Contacts of the helix formed by residues 115 - 128 (chain Q) in PDB entry 1KD1
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 115 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114Q LEU* 1.3 72.7 - - - +
116Q SER* 1.3 55.1 + - - +
117Q SER* 2.4 31.3 + - - -
118Q GLN* 2.6 57.3 + - - +
119Q TYR* 3.0 8.0 + - - -
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Residues in contact with SER 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1593A C 3.2 37.1 - - - +
1594A C 3.4 10.8 + - - -
109Q ARG* 4.5 9.9 - - - +
114Q LEU 3.7 2.0 + - - -
115Q SER* 1.3 69.4 - - - +
117Q SER* 1.3 56.6 + - - +
119Q TYR* 4.3 8.5 - - - -
120Q ARG* 3.3 14.9 + - - +
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Residues in contact with SER 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1593A C 2.6 36.2 + - - -
115Q SER* 2.4 34.4 + - - -
116Q SER* 1.3 72.3 + - - +
118Q GLN* 1.3 65.6 + - - +
119Q TYR 3.2 1.6 - - - -
120Q ARG* 3.6 2.5 - - - +
121Q ASP* 3.1 23.2 + - - +
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Residues in contact with GLN 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Q THR 4.0 5.5 + - - +
114Q LEU* 3.5 24.6 - - + +
115Q SER* 2.6 57.8 + - - +
117Q SER* 1.3 75.2 - - - +
119Q TYR* 1.3 56.0 + - - +
121Q ASP* 3.3 7.2 + - - +
122Q LEU* 3.0 36.2 + - + +
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Residues in contact with TYR 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1594A C 3.2 31.0 - - - -
1595A G 2.6 31.3 + - - -
1596A U 5.3 0.5 + - - -
102Q ARG 5.0 1.7 + - - -
105Q LEU* 3.4 48.0 - - + +
106Q ARG* 3.9 13.0 + - - +
109Q ARG* 3.0 40.6 + - + -
114Q LEU* 4.4 16.5 - - + +
115Q SER 3.0 12.4 + - - +
116Q SER* 4.3 1.8 - - - -
118Q GLN* 1.3 74.5 - - - +
120Q ARG* 1.3 58.5 + - - +
122Q LEU* 3.2 3.6 + - - +
123Q TYR* 2.7 60.7 + + + +
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Residues in contact with ARG 120 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1593A C 3.6 46.4 - - + +
1594A C 2.8 62.0 + - - +
1595A G 2.9 34.6 + - - -
116Q SER 3.3 12.3 + - - +
117Q SER 3.5 6.7 + - - +
119Q TYR* 1.3 83.2 - - - +
121Q ASP* 1.3 64.5 + - - +
123Q TYR* 2.7 39.4 - - - +
124Q ASP* 2.9 54.9 + - - +
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Residues in contact with ASP 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A G 5.0 3.7 + - - -
117Q SER 3.1 12.2 + - - +
118Q GLN* 3.5 11.7 - - - +
120Q ARG* 1.3 81.9 - - - +
122Q LEU* 1.3 66.4 + - + +
124Q ASP* 3.5 5.4 + - - +
125Q LYS* 3.2 56.1 + - - +
140Q TYR* 5.6 0.2 - - - -
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Residues in contact with LEU 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105Q LEU* 3.7 17.7 - - + -
114Q LEU* 3.8 34.1 - - + -
118Q GLN* 3.0 21.7 + - + +
119Q TYR* 3.6 3.6 - - - +
121Q ASP* 1.3 77.2 - - - +
123Q TYR* 1.3 67.4 + - - +
125Q LYS* 3.1 7.1 + - + +
126Q ALA* 2.8 23.7 + - - +
131Q PHE* 3.5 11.2 - - + -
137Q LEU* 4.2 6.7 - - + -
140Q TYR* 3.5 38.4 - - + -
141Q ILE* 4.0 19.3 - - + -
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Residues in contact with TYR 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1595A G 3.4 25.2 - + - -
1596A U 2.5 55.1 + + - -
102Q ARG* 3.5 35.8 + - + -
105Q LEU* 3.4 12.7 - - + +
106Q ARG* 5.7 0.4 - - - -
119Q TYR* 2.7 50.8 + + + +
120Q ARG* 2.7 39.9 - - - +
122Q LEU* 1.3 70.5 - - - +
124Q ASP* 1.3 65.5 + - - +
126Q ALA* 2.9 16.1 + - - +
127Q GLY* 3.0 12.4 + - - -
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Residues in contact with ASP 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A G 3.9 2.1 + - - -
801A U 3.2 37.2 + - - +
1593A C 5.7 3.1 + - - -
1594A C 5.2 2.0 + - - -
1595A G 4.0 5.9 - - - +
120Q ARG* 2.9 51.3 + - - +
121Q ASP* 3.7 5.8 - - - +
123Q TYR* 1.3 77.2 - - - +
125Q LYS* 1.3 56.7 + - + +
127Q GLY* 3.6 3.2 + - - -
128Q GLY 3.1 19.6 + - - -
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Residues in contact with LYS 125 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801A U 3.9 16.2 - - - +
802A G 3.6 27.1 - - - +
121Q ASP* 3.2 35.3 + - - +
122Q LEU* 3.1 10.2 + - - +
124Q ASP* 1.3 75.5 - - + +
126Q ALA* 1.3 63.6 + - - +
128Q GLY 3.1 6.2 + - - -
130Q GLU* 3.0 46.9 + - + +
131Q PHE* 3.8 11.9 - - + -
140Q TYR* 2.6 35.8 + - + +
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Residues in contact with ALA 126 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Q TRP* 3.9 6.8 - - - -
98Q ILE* 4.5 12.8 - - + +
101Q GLN* 3.6 24.7 - - + +
102Q ARG* 5.5 2.9 - - + -
105Q LEU* 4.7 7.6 - - + -
122Q LEU 2.8 11.7 + - - +
123Q TYR* 3.2 12.3 - - - +
125Q LYS* 1.3 72.4 - - - +
127Q GLY* 1.3 54.9 + - - +
128Q GLY 2.8 4.0 - - - -
129Q GLY* 2.4 30.4 + - - +
130Q GLU 4.4 1.1 - - - +
131Q PHE* 3.6 18.1 - - + -
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Residues in contact with GLY 127 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800A G 3.9 11.3 + - - +
814A G 5.3 4.9 + - - +
815A U 5.7 0.7 - - - +
1596A U 5.2 5.2 - - - -
1598A A 4.8 1.8 + - - -
94Q TRP* 3.9 14.9 - - - -
98Q ILE* 4.4 5.7 - - - +
102Q ARG* 4.2 21.5 - - - +
123Q TYR* 3.0 10.1 + - - -
124Q ASP* 3.8 4.7 - - - -
126Q ALA* 1.3 78.8 - - - +
128Q GLY* 1.3 56.3 + - - +
129Q GLY 3.1 2.8 + - - -
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Residues in contact with GLY 128 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800A G 3.2 32.7 + - - -
801A U 3.2 30.6 - - - +
813A C 4.6 1.4 - - - +
814A G 4.7 5.3 + - - -
124Q ASP 3.1 6.1 + - - -
125Q LYS 3.1 9.3 + - - -
126Q ALA 2.8 1.8 - - - -
127Q GLY* 1.3 76.2 - - - +
129Q GLY* 1.3 61.7 + - - +
130Q GLU* 3.4 4.7 + - - +
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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