Contacts of the helix formed by residues 120 - 145 (chain A) in PDB entry 1KRQ
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 LEU 120 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.6 4.5 - - + -
13A GLN* 6.2 0.2 - - + -
57A LEU* 4.4 10.8 - - + -
101A ILE* 5.3 4.0 - - + -
104A LEU* 3.8 41.1 - - + -
105A VAL* 4.2 22.2 - - + +
108A MET* 4.2 12.8 - - + -
116A THR* 3.0 28.8 + - + +
117A PHE* 3.9 5.4 - - - +
118A ASN 3.1 0.4 - - - -
119A PHE* 1.3 86.1 - - + +
121A GLN* 1.3 66.1 + - - +
122A TRP 3.0 3.1 - - - -
123A TYR* 3.0 39.3 + - + +
124A VAL* 3.2 12.4 + - - +
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Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL* 4.4 4.4 - - - +
117A PHE* 3.1 54.3 + - + +
118A ASN* 3.0 22.7 + - - +
120A LEU* 1.3 80.3 - - - +
122A TRP* 1.3 61.3 + - - +
124A VAL* 3.3 22.5 + - - +
125A SER* 3.1 25.5 + - - -
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Residues in contact with TRP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A HIS* 3.4 39.3 - + - -
56A LYS* 3.7 34.7 - - + +
118A ASN 4.5 0.4 + - - -
119A PHE 3.8 13.3 + - - +
120A LEU 3.0 0.2 - - - -
121A GLN* 1.3 79.6 - - - +
123A TYR* 1.3 95.1 + + - +
125A SER* 3.4 6.0 + - - -
126A GLU* 2.8 56.6 + - + +
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Residues in contact with TYR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 4.1 10.5 - - - -
53A HIS* 2.7 46.8 + + + -
56A LYS* 3.4 18.4 - - + +
57A LEU* 3.4 17.4 + - + +
101A ILE* 4.0 33.4 - - + -
119A PHE* 4.0 24.5 - + - -
120A LEU* 3.0 28.0 + - + +
122A TRP* 1.3 106.7 - + + +
124A VAL* 1.3 65.8 + - - +
126A GLU* 3.8 3.3 - - + +
127A GLN* 2.9 32.8 + - + +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 4.1 10.1 - - + -
102A ASN* 5.4 7.9 - - - +
105A VAL* 3.8 28.3 - - + -
120A LEU 3.2 11.5 + - - +
121A GLN* 3.6 23.3 - - - +
122A TRP 3.3 0.2 - - - -
123A TYR* 1.3 80.0 - - - +
125A SER* 1.3 66.5 + - - +
127A GLN* 3.3 4.2 + - - +
128A HIS* 3.2 18.8 + - + +
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN 3.1 14.8 + - - -
122A TRP* 3.5 7.2 - - - -
124A VAL* 1.3 82.2 - - - +
126A GLU* 1.3 63.0 + - - -
128A HIS* 3.2 22.0 + - - +
129A GLU* 3.4 15.7 + - - +
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 4.7 4.9 - - - +
53A HIS* 3.8 19.5 - - + +
122A TRP* 2.8 48.8 + - + +
123A TYR* 3.8 9.2 - - + +
125A SER* 1.3 73.3 - - - +
127A GLN* 1.3 59.8 + - + +
129A GLU* 3.1 21.0 + - - +
130A GLU* 3.0 50.2 + - - +
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 5.4 0.5 - - - +
50A GLU* 4.5 3.1 - - - +
53A HIS* 4.5 12.8 + - - -
94A GLU* 3.2 36.4 + - - +
97A ILE* 3.7 18.4 - - - +
98A THR* 3.2 32.2 + - + +
101A ILE* 4.3 19.3 - - + -
123A TYR* 2.9 25.2 + - + +
124A VAL* 3.9 4.3 - - - +
126A GLU* 1.3 74.7 - - + +
128A HIS* 1.3 66.5 + - - +
130A GLU* 3.8 12.9 - - - +
131A GLU* 2.9 28.1 + - - +
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Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 3.2 10.8 + - + +
125A SER* 3.2 14.4 + - - +
127A GLN* 1.3 76.6 - - - +
129A GLU* 1.3 82.5 + - - +
131A GLU* 4.0 4.1 - - - +
132A ALA* 3.1 31.7 + - + +
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Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A SER* 3.5 16.9 + - - +
