Contacts of the helix formed by residues 264 - 270 (chain D) in PDB entry 5LSJ
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 GLN 264 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 3.6 12.2 - - + +
159B ASN* 2.6 42.0 + - - +
160B GLN* 2.9 26.8 - - - +
163B ALA* 3.1 23.8 - - + +
164B ASP* 5.3 0.3 - - - +
262D SER 3.5 0.2 + - - -
263D SER* 1.3 93.5 + - - +
265D ASN* 1.3 66.2 + - - +
266D GLU* 3.2 5.2 - - - +
267D VAL* 3.4 24.3 + - + +
268D LEU* 3.6 10.9 + - - +
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Residues in contact with ASN 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU* 3.0 41.4 + - - +
261D GLY* 4.0 8.2 - - - +
262D SER* 3.4 21.3 + - - +
263D SER 3.3 2.2 + - - -
264D GLN* 1.3 74.3 - - - +
266D GLU* 1.3 61.0 + - + +
268D LEU* 3.1 9.1 + - - +
269D ASN* 2.8 50.7 + - - +
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Residues in contact with GLU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D GLN* 3.2 2.8 - - - -
265D ASN* 1.3 77.7 - - - +
267D VAL* 1.3 55.4 + - + +
269D ASN* 3.0 6.4 + - - +
270D THR* 2.6 45.2 + - - +
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Residues in contact with VAL 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.0 13.1 - - + +
141A GLU* 4.8 2.4 - - - +
163B ALA* 3.7 22.0 - - + +
166B VAL* 4.8 2.5 - - + -
167B LEU* 3.6 36.1 - - + -
170B ARG* 3.7 14.8 + - - +
264D GLN* 3.4 28.4 + - + +
265D ASN 3.3 0.2 - - - -
266D GLU* 1.3 79.1 - - + +
268D LEU* 1.3 58.1 + - - +
270D THR* 3.0 25.8 - - - +
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Residues in contact with LEU 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A THR* 3.8 20.4 - - + +
137A ALA* 3.8 26.2 - - + -
138A LEU* 3.6 30.3 - - + +
141A GLU* 5.0 5.0 - - - +
260D LEU* 3.6 42.2 - - + -
262D SER* 4.9 0.7 - - - +
264D GLN 3.6 7.3 + - - +
265D ASN* 3.1 17.1 + - - +
267D VAL* 1.3 81.4 - - - +
269D ASN* 1.3 63.2 + - - +
271D LYS* 4.1 16.6 - - - +
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Residues in contact with ASN 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU* 4.9 7.4 - - - +
265D ASN* 2.8 41.3 + - - +
266D GLU* 3.8 5.7 - - - +
268D LEU* 1.3 78.5 - - - +
270D THR* 1.3 60.6 + - - +
271D LYS* 3.3 8.1 + - - +
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Residues in contact with THR 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ARG* 2.5 55.3 + - - +
266D GLU* 2.6 27.1 + - - +
267D VAL* 3.0 6.4 - - - +
269D ASN* 1.3 71.1 - - - +
271D LYS* 1.3 52.6 + - - +
272D PRO* 4.9 4.9 - - + -
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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