Contacts of the strand formed by residues 284 - 289 (chain A) 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 THR 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A CYS 3.8 0.9 - - - +
278A TYR* 3.3 7.3 - - - -
279A ASP 2.9 29.5 + - - -
282A ASN* 3.0 30.4 + - - -
283A LYS* 1.3 75.1 - - - +
285A LEU* 1.3 66.0 + - - +
286A TYR* 3.5 34.6 - - + +
297A ALA* 4.4 3.6 - - + -
298A VAL 3.6 12.3 - - - +
299A THR* 2.9 25.8 + - - +
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Residues in contact with LEU 285 (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 VAL* 4.0 20.4 - - + -
52A ILE* 4.3 10.4 - - + +
53A GLY 4.1 4.5 - - - +
54A VAL* 3.9 21.1 - - + -
276A ASN* 3.9 16.6 - - + +
277A CYS 3.9 2.7 - - - +
278A TYR* 3.6 36.8 - - + -
283A LYS 4.4 0.2 + - - -
284A THR* 1.3 72.9 - - - +
286A TYR* 1.3 75.5 + - - +
287A TYR* 4.2 9.6 - - + -
296A VAL 3.6 0.3 - - - +
297A ALA* 3.2 4.5 - - - -
298A VAL* 2.8 58.1 + - + +
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Residues in contact with TYR 286 (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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241A VAL* 5.2 2.3 - - - +
245A ILE* 3.4 42.0 - - + +
249A PHE* 3.6 12.5 - - + -
276A ASN* 3.2 5.9 - - - +
277A CYS* 2.8 47.3 + - + +
279A ASP* 4.2 11.8 + - + -
282A ASN* 4.8 7.3 + - - -
284A THR* 3.5 34.0 - - + +
285A LEU* 1.3 74.2 - - - +
287A TYR* 1.3 60.4 + - - +
295A ILE* 3.8 21.1 - - + -
296A VAL 3.1 4.5 - - - -
297A ALA* 3.7 25.1 - - + -
320B ILE* 4.1 15.5 - - + -
322B LYS* 6.0 2.0 - - - -
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Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.7 21.6 - - + +
54A VAL* 5.6 0.2 - - + -
249A PHE* 3.9 2.9 - - - -
274A TYR* 5.3 0.7 - - + -
275A SER 3.3 12.6 - - - +
276A ASN* 3.8 9.4 - - + +
285A LEU* 4.2 14.6 - - + -
286A TYR* 1.3 77.7 - - - +
288A THR* 1.3 72.0 + - - +
289A THR* 4.2 7.4 - - + -
294A GLN 3.9 1.2 - - - +
295A ILE* 3.4 5.2 - - - +
296A VAL* 2.8 80.2 + - + +
298A VAL* 4.9 3.4 - - + -
312A TYR 4.8 0.3 + - - -
313A PRO 4.4 4.2 + - - -
314A PHE* 3.4 61.6 - + + -
315A GLU* 4.8 3.7 + - - +
323B LEU* 4.5 5.4 - - + +
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 3.7 16.0 - - + -
274A TYR* 3.2 8.3 - - - +
275A SER* 2.9 48.1 + - - +
287A TYR* 1.3 81.6 - - - +
289A THR* 1.3 67.5 + - - +
292A ASN 3.8 6.5 - - - -
293A ARG 3.6 10.5 - - - +
294A GLN 4.5 2.0 - - - -
295A ILE* 3.7 15.5 - - + +
293B ARG* 3.4 34.4 + - - +
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Residues in contact with THR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL 3.5 10.5 - - - +
274A TYR* 4.1 1.3 - - - +
287A TYR* 4.2 7.9 - - + -
288A THR* 1.3 83.4 - - - +
290A TYR* 1.3 67.0 + - - +
291A GLU* 3.0 13.4 + - - -
292A ASN* 3.0 38.4 + - + +
293A ARG* 4.9 0.5 - - - -
314A PHE* 3.6 33.4 - - + -
315A GLU 3.2 23.9 + - - +
316A ARG* 5.2 2.0 - - + +
250B HIS* 5.0 2.3 + - - -
293B ARG* 5.4 0.7 + - - -
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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