Contacts of the helix formed by residues 278 - 290 (chain D) in PDB entry 1P4E
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 ASN 278 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258D ARG* 5.5 2.1 + - - -
276D LYS* 3.1 4.0 - - + +
277D ASP* 1.3 78.3 - - - +
279D LEU* 1.3 66.0 + - - +
280D VAL* 3.0 4.0 - - - -
281D ARG* 2.9 21.2 + - - +
282D SER* 3.7 4.9 + - - -
5H T 4.6 5.4 + - + -
6H T 3.0 71.9 + - + +
7H C 4.0 13.3 + - - -
8H C 5.6 0.3 + - - -
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Residues in contact with LEU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D THR* 6.4 0.2 - - + -
177D LEU* 4.2 33.2 - - + -
178D TYR* 4.0 23.8 - - + -
181D LEU* 4.1 20.4 - - + -
192D PHE* 4.3 2.2 - - + -
275D LEU* 3.9 37.7 - - + -
276D LYS* 2.9 27.5 + - + +
278D ASN* 1.3 76.5 - - - +
280D VAL* 1.3 55.9 + - - +
282D SER* 3.0 17.2 + - - +
283D TYR* 2.8 27.7 + - + +
5H T 5.3 2.2 - - - +
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D PHE* 3.6 36.1 - - + -
277D ASP 3.7 13.9 - - - +
278D ASN* 3.0 2.1 + - - +
279D LEU* 1.3 80.6 - - - +
281D ARG* 1.3 64.8 + - + +
283D TYR* 3.6 5.3 - - - +
284D ASN* 2.8 46.6 + - - +
304D SER* 3.9 22.0 - - - +
24J T 4.9 6.5 - - + -
25J A 4.2 7.4 - - + +
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Residues in contact with ARG 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D ASN* 2.9 11.0 + - - +
280D VAL* 1.3 86.7 - - + +
282D SER* 1.3 58.7 + - - +
284D ASN* 4.4 8.5 - - - +
285D LYS* 2.9 56.2 + - - +
5H T 4.2 7.0 - - + -
6H T 3.2 34.5 + - + +
7H C 4.0 2.0 - - - +
26J G 3.1 50.1 + - - +
27J G 2.7 49.4 + - - -
28J A 4.5 3.4 - - - +
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Residues in contact with SER 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D TYR* 3.5 17.5 + - - -
278D ASN 3.7 2.1 + - - -
279D LEU* 3.0 19.9 + - - +
281D ARG* 1.3 79.7 - - - +
283D TYR* 1.3 57.3 + - - +
285D LYS* 3.3 3.6 + - - +
286D ALA* 2.8 31.2 + - - +
4H G 3.5 20.1 + - - -
5H T 3.1 40.2 + - - +
6H T 5.5 0.2 - - - +
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Residues in contact with TYR 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D PHE* 3.7 20.1 - + - -
178D TYR* 3.5 50.7 - + + -
181D LEU* 3.9 20.2 - - + -
182D PHE* 3.0 41.4 - - + +
185D THR* 5.0 1.6 + - + -
279D LEU* 2.8 21.7 + - + +
280D VAL* 3.6 6.1 - - - +
282D SER* 1.3 78.3 + - - +
284D ASN* 1.3 59.9 - - - +
286D ALA* 3.2 2.8 + - - +
287D LEU* 2.8 43.6 + - + +
304D SER* 3.6 37.3 + - - -
306D ILE* 4.8 1.4 - - - +
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Residues in contact with ASN 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D VAL* 2.8 32.8 + - - +
281D ARG* 3.9 11.9 - - - +
283D TYR* 1.3 72.2 - - - +
285D LYS* 1.3 56.5 + - - +
287D LEU* 3.2 6.4 + - - +
288D LYS* 2.7 36.6 + - - +
303D LYS* 2.9 33.9 - - + +
304D SER* 2.9 19.1 + - - -
25J A 3.1 39.3 + - - +
26J G 4.9 6.6 + - - +
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Residues in contact with LYS 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ARG* 2.9 35.6 + - - +
282D SER* 3.5 6.3 - - - +
284D ASN* 1.3 75.9 - - - +
286D ALA* 1.3 63.3 + - - +
288D LYS* 3.3 8.8 - - + +
289D LYS* 3.1 33.6 + - + +
3H A 4.4 12.5 + - + +
4H G 2.8 44.8 + - + +
5H T 3.2 27.0 + - + -
28J A 5.5 2.9 - - - +
29J A 4.2 4.1 - - - +
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Residues in contact with ALA 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D PHE* 4.1 10.5 - - + -
178D TYR* 3.8 25.6 - - + -
282D SER 2.8 17.7 + - - +
283D TYR 3.5 4.3 - - - +
285D LYS* 1.3 73.5 - - - +
287D LEU* 1.3 66.8 + - - +
288D LYS 3.0 1.1 - - - -
289D LYS* 3.1 5.0 + - - -
290D ASN* 3.0 39.3 + - - +
4H G 4.2 8.7 - - - +
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Residues in contact with LEU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D ILE* 4.0 18.8 - - + -
164D SER* 5.0 1.3 - - - +
165D PHE* 3.5 27.7 - - + -
283D TYR* 2.8 33.6 + - + +
284D ASN* 3.6 6.1 - - - +
286D ALA* 1.3 76.1 - - - +
288D LYS* 1.3 61.8 + - - +
290D ASN* 4.0 2.0 - - - +
291D ALA* 3.3 21.1 + - - -
292D PRO* 4.1 6.2 - - + +
296D PHE* 3.6 37.1 - - + +
303D LYS* 3.3 38.4 - - + +
306D ILE* 4.3 2.9 - - + -
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Residues in contact with LYS 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D ASN 2.7 18.6 + - - +
285D LYS* 3.3 11.0 - - + +
287D LEU* 1.3 75.9 - - - +
289D LYS* 1.3 67.8 + - + +
291D ALA* 3.4 15.6 - - - +
296D PHE 3.8 23.5 - - - +
297D ALA* 4.0 20.3 + - - +
298D ILE 4.6 0.2 + - - -
299D LYS* 4.0 14.1 - - - +
303D LYS* 3.9 13.4 - - - +
26J G 3.6 24.4 + - - +
27J G 5.4 6.8 + - - -
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Residues in contact with LYS 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D LYS* 3.1 21.7 + - + +
286D ALA* 3.1 6.4 + - - +
288D LYS* 1.3 81.5 - - + +
290D ASN* 1.3 62.1 + - - +
291D ALA* 2.6 19.3 + - - +
2H A 5.2 1.1 - - - -
3H A 2.9 41.3 - - - +
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Residues in contact with ASN 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D SER* 3.7 23.5 + - - +
165D PHE* 4.1 9.5 - - - -
168D THR* 3.0 45.3 + - + +
286D ALA* 3.0 34.3 + - - +
287D LEU* 4.0 2.2 - - - +
289D LYS* 1.3 75.5 - - - +
291D ALA* 1.3 50.3 + - - +
292D PRO* 2.5 31.8 - - + +
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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