Contacts of the strand formed by residues 328 - 334 (chain X) in PDB entry 1T6B
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 ASN 328 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261X ILE* 3.8 22.8 - - - +
262X VAL 3.1 26.8 + - - +
263X HIS* 4.9 3.6 - - + -
297X ARG* 4.7 9.0 - - + +
326X ASN 4.2 5.3 + - - -
327X SER* 1.3 83.7 + - - +
329X SER* 1.3 63.1 + - - +
451X ASP* 3.8 3.5 - - - +
452X THR* 3.1 36.5 + - - +
453X ASP 3.5 14.7 - - - +
454X GLN* 3.9 5.3 - - - +
456X TYR* 2.9 24.4 + - - -
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Residues in contact with SER 329 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263X HIS* 4.8 2.3 - - - +
297X ARG* 3.4 9.5 - - - +
298X THR* 2.9 45.5 + - - +
327X SER* 4.3 4.9 + - - -
328X ASN* 1.3 76.7 - - - +
330X SER* 1.3 62.4 + - - +
449X ARG* 3.7 14.6 - - - +
450X LEU 3.4 5.9 + - - -
451X ASP* 2.8 22.4 + - - -
802X NA 4.1 2.5 - - - -
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Residues in contact with SER 330 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263X HIS* 4.0 8.5 - - - -
264X VAL 2.9 27.1 + - - -
295X THR* 3.6 11.3 - - - +
296X SER 3.2 15.3 - - - -
298X THR* 4.4 1.8 - - - -
329X SER* 1.3 76.7 - - - +
331X THR* 1.3 62.7 + - - +
332X VAL* 5.3 0.4 - - - -
449X ARG* 3.3 7.2 - - - +
450X LEU* 2.9 39.4 + - - +
802X NA 3.2 11.3 - - - -
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Residues in contact with THR 331 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294X SER 3.9 0.9 - - - +
295X THR* 3.3 1.8 - - - -
296X SER 2.9 32.1 + - - -
298X THR* 4.0 11.7 + - - +
330X SER* 1.3 73.7 + - - +
332X VAL* 1.3 64.8 + - - +
447X GLN* 3.7 32.8 - - + +
448X LEU 3.3 10.8 - - - +
449X ARG* 4.2 13.4 - - + +
601X ASN* 3.8 16.7 + - - +
603X ILE* 4.4 9.4 - - - -
804X PG4 3.8 17.9 - - - +
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Residues in contact with VAL 332 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266X MET* 3.9 16.2 - - + -
293X THR* 3.3 39.0 - - + +
294X SER 3.4 3.1 - - - +
295X THR* 3.5 20.0 - - + +
331X THR* 1.3 78.2 - - - +
333X ALA* 1.3 60.7 + - - +
334X ILE* 3.9 5.3 + - + -
447X GLN* 3.2 11.6 - - - +
448X LEU* 2.6 50.2 + - + +
450X LEU* 3.8 27.8 - - + -
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Residues in contact with ALA 333 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293X THR* 3.1 7.1 - - - -
294X SER* 2.8 37.8 + - - +
332X VAL* 1.3 70.8 - - - +
334X ILE* 1.3 65.5 + - - +
335X ASP 3.7 0.5 + - - -
446X LYS 3.8 4.0 - - - +
447X GLN* 4.9 4.7 - - - +
703X LYS* 4.2 9.4 - - - +
804X PG4 3.7 43.9 - - - +
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Residues in contact with ILE 334 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269X ILE* 4.0 23.3 - - + -
291X LYS* 3.7 24.5 - - + -
292X ASN 4.0 2.0 - - - -
293X THR* 3.9 13.7 - - + -
332X VAL* 4.5 7.0 - - + +
333X ALA* 1.3 76.6 - - - +
335X ASP* 1.3 68.3 + - - +
336X HIS* 3.3 4.9 + - - +
346X TRP* 3.9 23.1 - - + -
442X LEU* 3.7 35.4 - - + -
446X LYS* 2.7 40.2 + - + +
447X GLN 4.1 2.0 - - - +
448X LEU* 4.2 11.9 - - + -
804X PG4 5.8 2.8 - - - +
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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