Contacts of the strand formed by residues 266 - 271 (chain A) in PDB entry 3L49
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 ALA 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A THR* 3.8 4.3 - - + +
245A ARG* 4.4 0.2 - - - -
246A THR* 3.5 8.5 - - - +
255A PHE* 3.7 23.8 - - + -
258A MET* 3.6 38.1 - - + -
259A VAL* 3.6 8.2 - - + +
264A SER* 3.2 5.3 + - - +
265A PRO* 1.3 74.8 - - - +
267A GLY* 1.3 58.4 + - - +
268A ALA 3.9 0.4 - - - -
307A LYS* 2.7 31.0 + - - +
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Residues in contact with GLY 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASP* 4.3 6.0 - - - +
245A ARG* 4.1 17.3 - - - -
246A THR 2.8 18.2 + - - -
247A TYR* 3.8 14.3 - - - -
259A VAL* 4.4 1.8 - - - -
265A PRO 3.4 2.4 + - - -
266A ALA* 1.3 74.3 - - - +
268A ALA* 1.3 62.0 + - - +
306A THR* 3.7 2.8 - - - -
307A LYS* 3.6 26.1 + - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 4.1 8.7 - - + -
143A GLN* 4.0 7.9 - - + -
246A THR 3.4 3.6 + - - -
247A TYR* 3.5 22.6 - - + -
248A GLY 3.3 21.7 + - - +
255A PHE* 3.5 6.9 - - - -
259A VAL* 4.0 6.0 - - - +
266A ALA 3.9 0.6 - - - -
267A GLY* 1.3 78.0 - - - +
269A VAL* 1.3 62.2 + - - +
304A LEU* 4.4 3.4 - - + -
305A ILE 3.2 14.8 - - - +
306A THR* 4.0 15.5 - - + -
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASP* 3.3 27.1 - - - +
248A GLY 3.3 8.3 - - - +
250A ASP 3.9 1.6 - - - +
251A GLY* 3.6 24.0 - - - +
255A PHE* 3.7 10.3 - - + -
256A VAL* 4.2 21.5 - - + -
259A VAL* 4.1 12.3 - - + -
268A ALA* 1.3 77.1 - - - +
270A ALA* 1.3 62.5 + - - +
271A ALA 3.4 3.4 + - - +
304A LEU* 3.6 5.2 - - - -
305A ILE* 2.8 57.6 + - + +
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Residues in contact with ALA 270 (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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136A ILE* 3.7 40.6 - - + +
140A LEU* 4.3 3.9 - - + +
248A GLY 3.2 8.1 + - - +
249A VAL* 3.9 14.8 - - + +
250A ASP* 2.8 25.7 + - - -
269A VAL* 1.3 70.0 - - - +
271A ALA* 1.3 62.2 + - - +
272A GLN* 3.4 3.6 + - - +
302A ALA* 5.2 0.4 - - - -
303A VAL 3.4 9.2 - - - +
304A LEU* 4.5 10.3 - - + +
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Residues in contact with ALA 271 (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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250A ASP 3.6 6.5 - - - -
251A GLY* 4.0 13.9 - - - -
256A VAL* 5.2 0.9 - - + -
269A VAL* 3.4 2.5 + - + +
270A ALA* 1.3 70.0 - - - +
272A GLN* 1.3 63.0 + - - +
273A GLN* 5.3 1.4 + - - +
302A ALA* 3.3 5.4 - - - -
303A VAL* 2.7 37.3 + - + +
305A ILE* 3.6 29.6 - - + -
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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