Contacts of the helix formed by residues 267 - 282 (chain A) in PDB entry 1LK9
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 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A TYR* 4.2 1.6 - - - -
243A ASP* 4.7 13.5 + - + +
265A ILE* 3.3 8.2 - - - +
266A LYS* 1.3 95.2 - - - +
268A GLU* 1.3 66.0 + - - +
269A SER* 4.4 6.9 + - - +
270A VAL* 3.1 25.0 + - + +
271A TYR* 3.0 17.7 + - - +
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Residues in contact with GLU 268 (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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125A TYR* 3.4 42.1 + - + +
266A LYS 3.6 4.0 + - - -
267A ASP* 1.3 71.8 - - - +
269A SER* 1.3 57.4 + - - +
271A TYR* 3.3 5.2 + - + +
272A ASN* 2.9 47.0 + - - +
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Residues in contact with SER 269 (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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267A ASP* 3.2 7.0 + - - +
268A GLU* 1.3 78.1 - - - +
270A VAL* 1.3 72.1 + - - +
272A ASN* 3.4 8.0 + - - +
273A ASN* 3.0 34.8 + - - -
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Residues in contact with VAL 270 (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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139A LEU* 3.9 26.7 - - + -
142A SER* 4.3 10.9 + - - +
143A LEU* 4.1 21.1 - - + -
244A ILE* 4.2 14.6 - - + -
265A ILE* 3.9 13.9 - - + -
267A ASP* 3.1 25.6 + - + +
269A SER* 1.3 79.1 + - - +
271A TYR* 1.3 61.2 + - - +
273A ASN* 3.2 8.7 + - - +
274A LEU* 2.8 28.6 + - - +
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Residues in contact with TYR 271 (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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99A ASN* 3.6 21.7 + - - +
101A ILE* 5.0 1.9 - - - +
125A TYR* 3.4 53.8 - + + -
126A ILE 3.6 22.4 + - - -
127A VAL* 3.5 21.5 - - + -
265A ILE* 3.7 12.0 - - + +
267A ASP 3.0 12.8 + - - +
268A GLU* 3.4 12.1 - - + +
270A VAL* 1.3 77.3 - - - +
272A ASN* 1.3 69.3 + - - +
274A LEU* 3.1 2.8 + - - +
275A LEU* 2.9 53.2 + - + +
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Residues in contact with ASN 272 (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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268A GLU* 2.9 38.7 + - - +
269A SER* 3.8 6.7 - - - +
270A VAL 3.3 0.2 - - - -
271A TYR* 1.3 92.3 - - - +
273A ASN* 1.3 60.4 + - - +
275A LEU* 3.4 12.1 + - - +
276A ASN* 3.0 26.9 + - - +
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Residues in contact with ASN 273 (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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142A SER* 3.3 39.7 + - - +
269A SER* 3.0 26.3 + - - +
270A VAL* 3.2 3.8 + - - +
272A ASN* 1.3 77.9 - - - +
274A LEU* 1.3 58.6 + - - +
276A ASN* 3.3 9.3 + - - +
277A TYR* 3.1 23.6 + - - +
174B TYR* 4.3 3.6 + - - -
1C NAG 5.5 7.4 - - - +
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Residues in contact with LEU 274 (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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127A VAL* 3.7 32.1 - - + -
135A LEU* 4.1 17.5 - - + +
138A GLY* 3.5 37.7 - - - -
139A LEU* 3.8 19.5 - - + +
142A SER* 3.4 4.2 + - - +
263A ALA* 4.2 4.7 - - + -
265A ILE* 3.7 20.0 - - + -
270A VAL 2.8 16.9 + - - +
271A TYR 3.7 3.4 - - - +
273A ASN* 1.3 74.4 - - - +
275A LEU* 1.3 67.6 + - - +
277A TYR* 3.2 11.9 + - + +
278A MET* 2.9 22.8 + - + +
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Residues in contact with LEU 275 (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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99A ASN* 3.7 41.7 - - + +
101A ILE* 4.0 18.6 - - + -
127A VAL* 4.0 16.2 - - + -
