Contacts of the helix formed by residues 267 - 284 (chain A) in PDB entry 1TJY
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A TRP* 1.3 74.6 - - - +
268A VAL* 1.3 55.6 + - - +
269A VAL* 3.2 13.5 + - - +
270A GLN* 3.0 42.4 + - + +
271A GLN* 2.9 24.4 + - - +
324A LEU* 4.2 6.3 - - + +
326A GLU 4.9 2.4 + - - -
328A VAL* 4.9 5.5 - - + +
338A TYR* 5.8 4.5 - - + -
340A PHE* 3.9 21.2 - - + -
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.5 59.7 - - + +
44A SER* 3.7 25.4 - - - -
45A GLY* 3.6 8.0 - - - -
115A TRP* 3.9 10.5 - - + -
247A THR* 4.8 0.4 - - + -
265A LEU* 4.6 1.8 - - + -
266A TRP* 2.9 12.8 + - - +
267A ASP* 1.3 69.2 + - - +
269A VAL* 1.3 68.5 + - - +
271A GLN* 3.2 12.9 + - - +
272A GLY 3.0 18.7 + - - -
340A PHE* 3.8 18.5 - - + -
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 3.6 21.8 - - - +
47A ASN* 4.8 5.2 - - + -
48A GLY* 3.3 25.4 - - - +
51A GLU* 6.3 0.7 - - + -
267A ASP* 3.2 7.8 - - - +
268A VAL* 1.3 77.3 - - - +
270A GLN* 1.3 61.9 + - - +
272A GLY 3.2 2.3 + - - -
273A LYS* 3.0 20.0 + - + +
339A ASP 5.2 1.3 - - - +
340A PHE* 3.6 33.9 - - + -
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Residues in contact with GLN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP* 3.0 36.0 + - - +
269A VAL* 1.3 76.5 - - - +
271A GLN* 1.3 57.3 + - - +
273A LYS* 3.2 10.1 + - + +
274A ILE* 2.8 47.0 + - + +
298A GLY 4.2 7.4 - - - +
299A ILE* 3.4 40.5 - - + +
324A LEU* 4.9 5.5 - - - +
325A PRO* 4.2 18.2 - - - +
326A GLU* 5.8 1.2 + - - +
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Residues in contact with GLN 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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41A PHE* 4.1 1.6 - - - -
115A TRP* 3.7 18.3 - - + -
116A ASP* 3.4 8.1 - - - +
128A ILE* 3.1 26.1 + - + +
130A GLN* 2.8 32.7 + - - +
266A TRP* 2.9 26.9 + - - -
267A ASP 2.9 13.5 + - - +
268A VAL* 3.4 18.6 - - + +
269A VAL 3.2 0.4 - - - -
270A GLN* 1.3 75.4 - - - +
272A GLY* 1.3 62.6 + - - +
274A ILE* 3.3 2.7 + - - +
275A SER* 3.0 23.2 + - - -
324A LEU* 3.9 26.2 - - + +
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Residues in contact with GLY 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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32A PHE* 4.0 12.1 - - - -
45A GLY* 3.5 22.4 - - - -
49A ALA* 3.5 16.9 - - - -
115A TRP* 5.2 0.2 - - - -
268A VAL 3.0 11.5 + - - -
269A VAL 3.2 1.3 + - - -
271A GLN* 1.3 76.9 - - - +
273A LYS* 1.3 60.6 + - - +
275A SER* 2.8 23.6 + - - -
276A VAL 3.3 5.2 + - - -
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY* 3.6 17.3 - - - +
52A ALA* 3.9 9.0 - - + +
269A VAL* 3.0 13.3 + - + +
270A GLN* 3.2 14.1 + - + +
272A GLY* 1.3 73.2 - - - +
274A ILE* 1.3 66.1 + - - +
276A VAL* 3.2 4.9 + - - +
277A TYR* 3.0 47.4 + - + -
296A ILE* 3.9 12.6 - - - -
297A PRO* 2.7 33.2 + - - +
298A GLY* 4.4 4.9 - - - -
299A ILE* 4.2 13.9 - - + +
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 3.9 16.4 - - + -
270A GLN* 2.8 38.0 + - + +
271A GLN 3.8 4.3 - - - +
273A LYS* 1.3 72.0 - - - +
275A SER* 1.3 59.3 + - - +
277A TYR* 3.2 1.6 + - - +
278A VAL* 2.9 41.1 + - + +
296A ILE* 4.1 18.4 - - + -
299A ILE* 3.4 27.1 - - + -
302A VAL* 4.3 13.2 - - + -
322A VAL* 4.2 13.9 - - + -
323A LEU 5.7 0.2 - - - +
324A LEU* 4.0 23.8 - - + -
325A PRO* 4.4 4.5 - - + -
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 3.3 21.0 - - - -
89A ILE* 3.5 25.5 - - - +
113A LEU* 3.8 2.9 - - - +
115A TRP* 4.5 3.4 - - - -
128A ILE* 3.8 28.5 - - - +
271A GLN 3.0 14.7 + - - -
272A GLY 2.8 16.8 + - - -
273A LYS 3.2 0.2 - - - -
274A ILE* 1.3 75.6 - - - +
276A VAL* 1.3 57.0 + - - +
278A VAL* 3.4 2.3 + - - +
279A ALA* 3.0 27.0 + - - +
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 4.4 11.7 - - + +
32A PHE* 5.0 0.2 - - + -
49A ALA* 3.5 28.5 - - + +
52A ALA* 3.8 18.4 - - + -
53A GLY* 4.0 11.7 - - - +
56A LEU* 4.1 10.5 - - + -
58A ILE* 4.6 2.9 - - + -
