Contacts of the strand formed by residues 298 - 305 (chain B) in PDB entry 6T2C
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 LEU 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B ASP 6.1 0.7 - - - +
296B GLU 2.8 15.5 + - - +
297B GLU* 1.3 76.8 - - - +
299B SER* 1.3 60.6 + - - +
300B TYR* 4.2 25.4 - - + +
451B ILE 4.7 0.2 - - - -
452B ASN* 3.4 4.0 - - - +
453B GLY 2.9 35.2 + - - +
454B HIS 4.6 2.0 - - - +
455B PHE* 4.3 21.8 - - - +
456B LYS* 4.3 7.4 - - + +
459B ILE* 4.9 5.2 - - + -
486B LYS* 4.3 24.7 - - + +
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Residues in contact with SER 299 (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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290B MET* 3.7 25.0 - - - +
293B SER* 6.0 1.1 - - - -
297B GLU 3.8 3.5 + - - -
298B LEU* 1.3 78.0 - - - +
300B TYR* 1.3 65.6 + - - +
450B ILE* 4.0 4.9 - - - +
451B ILE 3.4 5.4 - - - -
452B ASN* 3.2 24.9 + - - -
486B LYS* 3.6 6.9 - - - +
487B THR* 2.3 47.6 + - - +
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Residues in contact with TYR 300 (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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257A ILE* 6.4 0.4 - - + -
672A ASP* 3.3 36.4 + - - -
298B LEU* 4.2 26.6 - - + +
299B SER* 1.3 80.7 - - - +
301B THR* 1.3 68.3 + - - +
450B ILE* 3.4 2.4 - - - +
451B ILE* 2.9 33.6 + - + +
456B LYS* 4.2 24.5 - - + +
459B ILE* 3.9 30.5 - - + -
484B ILE* 3.8 29.4 - - + -
485B ASN 3.2 22.9 - - - -
486B LYS* 4.0 23.3 - - + -
487B THR* 3.8 1.7 + - - -
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Residues in contact with THR 301 (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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300B TYR* 1.3 78.6 + - - +
302B ILE* 1.3 72.1 + - - +
303B THR* 4.0 0.6 + - - +
448B ALA* 5.4 0.2 - - + -
449B LEU 3.4 10.1 - - - +
450B ILE* 3.6 15.3 - - + +
483B TYR 3.8 1.2 - - - +
484B ILE* 3.1 3.0 - - - -
485B ASN* 2.9 42.9 + - - +
486B LYS 4.6 0.2 - - - -
487B THR* 3.4 29.2 + - - +
488B GLY 4.8 0.2 + - - -
489B THR 5.3 0.4 - - - -
490B PHE* 3.8 36.1 - - + -
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Residues in contact with ILE 302 (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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676A PHE* 3.9 26.2 - - + -
301B THR* 1.3 73.8 - - - +
303B THR* 1.3 75.1 + - - +
304B GLY 3.9 1.9 + - - +
447B PHE* 4.1 15.5 - - + +
448B ALA* 3.5 5.0 - - - -
449B LEU* 2.9 47.5 + - + +
451B ILE* 4.1 10.5 - - + -
463B VAL* 3.8 31.9 - - + -
466B PHE* 5.8 1.1 - - + -
477B MET* 4.6 8.3 - - - -
482B SER* 4.5 3.1 - - - -
483B TYR 3.5 6.7 - - - +
484B ILE* 3.7 23.3 - - + -
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Residues in contact with THR 303 (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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659A LYS* 6.2 0.9 - - - +
301B THR* 4.0 1.4 + - - +
302B ILE* 1.3 70.3 - - - +
304B GLY* 1.3 61.5 + - - +
447B PHE 4.1 2.5 - - - -
448B ALA* 4.9 1.1 - - - +
481B LYS 4.3 1.7 - - - +
482B SER* 3.2 4.9 - - - -
483B TYR* 2.9 66.4 + - + +
490B PHE* 3.5 15.1 - - - +
491B GLU* 3.3 51.4 + - + +
801B MG 4.4 6.5 - - - -
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Residues in contact with GLY 304 (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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302B ILE* 3.9 1.4 + - - +
303B THR* 1.3 79.6 - - - +
305B ASP* 1.3 61.0 + - - -
447B PHE* 3.0 54.9 + - - +
481B LYS 4.4 0.9 - - - -
482B SER* 3.3 13.9 - - - -
801B MG 3.4 10.8 - - - -
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Residues in contact with ASP 305 (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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659A LYS* 4.8 11.1 + - - -
304B GLY* 1.3 73.5 - - - -
306B ASN* 1.3 66.6 + - - +
445B ASP* 3.6 22.2 - - - +
446B ASP* 3.7 12.4 - - - +
447B PHE* 4.2 1.8 - - - -
477B MET* 4.0 2.4 - - - -
478B SER* 3.0 26.5 + - - -
481B LYS* 3.8 27.3 + - + +
482B SER* 3.6 6.9 + - - -
801B MG 4.1 11.2 - - - -
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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