Contacts of the helix formed by residues 137 - 150 (chain N) in PDB entry 1KYO
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 GLY 137 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62N PHE* 3.9 4.0 - - - -
135N VAL 3.3 2.0 - - - -
136N TYR* 1.3 79.9 - - - +
138N GLN* 1.3 68.2 + - - -
140N SER* 3.0 7.7 + - - -
141N HIS 3.0 16.8 + - - -
256N ASN* 3.1 25.5 - - - -
258N ILE 3.3 13.2 - - - -
260N GLY* 3.6 6.7 - - - -
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Residues in contact with GLN 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137N GLY* 1.3 70.4 - - - +
139N MET* 1.3 68.7 + - + +
141N HIS* 3.4 0.7 + - - +
142N TRP* 2.8 54.4 + - - -
255N ASP* 3.5 15.1 + - + +
258N ILE* 2.8 27.5 + - + +
259N PRO 3.9 11.6 + - - +
260N GLY* 3.8 1.7 - - - +
261N ASN* 3.2 31.0 + - - +
264N VAL* 2.9 27.9 + - - +
266N PRO* 3.5 25.5 - - + +
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Residues in contact with MET 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132N TYR* 3.2 33.7 - - + +
138N GLN* 1.3 86.0 - - + +
140N SER* 1.3 53.1 + - - +
142N TRP* 3.4 0.4 + - - -
143N GLY* 2.8 34.5 + - - -
253N HIS* 3.8 34.5 - - + +
255N ASP* 3.4 34.0 + - + +
256N ASN* 3.2 10.1 + - - +
266N PRO* 4.1 9.2 - - + -
269N ILE* 3.9 35.0 - - + -
270N VAL 4.0 3.4 - - - +
525N SMA 3.6 13.9 - - - +
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Residues in contact with SER 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132N TYR* 2.8 34.0 + - - -
133N CYS* 3.6 11.0 - - - +
135N VAL* 3.7 0.2 - - - +
136N TYR* 3.1 17.2 + - - -
137N GLY 3.0 26.8 + - - -
139N MET* 1.3 73.8 - - - +
141N HIS* 1.3 60.3 + - - +
143N GLY* 2.9 2.8 + - - -
144N ALA* 2.8 32.4 + - - +
256N ASN* 3.0 15.3 + - - -
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Residues in contact with HIS 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136N TYR* 2.8 44.4 + - + -
137N GLY 3.0 10.8 + - - +
138N GLN 3.9 3.6 - - - +
140N SER* 1.3 79.3 - - - +
142N TRP* 1.3 92.2 + + + +
144N ALA* 3.2 8.8 - - - +
145N THR* 2.9 38.3 + - - -
170N SER* 6.3 0.4 - - - -
171N VAL* 3.5 35.2 - - + +
260N GLY* 4.3 6.7 - - - -
261N ASN 4.4 3.1 - - - -
262N PRO* 3.8 24.7 + - + +
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Residues in contact with TRP 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E GLY 3.7 20.2 - - - -
164E CYS* 4.1 8.7 - - - -
165E VAL* 3.5 17.0 - - + -
138N GLN* 2.8 47.0 + - - +
139N MET* 4.1 2.2 - - + +
141N HIS* 1.3 90.5 - + - +
143N GLY* 1.3 65.6 + - - +
145N THR* 3.6 17.7 - - + -
146N VAL* 3.0 30.5 + - - +
261N ASN 3.1 19.0 + - - -
262N PRO 3.5 13.9 - - - -
264N VAL 3.1 16.8 + - - -
265N THR* 3.4 29.8 - - + +
266N PRO* 3.7 15.3 - - + -
269N ILE* 3.7 22.0 - - + -
525N SMA 4.4 2.0 - - - -
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Residues in contact with GLY 143 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129N PHE* 4.0 8.3 - - - -
132N TYR* 5.8 3.4 - - - -
133N CYS* 5.6 0.2 - - - -
139N MET 2.8 17.5 + - - -
140N SER 3.5 1.1 - - - -
142N TRP* 1.3 75.0 - - - +
144N ALA* 1.3 64.3 + - - +
146N VAL* 5.0 0.2 - - - -
