Contacts of the helix formed by residues 118 - 130 (chain P) in PDB entry 1NK2
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 118 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116P PHE 3.6 2.0 + - - -
117P THR* 1.4 71.4 - - - +
119P ALA* 1.4 52.5 + - - +
121P THR* 3.3 14.3 - - + +
122P TYR* 2.5 39.2 + - + +
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Residues in contact with ALA 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117P THR* 2.9 12.7 + - - +
118P LYS* 1.4 77.4 - - - +
120P GLN* 1.4 52.2 + - + +
122P TYR* 2.7 26.3 + - - +
123P GLU* 2.7 37.3 + - - +
146P ILE* 6.1 0.2 - - + -
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Residues in contact with GLN 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P PHE* 3.1 15.4 - - + +
117P THR* 2.6 39.6 + - - +
119P ALA* 1.4 73.1 - - + +
121P THR* 1.4 57.1 + - - +
123P GLU* 3.4 1.2 + - - -
124P LEU* 2.8 35.3 + - - +
146P ILE* 2.6 61.6 + - + +
147P ARG* 4.6 5.9 + - - +
148P LEU* 2.9 28.1 - - - +
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Residues in contact with THR 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A A 5.1 2.9 + - - -
116P PHE* 3.6 20.1 + - - +
117P THR 2.5 20.9 + - - -
118P LYS* 3.3 18.6 - - + +
120P GLN* 1.4 67.0 - - - +
122P TYR* 1.4 52.6 + - - +
124P LEU* 2.7 16.4 + - - +
125P GLU* 2.4 58.8 + - + +
156P TRP* 4.2 18.6 + - + +
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Residues in contact with TYR 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P LYS* 2.5 30.0 + - + +
119P ALA* 2.7 14.3 + - - +
121P THR* 1.4 66.9 - - - +
123P GLU* 1.4 71.1 + - - -
125P GLU* 3.3 14.7 + - + +
126P ARG* 2.5 92.8 + - + +
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Residues in contact with GLU 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119P ALA* 2.7 40.1 + - - +
120P GLN 4.0 0.4 - - - +
122P TYR* 1.4 98.7 - - - +
124P LEU* 1.4 54.2 + - - +
126P ARG* 3.2 10.0 - - - +
127P ARG 2.8 28.2 + - - -
142P LEU* 3.1 32.7 - - + +
145P LEU* 5.2 6.1 - - + -
146P ILE* 2.8 33.1 - - + +
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Residues in contact with LEU 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P PHE* 3.2 33.4 - - + -
120P GLN 2.8 33.8 + - - +
121P THR* 2.7 17.2 + - - +
123P GLU* 1.4 66.8 - - - +
125P GLU* 1.4 52.1 + - - +
128P PHE 2.8 29.3 + - - -
142P LEU* 3.4 7.1 - - - +
146P ILE* 3.9 9.0 - - + -
148P LEU* 4.0 1.1 - - + -
152P GLN 4.1 1.8 - - - +
153P VAL* 3.5 37.0 - - + +
156P TRP* 3.4 44.1 - - + -
157P PHE* 2.9 15.7 - - + -
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Residues in contact with GLU 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121P THR* 2.4 48.9 + - + +
122P TYR* 3.4 14.9 - - + +
124P LEU* 1.4 64.2 - - - +
126P ARG* 1.4 55.0 + - - +
128P PHE* 2.8 3.9 + - - +
129P ARG* 2.4 58.1 + - + +
156P TRP* 3.6 19.9 - - + -
160P HIS* 6.0 2.0 - - - -
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Residues in contact with ARG 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P TYR* 2.5 90.0 + - + +
123P GLU* 3.2 13.9 - - - +
125P GLU* 1.4 75.3 - - - +
127P ARG* 1.4 58.2 + - - +
129P ARG* 3.0 16.0 + - - +
130P GLN* 2.8 48.6 + - - +
142P LEU* 5.5 2.0 - - + -
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Residues in contact with ARG 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P GLU 2.8 12.7 + - - +
126P ARG* 1.4 73.7 - - + +
128P PHE* 1.4 49.4 + - - +
130P GLN* 3.4 21.5 + - - +
131P GLN* 2.7 43.1 + - - +
134P LEU* 3.2 33.2 - - + -
138P GLU* 2.8 50.3 + - - -
141P HIS* 5.3 1.6 - - - +
142P LEU* 3.5 34.0 - - + +
145P LEU* 6.2 1.2 - - - +
157P PHE* 3.1 26.2 - - + -
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Residues in contact with PHE 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124P LEU 2.8 5.6 + - - +
125P GLU* 2.8 7.1 + - - +
127P ARG* 1.4 73.1 - - - +
129P ARG* 1.4 65.7 + - + +
130P GLN 2.8 15.4 + - - -
131P GLN 2.9 17.7 + - - +
132P ARG* 4.2 29.4 - - + -
156P TRP* 3.8 8.7 - + + -
157P PHE* 2.8 55.9 - + + -
160P HIS* 3.2 41.1 - + + -
161P ARG* 3.6 36.3 - - + -
164P THR* 4.9 7.9 - - + -
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Residues in contact with ARG 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P GLU* 2.4 58.2 + - + +
126P ARG* 3.6 12.6 - - - +
128P PHE* 1.4 79.6 - - + +
130P GLN* 1.4 57.5 + - + +
160P HIS* 4.9 15.2 + - - -
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Residues in contact with GLN 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P ARG* 2.8 57.0 + - - +
127P ARG* 3.4 31.9 + - - +
128P PHE 2.8 0.4 - - - -
129P ARG* 1.4 81.4 - - + +
131P GLN* 1.4 62.0 + - + +
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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