Contacts of the strand formed by residues 357 - 368 (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 THR 357 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274X ASN* 3.1 46.6 + - - +
352X LEU* 3.7 11.7 - - - +
355X ALA 5.3 1.3 - - - +
356X ASP* 1.3 81.3 - - - +
358X ALA* 1.3 61.9 + - - +
433X THR* 4.9 8.7 - - - +
434X MET 3.3 14.6 - - - +
435X ASN* 4.4 9.9 - - + -
436X TYR* 5.8 0.4 - - - +
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Residues in contact with ALA 358 (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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271X LEU* 5.7 0.2 - - + -
272X SER 3.3 10.3 - - - +
273X LYS* 4.7 0.2 - - - +
274X ASN* 4.5 2.5 - - - -
350X MET* 4.3 7.4 - - + -
352X LEU* 4.5 2.7 - - + +
357X THR* 1.3 76.5 - - - +
359X ARG* 1.3 61.8 + - - +
433X THR* 3.1 6.2 - - - -
434X MET* 2.7 48.8 + - + +
439X PHE* 3.6 38.4 - - + -
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Residues in contact with ARG 359 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270X ILE 3.9 0.6 - - - +
271X LEU* 3.5 7.6 - - - +
272X SER* 2.7 51.2 + - - +
274X ASN* 3.1 27.3 + - - +
358X ALA* 1.3 73.7 - - - +
360X LEU* 1.3 69.5 + - - +
361X ASN* 5.1 8.1 - - - +
422X ASN* 2.9 38.7 + - - +
429X SER* 5.2 2.4 + - - -
431X PRO* 4.9 14.8 - - + +
432X ILE 3.4 14.1 - - - +
433X THR* 4.4 3.6 - - + +
434X MET* 4.8 1.3 - - - -
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Residues in contact with LEU 360 (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* 5.3 0.2 - - + -
269X ILE* 3.9 29.2 - - + -
270X ILE 3.6 3.6 - - - -
271X LEU* 4.3 2.5 - - + -
359X ARG* 1.3 80.6 + - - +
361X ASN* 1.3 76.1 + - - +
362X ALA* 4.5 1.8 - - + -
383X LEU* 4.1 21.8 - - + -
391X LEU* 4.2 25.1 - - + -
421X LEU* 4.3 4.7 - - + -
422X ASN* 4.6 4.2 - - - +
432X ILE* 2.8 44.9 + - + +
434X MET* 4.1 17.7 - - + -
442X LEU* 4.8 3.4 - - + -
448X LEU* 4.2 12.1 - - + -
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Residues in contact with ASN 361 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269X ILE* 3.3 4.0 - - - +
270X ILE* 2.6 57.6 + - + +
359X ARG* 5.1 9.7 - - - +
360X LEU* 1.3 78.3 - - - +
362X ALA* 1.3 71.1 + - - +
420X ALA* 4.3 3.4 - - - +
421X LEU* 3.5 7.8 + - - +
422X ASN* 2.9 55.9 + - - +
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Residues in contact with ALA 362 (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* 3.7 33.0 - - + -
268X ASN* 3.1 13.9 - - - +
269X ILE* 4.1 2.5 - - + +
270X ILE* 4.8 0.9 - - - +
360X LEU* 4.5 3.6 - - + -
361X ASN* 1.3 84.4 + - - +
363X ASN* 1.3 64.9 + - - +
364X ILE* 4.8 0.2 - - + -
420X ALA* 3.3 5.4 - - - +
421X LEU* 2.9 40.0 + - + +
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Residues in contact with ASN 363 (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* 3.6 3.1 - - - +
267X GLU* 3.0 29.8 + - + +
268X ASN* 2.6 43.2 + - - +
362X ALA* 1.3 74.1 - - - +
364X ILE* 1.3 65.1 + - - +
418X PRO* 3.7 28.7 - - + +
419X ILE 3.2 9.2 - - - +
420X ALA* 3.8 15.4 - - - +
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Residues in contact with ILE 364 (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* 3.7 28.7 - - + -
265X ASP 3.3 7.2 - - - +
266X MET* 4.1 24.0 - - + -
267X GLU* 4.8 1.1 - - - +
363X ASN* 1.3 82.4 - - - +
365X ARG* 1.3 62.8 + - - +
366X TYR* 4.1 25.4 - - + +
394X ILE* 4.2 16.8 - - + -
418X PRO* 3.5 3.1 - - - +
419X ILE* 2.8 50.1 + - + +
421X LEU* 3.8 32.5 - - + -
450X LEU* 5.1 0.4 - - + -
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Residues in contact with ARG 365 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264X VAL* 3.6 4.2 - - - +
265X ASP* 2.7 40.4 + - + +
267X GLU* 3.1 31.3 + - + +
364X ILE* 1.3 79.1 - - - +
366X TYR* 1.3 68.8 + - - +
367X VAL* 4.6 0.2 - - - -
410X TYR* 4.2 10.7 - - + +
411X TYR 3.5 12.3 - - - +
412X PRO* 2.8 20.8 + - - +
413X SER 2.7 22.5 + - - -
414X LYS* 3.9 32.7 + - - +
416X LEU 2.3 33.1 + - - -
417X ALA 3.6 5.3 + - - -
418X PRO* 3.7 22.4 - - + +
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Residues in contact with TYR 366 (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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262X VAL* 3.9 18.8 - - + -
263X HIS 3.6 2.2 - - - -
264X VAL* 4.0 20.4 - - + -
364X ILE* 4.1 13.2 - - + -
365X ARG* 1.3 75.3 - - - +
367X VAL* 1.3 64.3 + - - +
368X ASN 4.3 0.2 - - - -
378X LEU* 3.6 36.3 - - + -
379X PRO* 4.0 24.2 + - + -
381X THR* 4.5 1.6 - - - -
394X ILE* 3.8 24.1 + - - +
396X ALA* 4.4 14.3 + - + +
405X LEU* 3.8 19.1 - - + -
410X TYR* 3.1 8.0 - - - +
411X TYR* 2.9 45.9 + + + +
419X ILE* 3.8 17.7 - - + -
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Residues in contact with VAL 367 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261X ILE 3.5 1.4 - - - +
262X VAL* 3.1 5.8 - - - +
263X HIS* 2.9 60.4 + - + +
265X ASP* 3.6 25.4 - - + +
365X ARG 4.1 0.2 - - - +
366X TYR* 1.3 80.1 - - - +
368X ASN* 1.3 60.4 + - - +
369X THR* 3.7 15.4 + - + -
405X LEU* 4.6 2.2 - - - -
409X ASN 3.7 6.7 - - - +
410X TYR* 3.4 35.2 - - + +
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Residues in contact with ASN 368 (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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260X PRO* 4.0 8.2 - - - +
261X ILE 3.1 18.9 + - - -
262X VAL* 4.5 3.0 - - - +
367X VAL* 1.3 71.6 - - - +
369X THR* 1.3 61.6 + - - +
370X GLY* 2.8 24.9 + - - -
372X ALA 2.9 25.2 + - - -
373X PRO* 4.2 0.4 - - - +
374X ILE* 4.5 1.2 - - - +
405X LEU* 3.2 33.7 + - + +
406X ALA 3.3 16.2 - - - +
407X PRO* 3.7 7.8 - - - -
408X ASN* 2.7 32.2 + - - -
409X ASN 3.1 9.6 + - - -
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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