126A GLU* 3.1 22.9 - - - +
128A HIS* 1.3 94.3 - - - +
130A GLU* 1.3 58.6 + - + +
132A ALA* 3.3 6.8 + - - +
133A LEU* 3.0 27.3 + - - +
165A ARG* 6.4 0.2 - - - -
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Residues in contact with GLU 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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46A HIS* 3.0 33.1 - - + -
49A GLU* 3.7 12.2 - - - +
50A GLU* 3.6 10.9 - - - +
53A HIS* 3.4 22.5 - - - -
94A GLU* 3.7 18.5 - - - +
126A GLU* 3.0 31.9 + - - +
127A GLN* 4.1 9.0 - - - +
129A GLU* 1.3 78.3 - - + +
131A GLU* 1.3 64.9 + - - +
133A LEU* 3.6 13.0 - - + +
134A PHE* 3.0 37.5 + - + -
165A ARG* 5.5 3.6 - - - +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 3.7 23.3 + - + -
94A GLU* 4.4 6.9 + - + +
95A GLN* 3.8 30.1 + - + +
98A THR* 2.7 40.2 + - - +
127A GLN* 2.9 18.3 + - - +
128A HIS* 4.0 4.3 - - - +
130A GLU* 1.3 73.4 - - - +
132A ALA* 1.3 66.6 + - - +
134A PHE* 4.1 0.2 - - - -
135A ARG* 3.0 43.0 + - - +
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Residues in contact with ALA 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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128A HIS* 3.1 28.9 + - + +
129A GLU* 3.5 6.3 - - - +
131A GLU* 1.3 79.0 - - - +
133A LEU* 1.3 62.9 + - - +
135A ARG* 3.4 24.1 + - - +
136A GLY* 3.0 20.1 + - - -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 4.0 19.7 - - + -
46A HIS* 5.7 0.9 - - - +
129A GLU 3.0 17.0 + - - +
130A GLU* 3.6 12.3 - - + +
132A ALA* 1.3 75.6 - - - +
134A PHE* 1.3 75.4 + - + +
136A GLY* 3.3 3.8 + - - -
137A ILE* 3.2 30.4 + - + +
161A ILE* 4.1 27.1 - - + -
165A ARG* 3.3 38.4 - - - +
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Residues in contact with PHE 134 (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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42A PHE* 3.4 32.8 - + - -
43A LEU* 4.4 1.6 - - + -
46A HIS* 3.3 47.6 - + - -
87A PHE* 4.2 19.3 - + - +
90A THR* 3.3 27.8 - - + -
91A TYR* 4.1 22.7 - - + -
94A GLU* 3.7 16.6 - - + -
130A GLU* 3.0 27.4 + - + +
133A LEU* 1.3 83.6 - - + +
135A ARG* 1.3 66.7 + - - +
136A GLY 3.1 1.3 - - - -
137A ILE* 3.2 8.0 + - + +
138A VAL* 3.1 26.0 + - - +
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Residues in contact with ARG 135 (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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91A TYR* 3.4 40.7 + - + +
131A GLU* 3.0 39.7 + - - +
132A ALA* 3.5 29.9 + - - +
134A PHE* 1.3 77.4 - - - +
136A GLY* 1.3 63.2 + - - +
138A VAL* 3.3 4.0 + - - +
139A ASP* 3.1 42.2 + - - +
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Residues in contact with GLY 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA 3.0 13.2 + - - -
133A LEU 3.3 4.7 + - - -
134A PHE 3.1 0.2 - - - -
135A ARG* 1.3 76.0 - - - +
137A ILE* 1.3 58.8 + - - +
139A ASP* 3.4 7.2 + - - +
140A LYS* 2.9 34.7 + - - +
157A TYR* 5.5 3.6 - - - -
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 5.1 6.5 - - + -
87A PHE* 3.7 28.7 - - + -
133A LEU* 3.2 26.6 + - + +
134A PHE* 3.2 19.9 + - + +
136A GLY* 1.3 74.8 - - - +
138A VAL* 1.3 58.7 + - - +
