Contacts of the helix formed by residues 122 - 133 (chain A) in PDB entry 1KL9
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 LYS 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.6 9.2 - - - +
120A TYR 3.7 0.2 - - - -
121A THR* 1.3 95.4 - - - +
123A ASP* 1.3 66.6 + - - +
124A GLU* 4.0 14.8 - - + -
125A GLN* 2.8 38.0 + - + +
126A LEU 3.5 2.9 + - - -
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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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3A LEU* 3.5 14.7 - - - +
4A SER* 3.2 45.9 + - - +
122A LYS* 1.3 72.0 - - - +
124A GLU* 1.3 58.2 + - - +
126A LEU* 3.1 7.9 + - - +
127A GLU* 2.9 27.6 + - - +
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Residues in contact with GLU 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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122A LYS* 4.0 16.2 - - + -
123A ASP* 1.3 79.8 - - - +
125A GLN* 1.3 63.7 + - + +
127A GLU* 3.8 10.6 - - + +
128A SER* 2.9 29.5 + - - -
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Residues in contact with GLN 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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119A GLU 5.1 1.4 + - - -
120A TYR* 3.3 46.7 + - + +
121A THR* 2.7 34.4 + - - +
122A LYS* 2.8 28.5 + - + +
124A GLU* 1.3 78.6 - - + +
126A LEU* 1.3 64.5 + - - +
128A SER* 3.3 6.6 + - - -
129A LEU 3.0 17.8 + - - -
132A ARG* 5.4 0.3 + - - -
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Residues in contact with LEU 126 (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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3A LEU* 4.1 33.0 - - + +
4A SER 3.9 13.5 - - - +
5A CYS* 3.6 26.5 - - + +
108A TYR* 4.4 10.5 - - + +
111A LEU* 3.7 28.7 - - + +
112A ARG* 4.2 7.4 - - + +
115A ALA* 4.1 9.2 - - + -
120A TYR* 3.7 6.4 - - + -
122A LYS 3.5 2.0 + - - -
123A ASP 3.1 8.4 + - - +
125A GLN* 1.3 77.3 - - - +
127A GLU* 1.3 65.9 - - - +
129A LEU* 3.2 9.3 + - + +
130A PHE* 3.1 35.0 + - + -
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Residues in contact with GLU 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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5A CYS* 3.8 17.5 - - - -
6A ARG* 3.1 40.1 + - - -
11A LYS* 5.2 4.6 - - - -
123A ASP 2.9 15.9 + - - +
124A GLU* 3.8 10.0 - - - +
126A LEU* 1.3 75.6 - - - +
128A SER* 1.3 58.4 + - - +
130A PHE* 3.2 3.7 + - - +
131A GLN* 2.8 33.2 + - + +
135A TRP* 4.0 10.3 - - + -
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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 GLU 2.9 18.2 + - - -
125A GLN* 3.6 7.6 - - - -
126A LEU 3.2 0.2 - - - -
127A GLU* 1.3 78.2 - - - +
129A LEU* 1.3 62.1 + - - +
131A GLN* 3.4 7.3 + - - +
132A ARG* 3.0 50.0 + - - +
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Residues in contact with LEU 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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111A LEU* 3.3 44.4 - - + +
114A VAL* 3.5 29.6 - - + -
115A ALA 4.2 0.2 - - - +
118A LEU* 5.2 1.6 - - + -
120A TYR* 4.1 24.5 - - + +
125A GLN 3.0 13.1 + - - +
126A LEU* 3.2 12.8 + - + +
128A SER* 1.3 76.3 + - - +
130A PHE* 1.3 56.6 + - - +
132A ARG* 3.3 14.3 + - - +
133A THR* 2.7 48.3 + - + +
167A LEU* 4.7 7.9 - - + -
171A GLU* 5.3 4.9 - - + +
175A LEU* 5.9 3.1 - - + -
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Residues in contact with PHE 130 (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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5A CYS* 3.9 14.8 - - + -
6A ARG 3.9 5.6 - - - -
7A PHE* 3.7 16.8 - - - -
104A SER 5.9 0.4 - - - -
107A VAL* 4.5 11.2 - - + -
108A TYR* 3.5 39.9 - + + -
111A LEU* 3.6 32.3 - - + -
126A LEU* 3.1 39.6 + - + -
127A GLU 3.4 7.4 - - - +
129A LEU* 1.3 73.9 - - - +
131A GLN* 1.3 65.2 + - - +
133A THR* 3.0 7.0 + - - -
134A ALA* 3.3 5.1 + - + -
135A TRP* 2.9 61.8 + + + -
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Residues in contact with GLN 131 (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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9A GLN* 2.6 46.1 + - - +
127A GLU* 2.8 25.9 + - + +
128A SER* 3.5 10.1 - - - +
130A PHE* 1.3 74.9 - - - +
132A ARG* 1.3 61.7 + - + +
135A TRP* 3.6 14.9 - - + +
136A VAL* 3.5 17.5 + - - +
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Residues in contact with ARG 132 (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 TYR* 4.2 9.5 + - - -
125A GLN 5.4 0.4 + - - -
128A SER* 3.0 34.6 + - - +
129A LEU* 3.3 14.3 + - - +
130A PHE 3.2 0.2 - - - -
131A GLN* 1.3 81.5 - - + +
133A THR* 1.3 66.4 + - + +
136A VAL* 3.6 9.7 - - - +
165A LEU* 3.5 24.8 - - - +
166A ASP* 2.9 49.8 + - + +
167A LEU* 3.6 8.2 - - + +
171A GLU* 2.9 40.4 + - - -
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Residues in contact with THR 133 (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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111A LEU* 3.6 18.1 - - + +
129A LEU* 2.7 28.6 + - + +
130A PHE 3.0 2.6 + - - -
131A GLN 3.4 0.2 - - - -
132A ARG* 1.3 84.7 - - - +
134A ALA* 1.3 73.9 + - - -
135A TRP 3.2 0.4 - - - -
136A VAL* 3.0 15.2 + - - +
137A PHE* 3.3 18.9 + - - -
152A PHE* 4.0 11.9 - - - -
165A LEU* 4.1 13.2 - - + -
167A LEU* 3.9 22.9 - - + -
175A LEU* 4.0 16.8 - - + -
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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