271A TYR* 2.9 53.0 + - + +
272A ASN* 3.6 14.4 - - - +
274A LEU* 1.3 78.9 - - - +
276A ASN* 1.3 62.4 + - - +
278A MET* 3.1 8.7 + - + +
279A THR* 3.0 25.2 + - - -
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Residues in contact with ASN 276 (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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272A ASN 3.0 14.1 + - - +
273A ASN* 3.5 13.1 + - - +
274A LEU 3.2 0.2 - - - -
275A LEU* 1.3 77.0 - - - +
277A TYR* 1.3 63.1 + - - +
279A THR* 3.2 8.6 + - - +
280A LYS* 2.9 45.1 + - - +
174B TYR* 3.4 29.4 - - - -
1C NAG 3.9 14.5 - - - +
4C FUC 5.3 3.4 + - - -
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Residues in contact with TYR 277 (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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134A GLN* 2.9 41.1 + - + -
137A HIS* 3.9 20.6 + - - +
138A GLY* 3.4 35.3 + - - +
141A ILE* 4.0 15.7 - - + -
273A ASN 3.1 11.5 + - - +
274A LEU* 3.4 17.9 - - + +
276A ASN* 1.3 76.0 - - - +
278A MET* 1.3 70.0 - - - +
280A LYS* 3.2 2.1 + - - +
281A ASN* 2.8 53.0 + - + +
174B TYR* 3.3 23.6 + - - +
175B PHE* 4.2 15.5 - + - -
281B ASN* 3.5 10.4 + - - -
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Residues in contact with MET 278 (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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100A PHE* 5.6 2.9 - - + -
127A VAL* 3.7 21.5 - - + -
128A PHE 3.3 20.0 - - - +
134A GLN* 3.2 43.1 - - - +
135A LEU* 4.2 8.5 - - - -
274A LEU* 2.9 17.8 + - + +
275A LEU* 3.1 11.8 + - + +
277A TYR* 1.3 89.1 - - + +
279A THR* 1.3 59.0 + - - +
281A ASN* 4.6 1.3 - - - +
282A THR* 3.2 19.9 + - - +
283A GLU 2.9 21.3 + - - -
284A GLY* 3.2 29.3 + - - +
285A THR* 4.0 2.5 - - + -
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Residues in contact with THR 279 (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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100A PHE* 3.8 15.9 - - + -
275A LEU* 3.0 12.4 + - - +
276A ASN* 3.2 12.7 + - - +
278A MET* 1.3 76.7 - - - +
280A LYS* 1.3 76.7 + - - +
282A THR 4.0 0.2 + - - -
283A GLU* 3.3 50.1 + - - +
133B THR* 4.2 2.3 - - - +
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Residues in contact with LYS 280 (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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276A ASN* 2.9 39.6 + - - +
277A TYR 3.7 3.1 - - - +
279A THR* 1.3 86.3 - - - +
281A ASN* 1.3 60.0 + - - +
133B THR* 3.8 2.4 - - - +
167B VAL* 5.9 0.2 - - - +
170B GLU* 3.6 36.0 + - + +
171B GLN* 2.9 41.6 + - + +
174B TYR* 3.7 49.4 - - + -
175B PHE* 3.9 3.9 - - + -
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Residues in contact with ASN 281 (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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134A GLN* 3.0 22.7 + - - +
277A TYR* 2.8 32.8 + - + +
278A MET 4.4 0.4 - - - +
280A LYS* 1.3 80.2 - - - +
282A THR* 1.3 59.8 + - - +
133B THR* 3.7 4.8 - - - +
134B GLN* 3.3 25.5 + - - +
137B HIS* 5.7 1.0 + - - +
171B GLN* 4.4 0.9 + - - +
175B PHE* 4.3 18.0 - - + -
277B TYR* 3.6 12.1 + - - -
281B ASN* 2.9 43.2 + - - +
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Residues in contact with THR 282 (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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130A VAL* 4.7 0.8 - - + +
134A GLN* 3.2 29.2 + - - +
278A MET* 3.2 4.7 + - - +
281A ASN* 1.3 89.3 - - - +
283A GLU* 1.3 66.3 + - - +
284A GLY 2.8 26.4 + - - +
130B VAL* 3.7 36.9 - - + +
133B THR* 4.2 3.1 - - - -
134B GLN* 4.0 12.3 - - + +
259B ARG* 2.9 27.9 + - - -
282B THR* 4.9 1.1 - - + -
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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