Contacts of the helix formed by residues 137 - 151 (chain G) in PDB entry 1K73
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 ASP 137 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29G VAL* 3.8 29.3 - - + +
30G THR 5.6 0.7 - - - +
31G ARG* 5.9 1.5 - - - +
121G ASP 6.2 1.8 - - - +
135G GLY 3.6 0.2 - - - -
136G PRO* 1.3 81.0 - - + +
138G ILE* 1.3 64.9 + - - +
139G GLU* 2.8 27.4 + - - +
140G ALA* 3.7 20.1 - - + +
141G VAL* 3.0 24.2 + - + +
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Residues in contact with ILE 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2781A U 3.8 28.1 - - - +
2782A G 4.5 2.2 - - - +
68G HIS* 6.0 1.1 - - - +
71G ASN* 3.7 38.6 - - + +
80G TRP* 3.6 45.9 - - + +
82G TYR* 4.0 22.2 - - + +
136G PRO 3.6 5.3 + - - -
137G ASP* 1.3 72.2 + - - +
139G GLU* 1.3 65.9 - - + +
141G VAL* 4.5 3.4 - - - -
142G GLY* 2.8 29.5 + - - -
172G PRO* 5.1 2.2 - - + -
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Residues in contact with GLU 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2780A C 4.1 4.7 + - - +
2781A U 2.6 45.0 + - - +
2794A G 3.0 25.9 + - - +
2795A C 4.6 8.8 + - - +
31G ARG* 4.7 27.7 + - - +
68G HIS* 4.1 5.4 - - - +
137G ASP* 2.8 14.5 + - - +
138G ILE* 1.3 89.5 - - + +
140G ALA* 1.3 62.3 + - - +
142G GLY* 3.9 0.5 - - - -
143G GLN* 3.1 24.7 + - - +
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Residues in contact with ALA 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G HIS* 3.5 36.5 - - + +
120G GLY* 4.5 5.6 - - - +
121G ASP 5.3 0.7 - - - +
122G THR* 3.6 5.8 - - - +
137G ASP* 3.1 25.0 + - + +
139G GLU* 1.3 79.9 - - - +
141G VAL* 1.3 53.8 + - - +
143G GLN* 3.4 2.1 + - - +
144G THR* 2.7 36.6 + - - -
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Residues in contact with VAL 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G TRP* 4.1 6.3 - - + +
82G TYR* 3.5 25.6 - - + -
122G THR* 3.6 16.4 - - - +
133G VAL* 3.6 28.4 - - + +
134G SER* 3.8 2.9 - - - -
135G GLY* 3.5 35.9 - - - +
137G ASP 3.0 17.2 + - - +
138G ILE* 4.0 5.2 - - - +
140G ALA* 1.3 74.5 - - - +
142G GLY* 1.3 64.6 + - - +
144G THR* 3.2 2.9 + - - -
145G ALA* 2.9 22.9 + - - +
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Residues in contact with GLY 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2780A C 3.6 19.3 + - - +
2781A U 4.8 0.4 - - - -
82G TYR* 3.8 27.4 - - - -
138G ILE 2.8 21.0 + - - -
141G VAL* 1.3 74.3 - - - +
143G GLN* 1.3 55.6 + - - +
145G ALA* 3.6 2.8 + - - +
146G ALA* 3.0 27.0 + - - +
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Residues in contact with GLN 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2779A G 2.8 36.6 + - - +
2780A C 3.0 29.7 + - - +
2795A C 4.2 4.9 + - - +
2796A U 3.5 28.4 + - - +
119G HIS* 4.2 11.7 - - + +
139G GLU 3.1 18.3 + - - +
140G ALA 3.8 3.6 - - - +
142G GLY* 1.3 71.3 - - - +
144G THR* 1.3 57.6 + - - +
145G ALA 3.1 0.2 - - - -
146G ALA* 4.2 4.5 - - - +
147G ASP* 2.6 70.8 + - - +
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Residues in contact with THR 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G VAL* 5.3 0.7 - - + -
116G THR* 6.3 1.1 - - + -
117G THR 5.4 0.4 - - - +
118G ILE* 3.7 31.9 - - + -
119G HIS* 3.2 21.6 + - - +
122G THR* 3.9 4.9 - - - +