60A VAL* 4.2 17.9 - - + -
89A ILE* 4.1 14.4 - - + -
272A GLY 3.3 10.1 + - - +
273A LYS 3.2 7.6 + - - +
275A SER* 1.3 81.9 + - - +
277A TYR* 1.3 59.6 + - - +
279A ALA* 3.3 2.6 + - - +
280A ASN* 2.9 27.5 + - - +
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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
----------------------------------------------------------
52A ALA* 3.9 17.3 - - + -
55A ALA* 3.9 20.0 + - + +
56A LEU* 3.7 37.1 - - + +
273A LYS* 3.0 36.5 + - + +
274A ILE 3.7 6.5 - - - +
276A VAL* 1.3 76.3 - - - +
278A VAL* 1.3 58.8 + - - +
280A ASN* 3.5 9.5 + - - +
281A ALA* 3.0 22.7 + - - +
294A LEU* 3.6 11.7 - - + +
295A ASP 4.6 3.8 - - - -
296A ILE* 3.7 40.2 - - + -
297A PRO* 3.5 34.7 - - + +
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.7 16.2 - - + -
126A TYR* 4.5 14.6 - - + -
128A ILE* 3.8 22.0 - - + -
274A ILE* 2.9 30.8 + - + +
275A SER 3.8 3.6 - - - +
277A TYR* 1.3 72.2 - - - +
279A ALA* 1.3 66.6 + - - +
281A ALA* 3.1 4.2 + - - +
282A LEU* 3.1 24.4 + - + +
288A MET* 3.9 17.9 - - + -
294A LEU* 4.0 17.0 - - + -
296A ILE* 5.1 0.2 - - + -
302A VAL* 4.8 2.7 - - + -
322A VAL* 4.3 13.7 - - + -
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Residues in contact with ALA 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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30A ILE* 3.8 20.2 - - + -
87A ALA* 4.2 7.2 - - + -
89A ILE* 4.2 8.3 - - + -
111A LYS* 5.1 0.7 - - - +
113A LEU* 3.8 26.4 - - + +
275A SER 3.0 17.1 + - - +
276A VAL 3.7 4.3 - - - +
278A VAL* 1.3 77.7 - - - +
280A ASN* 1.3 61.2 + - - +
282A LEU* 3.2 7.6 + - - +
283A LEU* 3.0 28.7 + - - +
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Residues in contact with ASN 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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28A GLU* 4.6 3.3 - - - +
30A ILE* 4.7 0.8 - - - +
56A LEU* 3.8 29.7 - - + +
58A ILE* 3.5 29.1 - - + +
276A VAL 2.9 18.3 + - - +
277A TYR* 3.5 8.6 + - - +
278A VAL 3.2 0.2 - - - -
279A ALA* 1.3 76.8 - - - +
281A ALA* 1.3 63.5 + - - +
283A LEU* 3.1 7.8 + - - +
284A LYS* 2.9 51.9 + - - +
286A MET* 4.3 10.7 - - - +
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Residues in contact with ALA 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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277A TYR 3.0 13.8 + - - +
278A VAL 3.4 8.7 - - - +
280A ASN* 1.3 76.4 - - - +
282A LEU* 1.3 63.4 + - - +
284A LYS 3.2 2.1 + - - -
285A ASN 3.0 4.9 + - - -
286A MET* 3.0 59.8 + - + +
288A MET* 4.2 11.7 - - + -
294A LEU* 3.9 19.5 - - + -
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Residues in contact with LEU 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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111A LYS* 3.8 35.4 + - + -
113A LEU* 4.1 26.9 - - + -
125A SER* 5.1 4.3 - - - -
126A TYR* 3.4 50.0 - - + +
278A VAL* 3.1 15.7 + - + +
279A ALA* 3.2 6.0 + - - +
281A ALA* 1.3 76.1 - - - +
283A LEU* 1.3 61.8 + - - +
285A ASN* 3.1 21.7 + - - +
286A MET 5.3 2.2 - - - +
288A MET* 4.1 17.5 - - + -
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Residues in contact with LEU 283 (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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28A GLU* 3.6 41.6 - - + +
30A ILE* 4.1 24.2 - - + -
58A ILE* 5.2 0.9 - - + -
86A ASP* 3.8 31.2 - - + +
87A ALA* 4.6 2.5 - - + -
111A LYS* 3.7 30.7 - - + +
279A ALA 3.0 19.0 + - - +
280A ASN* 3.1 9.2 + - - +
282A LEU* 1.3 77.2 - - - +
284A LYS* 1.3 62.0 + - + +
285A ASN* 3.3 7.7 + - - +
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 4.3 19.5 + - - -
280A ASN* 2.9 35.8 + - - +
281A ALA 3.8 0.9 - - - +
282A LEU 3.2 0.4 - - - -
283A LEU* 1.3 78.3 - - + +
285A ASN* 1.3 71.3 + - - +
286A MET* 3.2 31.3 + - + +
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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