Contacts of the strand formed by residues 287 - 292 (chain K) in PDB entry 1HZH
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 LYS 287 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286K VAL* 1.3 74.0 - - - +
288K PHE* 1.3 65.7 + - - +
289K ASN* 3.6 29.8 + - - +
341K LYS* 3.4 5.5 - - - +
342K VAL* 3.7 1.7 - - - -
343K SER* 2.9 49.6 + - - +
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Residues in contact with PHE 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274K CYS* 4.3 7.6 - - - -
276K VAL* 3.4 35.7 - - + -
286K VAL* 4.2 15.0 + - + -
287K LYS* 1.3 79.4 - - - +
289K ASN* 1.3 67.7 + - - +
290K TRP* 4.3 10.1 + - + +
304K ALA* 6.0 0.2 - - + -
306K THR* 3.3 37.0 - - + +
321K VAL* 3.8 21.1 - - + -
323K SER* 3.5 34.1 - - - +
340K CYS* 4.1 9.4 - - - -
341K LYS 3.5 0.7 - - - -
342K VAL* 3.5 19.5 - - + -
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Residues in contact with ASN 289 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287K LYS* 3.6 38.0 + - - +
288K PHE* 1.3 79.7 + - - +
290K TRP* 1.3 62.7 + - - +
291K TYR* 3.8 17.4 + - + +
300K GLU* 3.0 22.7 + - - +
339K LYS 3.6 1.2 - - - +
340K CYS* 3.6 0.8 - - - -
341K LYS* 2.7 68.5 + - + +
343K SER* 4.7 3.3 + - - -
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Residues in contact with TRP 290 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255K LEU* 3.5 24.2 - - + -
272K VAL* 3.7 23.8 - - + -
274K CYS* 3.3 32.3 - - + -
288K PHE* 4.5 10.0 - - + +
289K ASN* 1.3 73.1 - - - +
291K TYR* 1.3 73.1 + - - +
300K GLU* 3.3 4.5 - - - +
301K VAL* 3.2 47.9 + - + +
304K ALA* 3.1 24.5 - - + +
323K SER* 2.8 42.6 + - - -
325K LEU* 3.6 25.4 - - + -
338K TYR* 5.1 2.5 - - + -
339K LYS 3.1 21.5 - - - -
340K CYS* 3.8 11.0 - - + -
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Residues in contact with TYR 291 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289K ASN* 3.8 28.9 + - + +
290K TRP* 1.3 81.9 - - - +
292K VAL* 1.3 61.6 + - - +
295K ASP 3.6 1.0 + - - -
296K GLY* 3.4 26.4 + - - +
299K VAL 3.2 6.5 - - - +
300K GLU* 3.4 45.4 + - + -
301K VAL* 4.7 0.2 - - - -
325K LEU* 6.0 0.4 - - - -
337K GLU 3.4 4.3 - - - +
338K TYR* 3.6 1.9 - - - -
339K LYS* 2.8 76.3 + - + +
341K LYS* 3.9 23.0 + - + +
352K GLU* 4.5 2.2 - - - -
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Residues in contact with VAL 292 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291K TYR* 1.3 71.4 - - - +
295K ASP* 1.3 71.2 + - - +
296K GLY 3.1 0.9 + - - -
299K VAL* 2.8 26.2 + - + +
301K VAL* 3.5 31.9 - - + -
325K LEU* 4.7 2.7 - - + -
331K ASP* 5.3 3.6 - - - +
336K LYS* 4.0 35.2 - - + +
337K GLU 3.5 5.4 - - - +
338K TYR* 4.0 28.5 - - + +
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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