9 + - - +
124A HIS* 3.1 11.2 + - - -
126A TYR* 3.1 40.1 + - + -
128A THR* 3.9 15.7 - - + -
317A ILE* 3.8 20.9 - - + -
320A ILE* 3.7 33.2 - - + -
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Residues in contact with GLN 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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118A ASN* 3.0 34.9 + - - +
119A THR* 3.6 14.0 + - + +
121A LEU* 1.3 75.1 - - - +
123A ASP* 1.4 66.2 + - - +
125A GLY* 3.0 15.1 + - - -
126A TYR 3.5 16.7 + - - +
127A VAL* 5.5 0.4 - - - -
128A THR* 3.3 28.5 + - + +
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Residues in contact with ASP 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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119A THR* 2.8 35.6 + - - +
120A THR* 3.1 12.7 + - + +
122A GLN* 1.4 78.6 - - - +
124A HIS* 1.4 61.6 + - + +
125A GLY* 3.2 2.8 + - - -
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Residues in contact with HIS 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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84A VAL* 3.5 17.0 - - + +
85A ASP* 3.3 26.9 - - - -
88A ASP* 2.6 24.8 + - - +
120A THR* 3.0 42.9 + - + +
121A LEU 3.1 8.5 + - - +
123A ASP* 1.4 81.3 - - + +
125A GLY* 1.3 59.0 + - - +
126A TYR* 3.4 22.5 + - + -
322A LYS* 5.0 7.8 + - - -
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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