Contacts of the helix formed by residues 269 - 283 (chain A) in PDB entry 1P4D
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 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A VAL* 1.3 76.9 - - - +
270A PRO* 1.3 66.5 - - - +
271A GLU* 2.9 41.9 + - - +
272A ILE* 3.2 39.5 + - + +
273A LYS* 3.2 8.7 + - - +
6C GLN* 3.1 19.6 + - + +
77C ARG* 3.3 41.9 + - - +
78C PRO* 5.8 0.6 - - + +
80C TYR* 4.5 9.0 - - - -
176C SER* 4.6 0.3 - - - -
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Residues in contact with PRO 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP* 3.6 26.5 - - + +
24A TYR* 3.2 40.8 - - + -
268A VAL* 3.1 11.7 - - + +
269A ASP* 1.3 83.4 - - - +
271A GLU* 1.3 60.5 + - + +
273A LYS* 3.2 23.9 + - + +
274A MET* 2.8 31.5 + - - +
77C ARG* 3.5 21.5 - - - +
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.6 25.5 + - + +
269A ASP* 2.9 17.5 + - - +
270A PRO* 1.3 79.6 - - + +
272A ILE* 1.3 59.8 + - - +
274A MET* 3.7 3.2 - - - +
275A ALA* 3.1 21.0 + - - +
80C TYR* 3.6 7.1 + - - -
175C LEU 5.3 0.4 - - - +
176C SER* 3.1 31.5 - - - -
177C SER* 3.2 34.8 + - - +
184C GLY* 5.2 9.5 - - - -
185C PHE 5.6 1.2 + - - -
186C ILE* 3.6 22.0 - - + +
187C GLU* 6.2 0.9 - - + -
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Residues in contact with ILE 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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269A ASP* 3.2 29.5 + - + +
270A PRO 3.2 0.2 - - - -
271A GLU* 1.3 75.8 - - - +
273A LYS* 1.3 65.8 + - - +
275A ALA* 3.0 9.9 + - - +
276A GLU* 3.0 27.8 + - + +
4C ILE* 5.6 0.4 - - + -
5C ALA* 4.6 2.2 - - - +
6C GLN* 3.3 48.9 - - + +
80C TYR* 4.2 17.5 - - + -
186C ILE* 4.2 19.1 - - + -
190C TYR* 3.9 26.2 - - + +
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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
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21A ASP 4.5 9.7 + - - -
24A TYR* 5.3 0.8 - - - +
25A VAL* 4.1 6.8 - - - +
147A ASP* 3.8 6.1 + - - -
148A THR* 2.5 31.4 + - - +
152A GLN* 3.1 32.2 - - + +
268A VAL* 4.9 5.8 - - + +
269A ASP 3.2 10.4 + - - +
270A PRO* 3.2 30.1 + - + +
272A ILE* 1.3 79.6 - - - +
274A MET* 1.3 62.1 + - - +
276A GLU* 3.1 10.9 + - - +
277A TRP* 3.0 62.2 + - + +
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Residues in contact with MET 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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24A TYR* 4.7 6.7 - - + -
25A VAL* 3.8 32.1 - - + -
95A MET 3.5 21.8 - - - +
96A LEU* 4.3 3.6 - - - -
270A PRO 2.8 20.0 + - - +
271A GLU* 3.7 7.2 - - - +
273A LYS* 1.3 73.2 - - - +
275A ALA* 1.3 65.0 + - - +
277A TRP* 3.1 16.0 + - - +
278A MET* 2.8 52.7 + - + +
180C VAL* 5.3 11.2 - - + -
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Residues in contact with ALA 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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271A GLU 3.1 11.3 + - - +
272A ILE* 3.0 13.1 + - - +
274A MET* 1.3 80.6 - - - +
276A GLU* 1.3 62.3 + - - +
278A MET* 3.4 4.2 + - - +
279A GLN* 3.0 22.5 + - - +
186C ILE* 4.7 6.3 - - + +
187C GLU* 4.5 19.3 - - + +
190C TYR* 3.5 38.4 - - + +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 3.0 22.8 + - - +
273A LYS* 3.1 8.7 + - - +
275A ALA* 1.3 73.1 - - - +
277A TRP* 1.3 69.7 + - + +
279A GLN* 2.9 8.9 + - - +
