Contacts of the strand formed by residues 273 - 282 (chain M) in PDB entry 6LTJ
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 ILE 273 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268M ILE 3.7 1.0 - - - +
269M HIS* 3.4 3.8 - - - +
270M VAL 2.9 35.0 + - - +
271M GLY* 5.8 0.2 - - - -
272M ASN* 1.3 91.1 - - - +
274M SER* 1.3 63.8 + - - +
275M LEU 4.2 0.2 - - - -
303M LEU* 4.7 7.4 - - + -
307M PHE* 3.7 21.2 - - + -
353M LEU* 4.0 31.0 - - + -
354M GLU 3.5 6.1 - - - +
355M THR* 4.3 13.7 - - + -
361M MET* 4.6 0.2 - - - -
38R ARG* 5.6 4.7 - - - -
41R PHE* 3.8 30.7 - - + -
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Residues in contact with SER 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268M ILE 3.4 4.5 - - - -
269M HIS* 3.5 18.0 + - - +
273M ILE* 1.3 75.0 - - - +
275M LEU* 1.3 60.4 + - - +
276M VAL* 4.1 13.0 - - - +
352M LEU 3.5 0.5 - - - +
353M LEU* 2.8 26.2 - - - -
354M GLU* 2.9 24.8 + - - +
356M LEU* 3.6 31.7 - - - +
361M MET* 4.0 9.9 - - - -
364M LYS* 4.7 1.7 - - - +
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Residues in contact with LEU 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266M LEU* 3.6 4.3 - - + +
267M ASN* 3.5 1.4 + - - -
268M ILE* 2.9 45.6 + - + +
273M ILE 4.2 0.4 - - - -
274M SER* 1.3 72.6 + - - +
276M VAL* 1.3 78.1 + - - +
277M ASP* 4.8 5.6 - - + +
297M LEU* 4.8 5.4 - - + -
301M LEU* 4.2 20.9 - - + -
303M LEU* 4.3 9.6 - - + -
307M PHE* 4.2 14.1 - - + -
311M ILE* 3.8 31.9 - - + -
351M PRO* 3.8 28.3 - - + -
352M LEU 3.6 6.5 - - - +
353M LEU* 4.1 13.0 - - + -
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Residues in contact with VAL 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265M LYS* 6.4 0.7 - - + -
266M LEU 3.1 8.7 - - - +
267M ASN* 3.3 23.8 - - + +
274M SER* 4.1 13.2 - - - +
275M LEU* 1.3 82.6 - - - +
277M ASP* 1.3 68.5 + - - +
350M CYS 3.9 1.2 - - - +
351M PRO* 3.5 0.7 - - - +
352M LEU* 2.9 48.0 + - + +
354M GLU* 5.3 4.3 - - - +
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Residues in contact with ASP 277 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265M LYS* 3.2 6.4 - - - +
266M LEU* 2.9 54.0 + - - +
275M LEU* 4.8 4.4 - - - +
276M VAL* 1.3 81.3 - - - +
278M GLN* 1.3 64.1 + - - +
279M PHE* 3.5 15.3 - - - -
297M LEU* 3.8 11.8 - - - +
350M CYS 3.5 7.6 - - - +
351M PRO* 3.3 26.4 - - + +
487O ARG* 2.8 23.1 + - - +
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Residues in contact with GLN 278 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263M ILE* 3.3 39.6 - - + +
264M ILE 3.2 8.1 - - - +
265M LYS* 3.7 26.8 - - + +
277M ASP* 1.3 82.0 - - - +
279M PHE* 1.3 66.2 + - - +
348M GLN* 3.7 41.2 + - - +
349M TRP* 3.1 38.0 - - + +
350M CYS 4.3 2.0 + - - -
487O ARG* 3.5 1.4 + - - -
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Residues in contact with PHE 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263M ILE* 4.4 0.4 - - - -
264M ILE* 2.9 59.2 + - + +
266M LEU* 3.9 14.6 - - + -
277M ASP* 3.5 26.2 - - - -
278M GLN* 1.3 80.2 - - - +
280M GLU* 1.3 72.9 + - - +
281M TRP* 3.8 22.9 - + + -
293M PHE* 3.3 35.2 - + - -
315M ILE* 4.2 7.4 - - + -
341M ARG* 5.8 0.4 - - - +
349M TRP* 3.8 10.5 - - - -
487O ARG* 3.4 17.5 - - - +
494O VAL* 3.6 15.0 - - + -
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Residues in contact with GLU 280 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261M ARG* 3.4 29.2 + - + +
262M VAL 3.5 6.7 - - - +
263M ILE* 4.4 2.0 - - + +
279M PHE* 1.3 74.5 - - - +
281M TRP* 1.3 59.3 + - - +
333M LEU* 4.3 15.7 - - + +
341M ARG* 3.2 24.8 + - - +
349M TRP* 3.7 22.4 - - + -
491O ALA* 4.5 4.5 - - - +
492O GLY* 2.5 44.3 + - - +
493O ASP* 4.5 0.7 - - - +
494O VAL* 3.0 33.0 + - - +
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Residues in contact with TRP 281 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261M ARG* 3.1 5.0 - - - +
262M VAL* 2.9 35.4 + - + +
264M ILE* 4.4 15.7 - - + -
279M PHE* 3.8 15.3 - + + +
280M GLU* 1.3 78.1 - - - +
282M ASP* 1.3 79.6 + - - +
283M MET* 3.3 3.3 + - + +
288M ASN* 3.7 25.1 - - + +
289M SER 3.7 4.0 - - - -
290M PRO* 3.7 39.9 - - + -
293M PHE* 3.9 22.7 - + + -
315M ILE* 4.5 4.5 - - + -
319M LEU* 3.8 32.2 - - + +
493O ASP* 3.5 7.1 - - - +
494O VAL* 3.5 17.9 - - + -
495O CYS* 3.4 25.1 - - - -
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Residues in contact with ASP 282 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259M ASP* 3.1 22.3 - - - +
260M GLN 2.9 18.5 + - - -
261M ARG* 3.8 6.9 - - + +
281M TRP* 1.3 76.5 + - - +
283M MET* 1.3 65.8 + - - +
284M SER* 2.9 24.7 + - - -
285M GLU* 3.8 11.3 + - + +
288M ASN* 2.7 26.6 + - - +
454O ASN* 3.1 17.0 + - - -
457O LYS* 4.1 3.1 - - - -
493O ASP* 2.9 33.9 + - + +
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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