Contacts of the helix formed by residues 260 - 264 (chain A) in PDB entry 1LT8
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 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A HIS* 3.4 19.7 - - - -
219A PHE* 3.7 14.8 - - - -
256A ALA* 4.0 11.9 - - - +
257A ASN* 3.1 9.5 + - - -
258A LYS 3.3 2.4 + - - -
259A GLN* 1.3 80.4 - - - +
261A PHE* 1.3 65.4 + - - -
262A ILE 3.2 4.8 + - - -
263A ASP* 3.4 13.5 + - - +
264A LEU* 4.3 1.7 + - - +
370A PRO* 6.0 0.3 - - - +
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Residues in contact with PHE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.1 12.3 - + - -
217A CYS* 4.0 22.0 - - - -
218A HIS* 2.9 20.7 + - - +
249A LEU* 3.4 39.9 - - + -
251A TYR* 4.2 10.3 - + + -
253A THR* 3.9 13.7 - - + -
256A ALA* 4.3 0.8 - - - +
260A GLY* 1.3 70.0 - - - -
262A ILE* 1.3 91.5 + - + +
263A ASP 3.1 0.4 - - - -
264A LEU* 3.0 29.1 + - + +
267A PHE* 3.4 36.3 - + - +
271A LEU* 3.9 27.9 - - + +
300A CYS* 4.3 4.3 - - + -
601A CBH 5.1 2.5 - - + -
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Residues in contact with ILE 262 (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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160A TYR* 3.2 27.4 - - - +
162A GLU* 5.8 1.1 - - - +
218A HIS* 4.3 9.6 - - + -
259A GLN 5.0 5.8 - - - +
260A GLY 3.2 1.4 + - - -
261A PHE* 1.3 94.6 - - + +
263A ASP* 1.3 65.0 + - - +
267A PHE* 3.6 21.5 - - + +
601A CBH 3.4 19.3 - - + -
338B HIS* 4.1 12.8 - - + +
340B LYS* 5.0 6.5 - - + +
343B VAL* 3.8 22.7 - - + +
346B ARG* 3.1 26.2 + - - -
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Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ASN* 4.2 2.5 + - - +
259A GLN* 3.0 38.1 + - + +
260A GLY 3.4 9.4 + - - +
261A PHE 3.1 1.0 - - - -
262A ILE* 1.3 82.9 - - - +
264A LEU* 1.3 62.3 + - - +
370A PRO* 4.2 10.3 - - + -
371A ASP 2.7 42.9 + - - +
340B LYS* 4.6 4.9 - - - -
342B TRP* 2.8 40.6 + - - +
346B ARG* 3.3 7.4 + - - +
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Residues in contact with LEU 264 (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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253A THR* 4.2 8.5 - - + -
255A ASP* 3.8 34.5 - - - +
256A ALA* 4.1 7.2 - - + +
260A GLY 4.3 0.9 + - - +
261A PHE* 3.0 36.0 + - + +
263A ASP* 1.3 76.3 - - - +
265A PRO* 1.3 72.2 - - + +
266A GLU* 3.2 8.7 - - - +
267A PHE* 3.1 10.2 + - - +
271A LEU* 5.3 2.9 - - + -
274A ARG* 3.7 30.1 - - - +
368A SER* 3.8 18.4 - - - +
370A PRO* 4.0 13.2 - - + -
346B ARG* 3.1 18.2 + - - -
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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