Contacts of the strand formed by residues 262 - 273 (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 VAL 262 (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* 1.3 82.7 - - - +
263X HIS* 1.3 71.6 + - - +
328X ASN* 3.1 27.5 - - - +
366X TYR* 3.9 15.5 - - + -
367X VAL 3.1 7.9 - - - +
368X ASN* 4.5 4.5 - - - -
374X ILE* 3.3 35.0 - - + -
379X PRO* 3.6 27.8 - - + -
405X LEU* 3.8 16.4 - - + -
452X THR* 4.0 3.4 - - + +
456X TYR* 3.7 12.9 + - + -
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Residues in contact with HIS 263 (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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261X ILE 5.1 0.2 - - - -
262X VAL* 1.3 79.7 - - - +
264X VAL* 1.3 76.8 + - - +
265X ASP* 4.7 7.6 - - + -
295X THR* 5.3 2.5 - - + -
296X SER* 5.1 1.1 - - - -
297X ARG* 3.6 50.6 - - + +
328X ASN* 4.9 3.4 - - + -
329X SER 4.6 4.0 - - - +
330X SER* 4.0 10.8 - - - -
366X TYR* 3.6 2.8 - - - -
367X VAL* 2.9 70.8 + - + +
369X THR* 3.9 12.8 - - + +
452X THR* 4.5 1.6 - - - -
802X NA 3.5 13.9 - - - -
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Residues in contact with VAL 264 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263X HIS* 1.3 77.4 + - - +
265X ASP* 1.3 62.9 + - - +
295X THR* 3.4 7.4 - - - +
330X SER* 2.9 21.0 + - - -
364X ILE* 3.7 36.8 - - + -
365X ARG 3.6 4.9 - - - +
366X TYR* 4.0 23.1 - - + -
381X THR* 3.7 18.6 - - + +
394X ILE* 5.4 1.6 - - + -
450X LEU* 3.5 29.3 - - + +
452X THR* 3.7 16.8 - - + +
802X NA 2.9 10.8 - - - -
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Residues in contact with ASP 265 (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 6.0 + - + -
264X VAL* 1.3 76.5 - - - +
266X MET* 1.3 75.1 + - - +
267X GLU* 4.0 11.0 + - - +
295X THR* 3.9 25.4 + - + +
364X ILE* 3.3 2.6 - - - -
365X ARG* 2.7 39.8 + - + +
367X VAL* 3.6 23.8 - - + +
410X TYR* 4.9 10.1 + - + -
414X LYS* 6.3 0.4 - - - -
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Residues in contact with MET 266 (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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264X VAL 4.0 1.2 - - - -
265X ASP* 1.3 81.3 - - - +
267X GLU* 1.3 61.4 + - - +
268X ASN 4.1 7.0 - - - +
269X ILE* 4.4 13.5 - - + -
293X THR* 3.0 32.4 + - - +
294X SER* 4.5 0.2 - - - -
295X THR* 3.0 24.1 + - - +
332X VAL* 3.9 23.8 - - + -
360X LEU* 5.3 0.2 - - + -
362X ALA* 3.7 24.5 - - + -
363X ASN 3.6 12.3 - - - +
364X ILE* 4.1 14.1 - - + -
383X LEU* 4.2 34.1 - - + -
421X LEU* 4.5 1.6 - - + -
448X LEU* 4.5 7.4 - - + -
450X LEU* 4.4 10.0 - - + +
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Residues in contact with GLU 267 (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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265X ASP* 4.2 14.3 - - - +
266X MET* 1.3 73.3 - - - +
268X ASN* 1.3 78.5 + - - +
292X ASN* 3.6 6.4 - - - +
293X THR* 2.9 28.7 + - - +
363X ASN* 3.0 13.4 + - + +
365X ARG* 3.1 40.6 + - + -
414X LYS* 4.5 8.8 + - - -
418X PRO* 3.5 22.4 - - - +
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Residues in contact with ASN 268 (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* 4.1 1.4 - - - +
267X GLU* 1.3 94.0 + - - +
269X ILE* 1.3 63.2 + - - +
291X LYS 3.3 15.0 - - - +
292X ASN* 3.9 14.5 + - - +
293X THR* 3.4 5.8 + - - -
362X ALA* 3.1 6.1 - - - +
363X ASN* 2.6 61.5 + - - +
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Residues in contact with ILE 269 (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* 4.4 9.6 - - - -
268X ASN* 1.3 77.8 - - - +
270X ILE* 1.3 65.4 + - - +
271X LEU* 3.6 27.6 - - + -
289X ILE 3.9 1.0 - - - +
290X SER* 3.6 1.9 - - - -
291X LYS* 2.9 49.8 + - + +
293X THR* 3.8 17.3 - - + -
334X ILE* 4.0 18.4 - - + -
360X LEU* 3.9 13.9 - - + -
361X ASN 3.3 10.8 - - - +
362X ALA* 4.1 1.3 - - + +
442X LEU* 4.9 0.9 - - + -
448X LEU* 3.9 28.3 - - + -
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Residues in contact with ILE 270 (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* 1.3 75.3 - - - +
271X LEU* 1.3 65.7 + - - +
272X SER* 4.2 4.1 + - - +
288X THR* 3.8 32.8 - - + +
289X ILE 3.3 7.9 - - - +
290X SER* 3.9 13.2 - - - +
359X ARG 3.9 0.3 - - - +
360X LEU* 3.6 3.3 - - - -
361X ASN* 2.6 61.5 + - + +
362X ALA* 5.4 0.7 - - - -
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Residues in contact with LEU 271 (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* 3.6 35.0 - - + -
270X ILE* 1.3 76.0 - - - +
272X SER* 1.3 60.7 + - - +
288X THR* 3.5 6.6 + - - -
289X ILE* 2.8 51.4 + - + +
334X ILE* 6.3 0.2 - - + -
346X TRP* 3.6 36.1 - - + -
350X MET* 4.1 4.4 - - - +
359X ARG 3.5 5.6 - - - +
360X LEU* 4.3 14.1 - - + -
434X MET* 4.7 3.4 - - + -
439X PHE* 3.5 34.1 - - + -
442X LEU* 4.2 10.8 - - + -
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Residues in contact with SER 272 (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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270X ILE* 4.2 4.1 + - - +
271X LEU* 1.3 75.8 - - - +
273X LYS* 1.3 66.8 + - - +
288X THR* 3.9 18.6 - - - +
350X MET* 3.6 9.6 - - - -
358X ALA* 3.3 4.7 - - - +
359X ARG* 2.7 57.8 + - - +
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Residues in contact with LYS 273 (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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272X SER* 1.3 80.4 + - - +
274X ASN* 1.3 65.4 + - - +
275X GLU* 3.7 29.8 + - - +
288X THR 5.9 0.2 - - - +
350X MET* 3.2 32.2 - - + +
351X GLY* 3.1 27.1 + - - +
352X LEU* 3.7 18.2 - - + -
353X ASN* 4.2 5.3 - - - +
356X ASP* 3.2 25.1 + - - +
357X THR 3.9 3.6 - - - +
359X ARG* 5.3 0.2 - - - +
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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