Contacts of the helix formed by residues 136 - 146 (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 ALA 136 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134P LEU 4.1 0.6 + - - -
135P SER* 1.4 70.4 - - - +
137P PRO* 1.4 63.1 - - + +
139P ARG* 2.7 24.4 + - + +
140P GLU* 2.5 50.4 + - + +
150P PRO* 6.0 1.3 - - + -
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Residues in contact with PRO 137 (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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135P SER* 3.6 9.6 - - - -
136P ALA* 1.4 88.2 - - + +
138P GLU* 1.4 67.0 + - - +
140P GLU* 4.2 11.4 - - + +
141P HIS* 3.5 19.1 + - - +
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Residues in contact with GLU 138 (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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127P ARG* 2.8 46.7 + - - +
131P GLN* 5.7 0.9 - - - +
134P LEU* 3.3 27.1 - - + +
135P SER* 3.2 19.4 + - - +
137P PRO* 1.4 77.7 - - - +
139P ARG* 1.4 57.0 + - - +
141P HIS* 2.9 33.7 + - - +
142P LEU 3.4 3.6 + - - -
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Residues in contact with ARG 139 (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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21B C 4.8 6.3 + - - -
134P LEU* 2.8 64.9 + - + +
135P SER 3.1 1.5 + - - +
136P ALA* 2.7 34.3 + - + +
138P GLU* 1.4 71.8 - - - +
140P GLU* 1.4 51.5 + - - +
141P HIS 3.0 1.3 - - - -
142P LEU* 3.0 9.5 + - - +
143P ALA* 2.7 31.4 + - - +
150P PRO* 3.8 13.6 + - + +
153P VAL* 3.4 32.7 - - + +
154P LYS* 2.8 45.8 - - - +
157P PHE* 5.6 1.6 - - - -
161P ARG* 5.0 7.7 - - - +
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Residues in contact with GLU 140 (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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136P ALA* 2.5 55.3 + - + +
137P PRO* 4.2 8.1 - - + +
139P ARG* 1.4 68.2 - - - +
141P HIS* 1.4 50.4 - - - +
143P ALA* 2.7 15.0 + - + +
144P SER* 2.3 36.0 + - - -
150P PRO* 3.1 31.1 - - + +
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Residues in contact with HIS 141 (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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127P ARG* 5.3 2.5 - - - +
137P PRO 3.5 13.6 + - - +
138P GLU* 2.9 16.4 + - - +
140P GLU* 1.4 80.8 - - - +
142P LEU* 1.4 49.6 + - - +
144P SER* 3.1 20.9 + - - -
145P LEU* 2.8 52.0 + - + +
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Residues in contact with LEU 142 (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* 3.1 55.9 - - + +
124P LEU* 3.4 15.5 - - + +
126P ARG* 5.5 1.3 - - + -
127P ARG* 3.5 37.9 - - + +
138P GLU 3.4 2.8 + - - -
139P ARG* 3.0 13.7 + - - +
141P HIS* 1.4 73.5 - - - +
143P ALA* 1.4 65.0 + - - +
144P SER 3.0 1.1 - - - -
145P LEU* 3.1 19.4 + - + +
146P ILE* 3.0 29.0 - - + +
153P VAL* 4.0 19.5 - - + -
157P PHE* 4.1 2.5 - - + -
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Residues in contact with ALA 143 (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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139P ARG 2.7 6.7 + - - +
140P GLU* 2.7 23.5 + - - +
142P LEU* 1.4 73.7 - - - +
144P SER* 1.4 54.2 + - - -
147P ARG* 2.9 5.4 + - - -
148P LEU* 2.7 51.4 + - - +
150P PRO* 3.6 32.5 - - + -
153P VAL* 3.5 11.3 - - + +
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Residues in contact with SER 144 (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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140P GLU 2.3 23.1 + - - -
141P HIS* 3.2 26.5 + - - -
142P LEU 3.0 0.6 - - - -
143P ALA* 1.4 70.1 - - - +
145P LEU* 1.4 68.8 + - - +
146P ILE 3.4 0.2 + - - -
147P ARG* 3.5 14.3 + - - +
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Residues in contact with LEU 145 (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* 5.2 4.5 - - + -
127P ARG* 6.2 0.9 - - - +
141P HIS* 2.8 39.5 + - + +
142P LEU* 3.1 23.3 + - + +
144P SER* 1.4 76.8 - - - +
146P ILE* 1.4 66.1 + - + +
147P ARG* 4.6 2.6 - - - +
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Residues in contact with ILE 146 (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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120P GLN* 2.6 72.9 + - + +
123P GLU* 2.8 35.2 - - + +
124P LEU* 3.9 9.9 - - + -
142P LEU* 3.0 23.8 + - + +
145P LEU* 1.4 78.7 - - + +
147P ARG* 1.4 63.1 + - - +
148P LEU* 2.9 39.5 - - + +
153P VAL* 4.5 2.5 - - + -
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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