Contacts of the strand formed by residues 294 - 299 (chain K) in PDB entry 6X5A
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 VAL 294 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263K LEU* 5.4 1.3 - - + +
266K PHE* 4.0 12.6 - - + -
267K ARG* 3.4 54.3 - - + +
270K ILE* 3.7 38.6 - - + -
284K VAL* 5.1 7.0 - - + -
292K PRO 5.6 0.4 - - - -
293K ALA* 1.3 72.7 - - - +
295K THR* 1.3 59.9 + - - +
296K LEU* 5.5 1.1 - - + -
308K ILE* 3.0 41.1 + - + +
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Residues in contact with THR 295 (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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284K VAL* 3.5 2.2 - - - +
285K GLU* 2.7 76.8 + - + +
287K GLU* 5.4 6.5 - - + -
293K ALA 4.6 7.2 - - - +
294K VAL* 1.3 71.8 - - - +
296K LEU* 1.3 58.7 + - - +
297K LEU* 4.2 4.7 - - - +
305K SER* 2.4 30.6 + - - -
306K VAL 3.5 6.7 - - - -
307K ASP* 4.4 9.6 - - - +
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Residues in contact with LEU 296 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174K VAL* 5.3 5.6 - - + -
175K VAL* 5.7 3.8 - - + -
178K LEU* 4.2 12.6 - - + -
270K ILE* 5.1 6.5 - - + +
271K LYS* 5.5 0.4 - - - -
274K VAL* 3.6 34.1 - - + -
282K VAL* 3.6 25.1 - - + -
283K SER 3.0 11.9 - - - +
284K VAL* 3.7 28.5 - - + -
294K VAL* 3.9 1.3 + - + +
295K THR* 1.3 73.7 - - - +
297K LEU* 1.3 61.5 + - - +
298K ILE* 4.8 2.7 - - + -
304K ILE 3.0 13.5 - - - +
305K SER* 3.1 16.6 + - - -
306K VAL* 3.3 23.2 + - + +
308K ILE* 4.2 15.9 - - + -
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Residues in contact with LEU 297 (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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281K ASP 3.9 1.0 - - - +
282K VAL* 3.4 1.2 - - - -
283K SER* 2.4 51.7 + - - +
284K VAL 4.9 2.2 - - - -
285K GLU* 3.5 37.7 - - + +
295K THR* 4.2 5.4 - - - +
296K LEU* 1.3 72.2 - - - +
298K ILE* 1.3 60.6 + - - +
299K ARG* 4.1 10.9 + - - +
303K GLU* 3.2 30.5 - - - +
304K ILE 3.3 2.2 - - - -
305K SER* 4.1 13.0 - - - +
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Residues in contact with ILE 298 (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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170K THR* 5.8 1.3 - - + +
171K VAL* 4.0 21.1 - - + -
174K VAL* 3.7 30.1 - - + -
280K ILE* 3.6 17.3 - - + -
281K ASP 3.2 9.9 - - - +
282K VAL* 3.6 23.1 - - + -
296K LEU* 4.8 1.8 - - + -
297K LEU* 1.3 73.9 - - - +
299K ARG* 1.3 59.8 + - - +
300K ASN* 3.3 24.9 - - + +
302K GLU 2.7 25.1 - - - +
303K GLU* 3.2 6.1 + - - -
304K ILE* 2.7 38.1 + - + +
306K VAL* 4.8 8.1 - - + -
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Residues in contact with ARG 299 (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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281K ASP* 2.5 37.7 + - + +
297K LEU* 4.1 13.7 + - - +
298K ILE* 1.3 70.9 - - - +
300K ASN* 1.3 63.8 + - - +
301K PRO 4.0 9.8 - - - +
302K GLU* 4.2 7.1 + - - +
303K GLU* 2.3 68.8 + - - +
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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