Contacts of the strand formed by residues 267 - 272 (chain B) 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 ILE 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B LEU* 4.3 18.6 - - + -
266B GLY* 1.3 84.9 - - - +
268B SER* 1.3 65.5 + - - +
269B ILE* 3.9 14.6 - - + -
283B ILE* 3.4 33.0 - - + -
285B SER 3.3 10.3 - - - +
286B ILE* 4.3 8.3 - - + -
287B MSE 3.9 4.9 - - - +
292B VAL* 3.5 31.0 - - + -
304B LEU* 5.1 5.4 - - + -
324B LEU* 5.7 0.9 - - + -
336B LEU* 5.4 4.3 - - + -
7E THR* 3.2 2.4 - - - +
8E VAL* 2.8 47.1 + - + +
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ILE* 1.3 79.2 - - - +
269B ILE* 1.3 65.0 + - - +
283B ILE* 3.7 5.0 - - - -
284B GLY* 2.9 24.9 + - - -
285B SER* 3.0 33.6 + - - -
287B MSE 3.9 2.4 - - - +
289C GLY* 6.1 2.0 - - - -
4E LEU* 3.9 16.8 - - - +
6E THR 3.2 11.9 - - - -
7E THR* 3.6 17.9 - - - +
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Residues in contact with ILE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ILE* 3.9 28.3 - - + -
268B SER* 1.3 80.3 - - - +
270B VAL* 1.3 67.2 + - - +
281B ILE* 3.8 31.2 - - + -
282B TYR 3.5 10.5 - - - +
283B ILE* 4.4 0.4 - - + -
304B LEU* 4.3 15.5 - - + -
321B VAL* 4.5 5.6 - - + -
324B LEU* 4.2 24.7 - - + -
4E LEU* 3.6 3.6 - - - +
5E MET* 2.9 40.7 + - + +
6E THR* 3.0 21.0 + - - +
8E VAL* 4.7 4.5 - - + -
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLY* 5.7 4.5 - - - -
341A LEU* 4.5 14.1 - - + -
269B ILE* 1.3 79.6 - - - +
271B GLY* 1.3 63.6 + - - +
281B ILE* 3.1 3.1 - - - -
282B TYR* 2.7 47.7 + - + +
283B ILE 5.3 0.2 - - - +
284B GLY* 4.7 16.4 - - - -
2E LEU* 3.9 34.3 - - + -
3E LYS 3.3 19.3 - - - +
4E LEU* 4.1 11.9 - - + -
5E MET 4.4 0.2 - - - +
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Residues in contact with GLY 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B VAL* 1.3 76.8 - - - +
272B GLN* 1.3 62.0 + - - -
280B GLY 3.4 9.0 - - - -
281B ILE* 4.1 3.1 - - - -
282B TYR* 5.1 0.2 - - - -
317B ASN* 4.4 1.8 - - - -
2E LEU* 3.3 7.4 - - - -
3E LYS* 3.0 40.9 + - - -
5E MET* 3.7 20.5 - - - -
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Residues in contact with GLN 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLN* 3.1 33.1 + - - +
273A SER 4.8 3.6 - - - +
274A ASN* 4.4 17.5 - - - +
271B GLY* 1.3 74.8 - - - -
273B SER* 1.3 82.2 + - - +
274B ASN* 3.0 2.3 + - - +
277B GLY 4.7 2.3 - - - +
278B ASP 5.1 0.4 + - - -
279B GLY* 3.9 17.0 - - - -
280B GLY 3.1 12.1 + - - +
282B TYR* 2.9 34.7 + - + -
317B ASN* 2.8 15.8 + - - -
1D SER* 4.4 9.8 + - - +
2D LEU* 4.5 7.5 - - - +
1E SER 3.5 9.2 - - - +
2E LEU* 3.9 6.7 - - + -
3E LYS* 3.9 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