Contacts of the strand formed by residues 261 - 270 (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 ARG 261 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259M ASP* 3.4 30.8 + - - +
260M GLN* 1.3 76.5 - - - +
262M VAL* 1.3 63.9 + - - +
280M GLU* 3.4 42.0 + - + +
281M TRP 3.1 21.5 - - - +
282M ASP* 3.8 9.0 - - + +
332M PRO* 5.2 6.2 - - - +
333M LEU* 3.3 41.4 + - + +
334M PRO* 2.6 36.3 + - - +
335M THR 4.4 1.4 - - - -
336M VAL* 3.8 25.2 - - - +
456O SER* 4.4 1.5 + - - -
491O ALA* 6.2 0.4 - - - +
492O GLY* 4.3 3.0 - - - -
493O ASP* 5.1 10.8 - - + +
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Residues in contact with VAL 262 (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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260M GLN 4.1 2.0 - - - +
261M ARG* 1.3 79.7 - - - +
263M ILE* 1.3 60.5 + - - +
264M ILE* 3.8 12.5 + - + -
280M GLU* 3.5 0.9 - - - -
281M TRP* 2.9 35.6 + - - +
283M MET* 3.5 36.1 - - + -
319M LEU* 5.0 2.5 - - + -
322M HIS* 3.3 40.6 - - + +
326M TYR 4.8 10.1 - - - +
332M PRO* 6.3 2.9 - - + -
333M LEU* 4.1 7.9 - - - -
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Residues in contact with ILE 263 (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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262M VAL* 1.3 74.5 - - + +
264M ILE* 1.3 61.7 + - - +
265M LYS* 4.1 17.7 + - - +
278M GLN* 3.3 44.9 - - + +
279M PHE 3.6 4.0 - - - +
280M GLU* 4.4 1.6 - - - +
318M GLN* 4.9 1.0 - - - +
322M HIS* 4.1 16.2 + - + -
333M LEU* 4.4 13.4 - - + +
349M TRP* 3.4 28.5 - - + -
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Residues in contact with ILE 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262M VAL* 3.8 11.6 + - + -
263M ILE* 1.3 74.8 - - - +
265M LYS* 1.3 62.3 + - - +
266M LEU* 3.9 9.9 - - + -
278M GLN* 3.2 2.9 - - - -
279M PHE* 2.9 62.5 + - + +
281M TRP* 4.4 14.8 - - + -
315M ILE* 3.8 31.2 - - + +
318M GLN* 3.8 30.3 - - + +
319M LEU* 4.0 25.1 - - + +
322M HIS* 5.0 2.5 - - + +
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Residues in contact with LYS 265 (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 21.1 - - - +
264M ILE* 1.3 76.6 - - - +
266M LEU* 1.3 59.2 + - - +
267M ASN* 4.0 3.1 + - + +
276M VAL* 6.4 0.7 - - + -
277M ASP 3.2 11.0 - - - +
278M GLN* 3.7 30.0 - - + +
318M GLN* 2.3 36.3 + - - +
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Residues in contact with LEU 266 (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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264M ILE* 3.9 14.1 - - + -
265M LYS* 1.3 72.7 - - - +
267M ASN* 1.3 59.5 + - - +
268M ILE* 3.8 16.6 - - + -
275M LEU* 4.1 4.9 - - + +
276M VAL* 3.1 9.5 - - - +
277M ASP* 2.9 53.3 + - - +
279M PHE* 3.9 19.1 - - + -
293M PHE* 4.6 0.2 - - + -
297M LEU* 4.3 8.5 - - + -
311M ILE* 3.7 29.2 - - + +
314M SER* 3.4 25.8 - - - +
315M ILE* 3.8 19.7 - - + -
318M GLN* 3.9 1.3 - - - +
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Residues in contact with ASN 267 (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* 4.0 3.0 + - + +
266M LEU* 1.3 73.7 - - - +
268M ILE* 1.3 61.7 + - - +
269M HIS* 3.2 33.6 + - - -
275M LEU 3.5 2.2 - - - -
276M VAL* 3.3 27.1 - - + +
314M SER* 5.2 1.0 + - - -
364M LYS* 4.5 2.4 + - - +
367M ASP* 4.9 4.0 + - - -
368M GLN* 3.7 33.8 + - + +
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Residues in contact with ILE 268 (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* 3.8 20.9 - - + -
267M ASN* 1.3 84.3 - - - +
269M HIS* 1.3 65.3 + - - +
270M VAL* 4.1 6.0 + - + -
273M ILE 3.7 1.2 - - - +
274M SER* 3.4 2.4 - - - -
275M LEU* 2.9 46.1 + - + +
307M PHE* 3.9 18.3 - - + -
310M THR* 3.6 24.7 - - - +
311M ILE* 3.5 41.3 - - + +
314M SER* 4.3 13.0 - - - +
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Residues in contact with HIS 269 (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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267M ASN* 3.2 40.6 + - - -
268M ILE* 1.3 74.4 - - - +
270M VAL* 1.3 65.7 + - - +
271M GLY 4.9 1.6 - - - -
273M ILE 3.4 4.7 - - - -
274M SER* 3.5 16.3 + - - -
361M MET* 3.4 30.6 - - + +
364M LYS* 3.4 32.7 + - + -
365M ILE* 3.3 39.6 - - + +
368M GLN* 3.9 7.4 - - + +
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Residues in contact with VAL 270 (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* 4.1 4.1 - - + -
269M HIS* 1.3 78.7 - - - +
271M GLY* 1.3 62.7 + - - +
273M ILE* 2.9 34.8 + - - +
306M GLU* 3.3 45.3 - - + +
307M PHE* 3.6 35.6 - - + +
310M THR* 4.1 21.5 - - + +
41R PHE* 5.1 6.7 - - + -
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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