124G VAL* 4.0 19.1 - - + -
133G VAL* 4.0 8.7 - - + -
140G ALA 2.7 23.8 + - - -
141G VAL 3.6 4.0 - - - -
143G GLN* 1.3 77.1 - - - +
145G ALA* 1.3 63.5 + - - +
147G ASP* 3.9 8.1 - - + +
148G ILE* 3.1 34.6 + - + +
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Residues in contact with ALA 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G TYR* 4.0 24.0 - - + -
84G MET* 3.7 11.3 - - - +
133G VAL* 4.1 11.2 - - + +
141G VAL 2.9 16.7 + - - +
142G GLY 3.6 4.7 - - - +
144G THR* 1.3 77.1 - - - +
146G ALA* 1.3 65.1 + - - +
148G ILE* 3.0 14.6 + - - +
149G GLU 3.0 10.0 + - - -
168G ILE* 3.4 25.6 - - + +
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Residues in contact with ALA 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2779A G 3.8 10.3 - - - +
2780A C 3.7 29.4 - - - +
142G GLY 3.0 15.7 + - - +
143G GLN* 3.5 9.2 - - - +
145G ALA* 1.3 80.4 - - - +
147G ASP* 1.3 51.9 + - - +
149G GLU* 2.8 9.5 + - - +
150G GLN* 2.7 39.3 + - + +
168G ILE* 4.3 5.1 - - - +
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Residues in contact with ASP 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2796A U 3.5 13.1 + - - +
116G THR* 3.6 23.6 + - + +
117G THR 4.7 0.4 - - - +
119G HIS* 2.8 35.1 + - - -
143G GLN* 2.6 43.1 + - - +
144G THR* 3.9 5.3 + - + +
146G ALA* 1.3 72.5 - - - +
148G ILE* 1.3 52.8 + - - +
150G GLN* 3.3 10.7 + - - +
151G LEU* 2.7 36.2 + - - +
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Residues in contact with ILE 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G MET* 3.2 36.8 - - + -
102G VAL* 3.8 37.5 - - + -
104G ILE* 4.9 6.5 - - + +
116G THR* 4.5 5.6 - - + -
124G VAL* 4.2 16.6 - - + -
131G LEU* 4.5 4.9 - - + -
133G VAL* 4.3 2.7 - - + -
144G THR* 3.1 18.5 + - + +
145G ALA 3.0 9.4 + - - +
147G ASP* 1.3 76.7 - - - +
149G GLU* 1.3 66.3 + - - +
151G LEU* 3.0 22.1 + - - +
152G THR* 3.8 6.4 + - - +
166G VAL* 3.8 23.5 - - + +
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Residues in contact with GLU 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G MET* 5.4 0.4 - - - -
145G ALA 3.0 8.8 + - - +
146G ALA* 2.8 12.4 + - - +
148G ILE* 1.3 79.5 - - - +
150G GLN* 1.3 69.2 + - - +
152G THR* 3.0 21.5 + - - +
153G ARG* 3.9 1.9 + - - -
166G VAL 3.3 22.4 - - - +
167G TYR* 3.3 20.7 - - + +
168G ILE* 2.7 44.8 + - + +
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Residues in contact with GLN 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2778A A 2.8 45.5 + - + +
2779A G 3.8 29.0 + - - +
146G ALA* 2.7 26.8 + - + +
147G ASP* 3.6 11.0 - - - +
149G GLU* 1.3 80.7 - - - +
151G LEU* 1.3 55.1 + - - +
153G ARG* 2.6 45.2 + - + +
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Residues in contact with LEU 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G VAL* 4.3 5.8 - - + +
104G ILE* 4.2 20.0 - - + -
114G ARG* 2.8 46.3 + - + +
115G ARG* 3.1 40.8 - - - +
116G THR* 3.5 28.9 - - + -
147G ASP 2.7 11.7 + - - +
148G ILE* 3.0 15.9 + - - +
150G GLN* 1.3 77.3 - - - +
152G THR* 1.3 56.8 + - - +
153G ARG 3.3 0.4 - - - -
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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
------------------------------------------------------------
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