280A THR* 2.8 28.3 + - + +
4C ILE 5.0 2.4 - - - +
5C ALA* 5.7 1.4 - - - -
190C TYR* 3.0 34.6 + - + +
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Residues in contact with TRP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.4 33.4 - - + -
95A MET* 4.4 4.3 - - - -
96A LEU* 4.0 25.8 - - + -
147A ASP 3.8 10.8 - - - -
148A THR* 3.6 13.0 - - + -
152A GLN 3.0 21.1 + - - -
153A GLU* 3.4 13.4 + - - +
154A PRO* 3.4 44.3 - - + +
234A PHE* 3.8 8.4 - + + -
273A LYS* 3.0 49.5 + - + +
274A MET* 3.5 13.5 - - - +
276A GLU* 1.3 77.5 - - + +
278A MET* 1.3 58.2 + - - +
280A THR* 3.0 10.8 - - + +
281A LEU* 2.9 30.2 + - - +
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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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96A LEU* 3.8 41.3 - - - +
274A MET* 2.8 45.5 + - + +
275A ALA* 3.7 6.3 - - - +
277A TRP* 1.3 76.0 - - - +
279A GLN* 1.3 61.1 + - - +
281A LEU* 3.4 14.8 + - + +
282A LYS* 3.2 33.7 + - + +
187C GLU* 4.9 9.9 - - - +
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Residues in contact with GLN 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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275A ALA 3.0 13.8 + - - +
276A GLU* 2.9 10.5 + - - +
278A MET* 1.3 73.0 - - - +
280A THR* 1.3 62.2 + - - +
281A LEU 3.0 4.7 - - - -
282A LYS* 3.0 21.9 + - + +
283A GLU* 3.1 34.0 + - + +
190C TYR* 3.1 41.7 - - + +
193C GLN* 3.3 19.9 + - - +
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Residues in contact with THR 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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233A ALA* 3.8 22.6 + - - +
234A PHE* 3.6 13.1 - - + -
276A GLU* 2.8 20.7 + - + +
277A TRP* 3.0 23.3 - - + +
279A GLN* 1.3 74.3 - - - +
281A LEU* 1.3 60.3 + - - +
283A GLU* 3.6 18.4 + - - +
284A THR* 3.3 21.7 + - - +
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Residues in contact with LEU 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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92A MET* 5.8 2.9 - - + -
96A LEU* 4.0 30.7 - - + +
230A PRO* 4.8 6.3 - - + -
234A PHE* 4.0 17.3 - - + -
277A TRP 2.9 18.2 + - - +
278A MET* 3.4 19.1 - - + +
279A GLN 3.0 0.4 - - - -
280A THR* 1.3 77.3 - - - +
282A LYS* 1.3 64.4 + - + +
284A THR* 2.4 37.6 + - - +
285A GLY 3.9 1.0 + - - -
286A PHE* 4.4 11.2 + - + +
288A ILE* 3.2 40.6 - - + -
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Residues in contact with LYS 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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278A MET* 3.2 20.4 + - + +
279A GLN* 3.0 13.5 + - + +
281A LEU* 1.3 83.3 - - + +
283A GLU* 1.3 62.2 + - + +
285A GLY* 3.0 15.6 + - - -
286A PHE 5.7 2.5 - - - -
608A EDO 3.7 8.7 + - - -
187C GLU* 5.7 2.2 + - - -
191C ALA* 5.5 9.3 - - - +
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Residues in contact with GLU 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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279A GLN* 3.1 45.2 + - + +
280A THR* 3.9 16.4 - - - +
281A LEU 3.3 0.2 - - - -
282A LYS* 1.3 76.3 - - + +
284A THR* 1.3 60.7 + - - +
285A GLY 3.3 0.4 + - - -
608A EDO 3.9 15.2 + - - -
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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