140A LYS* 3.2 6.6 + - - +
141A ILE* 2.8 39.0 + - + +
157A TYR* 4.3 3.1 - - + -
158A ILE* 3.8 30.1 - - + -
161A ILE* 3.2 37.5 - - + -
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.1 11.2 - - + -
87A PHE* 3.3 35.7 - - + +
88A GLU* 4.4 8.5 - - + +
91A TYR* 4.3 15.7 - - + -
134A PHE 3.1 14.0 + - - +
135A ARG* 3.7 7.4 - - - +
137A ILE* 1.3 74.1 - - - +
139A ASP* 1.3 69.5 + - - +
141A ILE* 3.1 10.1 + - - +
142A LYS* 3.0 48.0 + - + +
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Residues in contact with ASP 139 (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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135A ARG* 3.1 35.0 + - - +
136A GLY* 3.9 5.7 - - - +
138A VAL* 1.3 80.4 - - - +
140A LYS* 1.3 52.8 + - - +
142A LYS* 3.1 14.6 + - - +
143A LEU* 2.8 37.2 + - - +
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Residues in contact with LYS 140 (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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136A GLY 2.9 19.2 + - - +
137A ILE 3.3 5.4 - - - +
139A ASP* 1.3 77.5 - - - +
141A ILE* 1.3 62.6 + - + +
143A LEU* 3.3 25.6 + - + +
144A ILE* 3.1 40.7 + - + +
157A TYR* 3.4 58.2 - - + -
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.0 31.9 - - + +
84A LEU* 4.3 26.9 - - + +
87A PHE* 4.0 28.0 - - + -
137A ILE* 2.8 43.4 + - + +
138A VAL* 3.1 6.5 + - - +
140A LYS* 1.3 74.5 - - + +
142A LYS* 1.3 62.0 + - - +
144A ILE* 3.4 5.8 + - - +
145A GLY* 3.1 22.7 + - - +
151A LEU* 6.1 1.3 - - + -
154A ALA* 4.6 11.4 - - + -
157A TYR* 6.4 0.7 - - + -
158A ILE* 4.2 7.2 - - + -
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Residues in contact with LYS 142 (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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84A LEU* 4.4 18.6 - - + -
88A GLU* 4.0 16.9 + - - -
138A VAL* 3.0 38.2 + - + +
139A ASP* 3.5 15.1 + - - +
141A ILE* 1.3 77.7 - - - +
143A LEU* 1.3 62.4 + - - +
144A ILE 3.2 1.0 + - - -
145A GLY* 3.2 13.0 + - - +
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP 2.8 21.5 + - - +
140A LYS* 3.3 30.0 + - + +
142A LYS* 1.3 72.9 - - - +
144A ILE* 1.3 61.2 + - + +
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Residues in contact with ILE 144 (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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140A LYS* 3.1 36.2 + - + +
141A ILE* 3.9 4.0 - - - +
142A LYS 3.1 0.4 - - - -
143A LEU* 1.3 82.8 - - + +
145A GLY* 1.3 66.2 + - - +
147A HIS 4.6 3.3 - - - +
150A GLY* 3.6 29.6 - - - +
153A LEU* 4.3 19.7 - - + +
154A ALA* 3.9 28.3 - - + +
157A TYR* 4.8 5.2 - - + -
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Residues in contact with GLY 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 3.1 16.0 + - - +
142A LYS* 3.2 11.7 + - - -
144A ILE* 1.3 83.0 - - - +
146A GLU* 1.3 59.9 + - - -
147A HIS* 3.4 3.8 - - - -
150A GLY* 3.2 21.1 - - - -
151A LEU* 6.0 0.2 - - - +
154A ALA* 5.7 0.9 - - - +
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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
------------------------------------------------------------
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