Contacts of the strand formed by residues 271 - 279 (chain B) in PDB entry 5HKE
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 TYR 271 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ASP* 3.3 2.8 - - - -
20B LEU 2.9 42.3 + - - +
21B ASP 4.5 2.0 - - - -
22B PHE* 4.5 9.6 - - - -
23B SER* 3.6 26.9 + - - -
257B GLN* 3.2 18.2 - - - +
259B LYS* 3.6 48.0 + - + +
269B GLU* 3.4 16.6 - - + -
270B GLU* 1.3 75.5 - - - +
272B THR* 1.3 61.2 + - - +
273B VAL* 3.1 28.0 + - + +
290B TYR* 3.6 28.7 - + + -
291B GLU* 4.6 5.8 + - - -
316B ARG* 4.4 8.0 + - - -
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Residues in contact with THR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASN* 3.7 11.0 + - - +
18B LEU 3.5 0.2 - - - -
19B ASP* 2.6 23.8 + - - +
256B GLU* 3.5 25.2 - - + +
257B GLN* 2.8 31.0 + - - +
271B TYR* 1.3 71.0 - - - +
273B VAL* 1.3 61.5 + - - +
274B TYR* 3.4 23.1 - - - +
275B SER* 3.5 17.0 - - - +
289B THR 4.8 0.3 - - - -
290B TYR* 3.3 24.5 + - - +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 2.8 20.8 + - + +
20B LEU* 4.1 13.7 - - + +
22B PHE 4.0 15.3 - - - +
23B SER* 3.9 11.2 - - - +
26B GLU* 3.6 34.4 - - - +
271B TYR* 3.7 39.7 - - + +
272B THR* 1.3 71.1 - - - +
274B TYR* 1.3 65.1 + - + +
289B THR* 3.5 5.7 - - - +
290B TYR* 2.9 21.0 + - - +
291B GLU* 4.5 2.7 - - - +
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Residues in contact with TYR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 3.8 14.1 - - - -
18B LEU* 2.9 60.1 + - + +
26B GLU* 4.0 13.7 - - + -
54B VAL* 3.5 25.2 - - + +
65B PHE* 3.4 18.6 - + - +
66B ASP* 2.7 20.8 + - - -
272B THR* 3.4 9.7 - - - +
273B VAL* 1.3 79.9 - - + +
275B SER* 1.3 73.2 + - - +
276B ASN* 3.5 23.6 - - + -
287B TYR* 5.3 0.7 - - + -
288B THR 3.2 16.2 - - - +
289B THR* 4.1 3.8 - - + +
290B TYR 4.6 0.2 - - - +
314B PHE* 3.9 26.0 - + + -
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Residues in contact with SER 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG 3.3 6.3 - - - -
17B ASN* 2.7 22.4 + - - -
249B PHE* 3.5 13.1 - - - -
252B LEU* 4.0 9.5 - - - +
256B GLU* 4.8 4.9 + - - -
272B THR* 3.5 9.4 - - - +
274B TYR* 1.3 75.5 - - - +
276B ASN* 1.3 63.0 + - - +
287B TYR* 3.3 3.6 - - - +
288B THR* 2.9 46.6 + - - +
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Residues in contact with ASN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY* 3.3 8.1 - - - -
16B ARG* 2.8 53.4 + - - +
54B VAL* 3.6 12.5 - - - +
66B ASP* 2.9 26.3 + - - -
248B PHE* 3.3 9.7 - - - -
249B PHE* 4.1 4.5 - - - -
252B LEU* 3.4 3.4 - - - +
274B TYR* 3.5 16.7 - - + -
275B SER* 1.3 77.1 - - - +
277B CYS* 1.3 61.5 + - - +
278B TYR* 3.6 12.4 - - - -
285B LEU* 3.9 4.6 - - + +
286B TYR 3.2 13.7 - - - +
287B TYR* 3.8 9.2 - - + -
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Residues in contact with CYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TYR* 3.9 27.4 - - - -
14B PHE 3.7 4.3 - - - -
245B ILE* 4.3 15.7 - - - -
248B PHE* 3.6 39.0 - - + -
249B PHE* 3.8 18.8 - - + -
276B ASN* 1.3 73.7 - - - +
278B TYR* 1.3 62.2 + - - +
285B LEU* 4.8 0.2 - - - -
286B TYR* 2.8 42.7 + - + -
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Residues in contact with TYR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TYR* 3.1 26.5 - - - +
14B PHE* 2.7 45.8 + + - +
15B GLY* 4.9 0.2 - - - -
52B ILE* 3.6 19.1 - - + -
53B GLY* 3.2 22.4 - - - -
54B VAL* 3.6 1.9 + - - +
66B ASP* 2.6 33.5 + - + -
67B ALA* 4.1 5.8 - - - -
68B ILE* 3.5 38.6 - - + -
276B ASN* 3.6 15.8 + - - -
277B CYS* 1.3 76.7 - - - +
279B ASP* 1.4 59.5 + - - +
280B LEU* 3.4 4.7 + - + -
284B THR 3.3 5.6 - - - +
285B LEU* 3.7 32.5 - - + -
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Residues in contact with ASP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B SER* 2.7 32.4 + - - -
12B ASN 3.7 3.4 - - - -
13B TYR* 3.9 12.1 - - + -
68B ILE* 4.4 0.9 - - - +
241B VAL* 3.8 21.3 - - - +
277B CYS 4.0 1.2 + - - -
278B TYR* 1.4 71.0 - - - +
280B LEU* 1.3 58.3 - - - +
281B ASP 3.1 8.0 + - - -
282B ASN* 3.1 35.2 + - - +
283B LYS* 2.8 26.5 + - - -
284B THR 2.9 16.9 + - - +
286B TYR* 4.2 14.8 + - + -
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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