Contacts of the helix formed by residues 249 - 259 (chain A) in PDB entry 1LC7
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 ASN 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PRO* 4.3 3.8 - - - -
83A ASN* 4.7 6.9 + - - -
223A LEU* 2.9 33.4 + - - +
224A ARG* 4.7 2.2 + - - +
246A TRP 5.4 0.7 - - - -
247A SER 3.8 3.2 + - - -
248A VAL* 1.3 78.5 - - - +
250A ALA* 1.3 65.6 + - - +
251A LEU* 3.2 13.3 + - - +
252A ALA* 2.9 28.8 + - - +
253A ALA* 3.1 18.5 + - - +
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Residues in contact with ALA 250 (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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52A CYS* 3.8 35.3 - - + +
53A ILE* 4.8 7.9 - - + -
55A ARG 4.9 2.5 - - - +
57A PRO* 3.8 26.9 - - + +
248A VAL 3.8 1.2 + - - -
249A ASN* 1.3 74.2 - - - +
251A LEU* 1.3 61.8 + - - +
253A ALA* 3.3 7.3 + - - +
254A LEU* 3.1 22.5 + - - +
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Residues in contact with LEU 251 (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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46A LEU* 3.7 26.0 - - + +
49A ASN 4.3 7.6 - - - +
50A LEU* 4.3 24.7 - - + -
52A CYS* 3.6 25.1 - - - -
53A ILE* 3.7 24.7 - - + +
223A LEU* 4.0 13.7 - - + -
249A ASN* 3.2 8.8 + - - +
250A ALA* 1.3 74.3 - - - +
252A ALA* 1.3 60.7 + - - +
254A LEU* 3.3 7.4 + - + +
255A ALA* 2.8 32.1 + - - +
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Residues in contact with ALA 252 (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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220A ILE* 6.0 0.2 - - - -
223A LEU* 3.5 40.8 - - + +
224A ARG 3.7 13.0 - - - +
225A LEU* 3.3 15.6 - - + +
248A VAL* 4.1 9.2 - - + -
249A ASN* 2.9 19.6 + - - +
251A LEU* 1.3 76.7 - - - +
253A ALA* 1.3 58.2 + - - +
255A ALA* 3.9 0.9 - - - +
256A GLY 2.9 24.8 + - - -
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Residues in contact with ALA 253 (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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57A PRO* 6.0 0.2 - - + -
61A TYR* 4.3 13.5 - - + -
64A LEU* 3.9 21.9 - - + +
248A VAL* 4.0 10.9 - - + +
249A ASN 3.1 11.6 + - - +
250A ALA* 3.6 10.8 - - - +
251A LEU 3.2 0.2 - - - -
252A ALA* 1.3 77.4 - - - +
254A LEU* 1.3 60.7 + - - +
256A GLY* 3.5 0.9 + - - -
257A GLU* 3.0 39.8 + - - +
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Residues in contact with LEU 254 (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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45A ALA* 3.4 42.2 - - + +
46A LEU* 3.8 17.9 - - + -
49A ASN* 3.9 29.2 - - + +
52A CYS* 5.1 2.9 - - - -
250A ALA 3.1 14.1 + - - +
251A LEU* 3.5 13.7 - - + +
252A ALA 3.2 0.2 - - - -
253A ALA* 1.3 74.0 - - - +
255A ALA* 1.3 66.0 + - - +
257A GLU* 3.3 18.2 + - - +
258A VAL* 3.0 33.0 + - + +
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.9 25.8 - - + +
45A ALA* 6.0 0.2 - - - -
46A LEU* 4.5 4.0 - - + -
220A ILE* 4.4 10.5 - - + -
223A LEU* 3.4 24.9 - - + -
251A LEU 2.8 20.5 + - - +
252A ALA 3.9 1.8 - - - +
254A LEU* 1.3 74.1 - - - +
256A GLY* 1.3 59.5 + - - +
258A VAL* 3.2 4.9 + - - +
259A ALA* 2.7 34.7 + - - +
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Residues in contact with GLY 256 (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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64A LEU* 4.5 6.5 - - - -
214A LEU* 4.0 10.3 - - - +
220A ILE* 5.0 1.3 - - - +
225A LEU* 3.6 24.8 - - - +
252A ALA 2.9 12.0 + - - -
253A ALA 3.9 1.3 - - - -
254A LEU 3.2 0.2 - - - -
255A ALA* 1.3 78.1 - - - +
257A GLU* 1.3 62.4 + - - +
259A ALA* 3.4 2.7 + - - +
260A LEU* 3.3 29.3 + - - +
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Residues in contact with GLU 257 (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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63A HIS* 3.7 17.4 - - - +
64A LEU* 3.4 37.2 + - + +
67A ALA* 4.1 21.4 - - + +
253A ALA* 3.0 30.1 + - - +
254A LEU* 3.7 17.1 + - - +
256A GLY* 1.3 76.1 - - - +
258A VAL* 1.3 64.7 + - + +
260A LEU* 3.5 9.1 + - - +
261A GLN* 3.3 18.5 + - - +
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Residues in contact with VAL 258 (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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41A SER* 3.6 46.0 + - - +
42A VAL* 3.7 6.7 - - + +
45A ALA* 3.6 22.4 - - + -
254A LEU* 3.0 25.5 + - + +
255A ALA 3.7 2.7 - - - +
257A GLU* 1.3 76.3 - - + +
259A ALA* 1.3 59.3 + - - +
261A GLN* 2.8 35.4 + - + +
262A ASP 3.7 2.6 + - - -
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Residues in contact with ALA 259 (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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39A PRO* 4.9 2.5 - - + -
41A SER* 5.4 0.2 - - - -
42A VAL* 3.8 17.2 - - + +
214A LEU* 5.1 1.3 - - + -
218A TYR* 3.5 50.3 + - + -
220A ILE* 5.6 3.1 - - + -
255A ALA 2.7 22.6 + - - +
256A GLY* 3.4 6.3 + - - +
258A VAL* 1.3 74.0 - - - +
260A LEU* 1.3 60.8 + - - +
261A GLN 3.1 1.2 + - - -
262A ASP* 3.2 19.0 + - - +
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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