Contacts of the strand formed by residues 280 - 286 (chain A) in PDB entry 1L6O
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 GLY 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A GLY* 3.7 0.2 - - - -
272A GLN* 3.0 28.6 + - - +
278A ASP 3.1 5.4 + - - -
279A GLY* 1.3 77.3 - - - +
281A ILE* 1.3 67.2 + - - -
282A TYR* 3.8 5.7 - - - -
303A MSE 5.0 7.2 - - - -
304A LEU 6.1 0.2 - - - -
312A PHE 6.1 0.9 - - - -
315A MSE 6.2 0.2 - - - -
317A ASN* 3.3 16.6 + - - +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ILE* 3.9 20.2 - - + -
270A VAL 3.4 5.2 - - - +
271A GLY* 4.5 2.9 - - - -
280A GLY* 1.3 63.3 - - - +
282A TYR* 1.3 62.0 + - - +
303A MSE 3.6 7.6 - - - +
304A LEU* 3.0 53.5 + - + +
312A PHE* 4.0 26.2 - - + -
317A ASN* 3.9 33.0 - - + +
320A ALA* 4.0 15.5 - - + -
321A VAL* 4.3 13.7 - - + -
324A LEU* 4.8 2.7 - - + -
5D MET* 4.9 0.4 - - + -
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Residues in contact with TYR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ILE* 3.4 9.8 - - - +
270A VAL* 2.9 46.2 + - + +
272A GLN* 2.7 47.9 + - + -
279A GLY 4.3 2.1 + - - -
280A GLY 3.8 10.1 - - - -
281A ILE* 1.3 73.3 - - - +
283A ILE* 1.4 69.1 + - - +
301A GLY* 3.4 24.7 - - - +
302A ASP 3.2 11.4 - - - +
303A MSE 3.8 33.2 - - + -
304A LEU* 4.5 2.2 - - - +
2D LEU* 5.3 2.0 - - + -
1E SER* 3.8 11.8 - - - -
2E LEU* 3.8 36.8 - - + -
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ILE* 3.9 29.2 - - + -
268A SER 3.4 6.3 - - - +
269A ILE* 4.4 6.3 - - + -
270A VAL* 5.0 0.7 - - - -
282A TYR* 1.4 74.3 - - - +
284A GLY* 1.3 57.0 + - - +
285A SER 4.2 7.0 - - - +
286A ILE* 3.8 34.8 - - + -
298A ILE* 4.0 15.3 - - + -
299A GLU 4.0 8.5 - - - +
300A PRO* 3.3 3.0 - - + +
301A GLY* 2.8 30.7 + - - -
302A ASP* 3.0 28.3 + - + +
304A LEU* 4.6 13.9 - - + -
336A LEU* 5.7 2.7 - - + -
338A VAL* 5.3 5.8 - - + -
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Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A SER* 2.9 19.5 + - - -
270A VAL* 3.9 18.9 - - - +
282A TYR 3.6 3.2 + - - -
283A ILE* 1.3 71.2 - - - +
285A SER* 1.3 60.8 + - - +
300A PRO* 3.2 19.9 - - - +
284B GLY 4.6 0.2 - - - +
285B SER* 5.9 0.2 - - - -
300B PRO* 4.0 19.0 - - - +
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLY 3.8 0.2 - - - +
267A ILE* 3.5 5.2 - - - +
268A SER* 2.7 42.1 + - - -
283A ILE* 4.2 0.5 - - - +
284A GLY* 1.3 77.0 - - - +
286A ILE* 1.3 71.4 + - - +
287A MSE 4.3 18.5 + - - +
300A PRO* 4.6 5.4 - - - -
300B PRO* 4.6 18.6 - - - +
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLY 3.3 5.8 - - - +
267A ILE* 4.5 1.3 - - + -
283A ILE* 3.8 14.4 - - + -
285A SER* 1.3 84.8 - - - +
287A MSE 1.3 65.9 + - - +
288A LYS 3.8 0.9 + - - -
292A VAL* 4.0 15.7 - - + -
293A ALA* 3.8 37.1 - - + +
298A ILE* 3.5 28.0 - - + +
299A GLU* 3.7 22.4 - - - -
300A PRO* 3.9 9.5 - - + +
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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