147N ILE* 3.1 32.0 + - - +
525N SMA 3.8 27.5 - - - -
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Residues in contact with ALA 144 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N PHE* 4.0 5.1 - - - -
133N CYS* 3.8 25.1 - - + -
140N SER 2.8 12.2 + - - +
141N HIS* 3.2 13.0 - - - +
143N GLY* 1.3 79.0 - - - +
145N THR* 1.3 52.2 + - - +
147N ILE* 4.5 0.3 - - - +
148N THR* 2.7 38.3 + - - +
171N VAL* 4.0 22.6 - - + +
176N ILE* 5.1 2.5 - - + -
179N PHE* 4.5 9.0 - - + -
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Residues in contact with THR 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E LEU 3.9 3.4 - - - +
163E GLY* 3.5 26.0 - - - +
141N HIS* 2.9 35.1 + - - -
142N TRP* 3.6 17.6 - - + -
144N ALA* 1.3 73.6 - - - +
146N VAL* 1.3 67.4 + - + +
148N THR* 2.9 17.3 + - - -
149N ASN* 3.1 28.5 + - - +
166N TRP* 4.8 5.2 - - + +
171N VAL* 3.7 16.1 - - + +
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Residues in contact with VAL 146 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E LEU* 3.3 43.4 - - + +
164E CYS* 3.5 31.0 - - - -
181E HIS* 3.7 4.5 - - + -
142N TRP 3.0 19.7 + - - +
143N GLY 4.2 1.1 - - - +
145N THR* 1.3 76.0 - - - +
147N ILE* 1.3 64.2 + - - +
149N ASN* 3.0 14.6 + - - +
150N LEU* 3.1 10.4 + - + +
525N SMA 3.6 42.2 - - + +
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Residues in contact with ILE 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N PHE* 3.3 45.5 - - + -
143N GLY 3.1 15.6 + - - +
146N VAL* 1.3 75.1 - - - +
148N THR* 1.3 62.0 + - - +
150N LEU* 2.9 31.5 - - + +
151N PHE* 4.0 5.4 - - - -
275N LEU* 5.1 0.4 - - + -
525N SMA 3.6 91.8 - - + +
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Residues in contact with THR 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N PHE* 5.0 2.7 - - + -
144N ALA 2.7 24.6 + - - +
145N THR 2.9 8.5 + - - -
147N ILE* 1.3 76.5 - - - +
149N ASN* 1.3 60.8 + - - +
150N LEU 3.1 1.4 + - - -
151N PHE* 3.2 28.6 + - - +
162N VAL* 3.7 11.1 - - - +
165N LEU* 4.4 12.1 - - + +
166N TRP* 2.8 34.0 + - + +
179N PHE* 3.8 27.4 - - + -
525N SMA 4.1 13.9 - - + -
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Residues in contact with ASN 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E LEU* 3.1 43.2 + - + +
163E GLY* 3.9 5.5 - - - -
145N THR* 3.1 24.6 + - - +
146N VAL 3.0 11.1 + - - +
148N THR* 1.3 73.5 + - - +
150N LEU* 1.3 57.0 + - - +
151N PHE 2.9 2.9 - - - -
152N SER* 2.7 46.4 + - - +
153N ALA 4.0 0.3 + - - -
162N VAL* 3.8 14.1 - - - +
166N TRP* 3.6 23.6 - - - -
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Residues in contact with LEU 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E LEU* 3.7 25.4 - - + -
146N VAL 3.1 4.8 + - - +
147N ILE* 2.9 46.4 + - + +
149N ASN* 1.3 77.0 - - - +
151N PHE* 1.3 69.0 + - + +
153N ALA* 3.3 21.8 - - - +
154N ILE* 5.4 0.3 - - - +
282N LEU* 4.1 11.7 - - + -
292N VAL* 3.5 35.0 - - + +
295N MET* 4.0 20.2 - - + -
296N PHE* 5.0 9.7 - - + -
525N SMA 4.6 16.6 - - + -
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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