Contacts of the helix formed by residues 245 - 256 (chain A) in PDB entry 1LL9
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 GLU 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A PRO* 3.7 43.9 - - + +
243A ILE* 3.6 15.0 - - + +
244A ASN* 1.3 82.2 + - - +
246A LYS* 1.3 65.3 - - - +
247A THR* 3.5 2.9 - - - +
248A LEU* 3.7 18.5 - - + +
249A GLN* 3.0 22.2 + - - +
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Residues in contact with LYS 246 (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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244A ASN 2.9 10.9 + - - +
245A GLU* 1.3 70.1 - - - +
247A THR* 1.3 66.9 + - + +
249A GLN* 3.1 12.5 + - - +
250A GLN* 3.1 31.5 + - - +
241B LEU* 3.6 37.3 - - + +
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Residues in contact with THR 247 (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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76A ASP* 2.8 24.2 + - - +
79A ALA* 3.5 34.8 - - + +
80A ARG* 3.6 40.7 + - + +
245A GLU* 5.2 2.8 - - - +
246A LYS* 1.3 80.6 - - + +
248A LEU* 1.3 51.9 + - - +
250A GLN* 3.3 6.4 + - - +
251A GLY* 2.7 30.7 + - - -
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Residues in contact with LEU 248 (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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72A VAL* 3.8 25.6 - - + -
76A ASP* 3.5 13.0 - - + +
177A ARG 3.6 26.2 - - - +
178A VAL* 4.3 11.9 - - + +
181A PRO* 3.7 23.1 - - + -
182A LEU* 3.8 26.5 - - + -
243A ILE* 4.2 15.0 - - + -
245A GLU* 3.3 17.3 + - + +
246A LYS 3.2 0.6 - - - -
247A THR* 1.3 79.5 + - - +
249A GLN* 1.3 66.4 + - - +
251A GLY 4.3 0.2 - - - +
252A ILE* 3.0 32.0 + - + +
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Residues in contact with GLN 249 (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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240A PRO* 3.5 24.8 - - - +
241A LEU* 3.1 38.9 + - - +
243A ILE* 3.4 24.8 + - + +
244A ASN 5.1 1.2 + - - -
245A GLU 3.0 13.2 + - - +
246A LYS* 3.4 13.5 + - - +
248A LEU* 1.3 77.4 - - - +
250A GLN* 1.3 65.5 + - + +
252A ILE* 3.5 3.5 + - - +
253A GLN* 3.3 31.8 + - - +
241B LEU* 4.6 18.5 - - - +
249B GLN* 3.9 8.3 - - - +
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Residues in contact with GLN 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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79A ALA* 3.5 28.1 + - + +
246A LYS* 3.1 31.4 + - - +
247A THR* 3.6 13.6 - - - +
249A GLN* 1.3 77.7 - - + +
251A GLY* 1.3 59.3 + - - +
253A GLN* 3.0 15.3 + - - +
254A LEU* 2.9 36.8 + - + +
241B LEU* 5.2 8.6 - - + +
253B GLN* 4.5 25.3 + - - +
306B PRO* 4.7 12.0 - - - +
307B ALA 5.4 3.3 - - - +
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Residues in contact with GLY 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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72A VAL* 4.2 8.3 - - - -
75A GLY* 3.4 35.3 + - - -
76A ASP* 3.5 4.7 - - - -
247A THR 2.7 17.4 + - - -
248A LEU 3.2 2.4 + - - -
250A GLN* 1.3 73.8 - - - +
252A ILE* 1.3 60.5 + - - +
254A LEU* 3.3 4.5 + - - +
255A ALA* 3.1 22.7 + - - +
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Residues in contact with ILE 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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72A VAL* 3.6 27.4 - - + -
182A LEU* 4.7 3.8 - - + -
233A TRP* 4.5 5.8 - - + -
236A SER* 4.0 16.2 - - - +
237A ASN* 3.5 33.2 - - - +
240A PRO* 3.8 19.1 - - + -
243A ILE* 3.7 24.2 - - + -
248A LEU* 3.0 18.2 + - + +
249A GLN 3.8 4.9 - - - +
251A GLY* 1.3 75.2 - - - +
253A GLN* 1.3 63.7 + - - +
255A ALA* 3.3 11.8 + - - +
256A GLN* 3.4 23.4 + - - +
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Residues in contact with GLN 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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240A PRO* 4.0 18.0 - - + +
241A LEU* 4.1 14.8 - - - +
249A GLN* 3.3 28.7 + - - +
250A GLN* 3.0 19.6 + - - +
252A ILE* 1.3 78.5 - - - +
254A LEU* 1.3 63.8 + - + +
256A GLN* 3.2 13.5 + - - +
257A SER* 3.4 13.3 + - - -
307A ALA* 4.1 16.6 + - + +
250B GLN* 3.6 32.1 + - - +
253B GLN* 5.2 5.4 + - - -
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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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75A GLY* 3.7 28.7 - - - +
78A ILE* 3.8 26.9 - - + -
79A ALA* 4.6 4.7 - - + +
250A GLN* 2.9 22.2 + - + +
251A GLY 3.6 4.7 - - - +
253A GLN* 1.3 80.3 - - + +
255A ALA* 1.3 60.5 + - - +
257A SER* 3.3 17.9 + - - +
259A TYR* 2.8 32.7 + - - +
269A LEU* 3.8 4.6 - - + +
306B PRO* 4.1 21.5 - - + -
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Residues in contact with ALA 255 (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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71A GLY 4.1 5.2 - - - +
72A VAL* 3.9 22.0 - - + -
251A GLY 3.1 15.2 + - - +
252A ILE 3.7 5.8 - - - +
253A GLN 3.3 0.6 - - - -
254A LEU* 1.3 75.9 - - - +
256A GLN* 1.3 59.0 + - - +
257A SER 3.4 0.2 - - - -
268A GLY* 3.5 5.9 - - - -
269A LEU* 2.9 53.5 + - + +
271A TRP* 4.0 13.5 - - + +
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Residues in contact with GLN 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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237A ASN* 3.0 38.2 + - - +
240A PRO* 5.6 1.2 - - - +
252A ILE* 3.4 15.2 + - - +
253A GLN* 3.2 6.5 + - - +
254A LEU 3.1 1.0 - - - -
255A ALA* 1.3 79.5 - - - +
257A SER* 1.3 64.1 + - - +
258A ARG* 3.8 3.1 + - - +
271A TRP* 4.2 13.7 - - + -
273A MET* 3.6 18.8 - - + +
307A ALA* 3.5 33.4 - - + +
308A VAL 4.7 2.8 + - - +
313A VAL* 4.1 18.4 - - + +
328A PHE* 3.7 26.1 - - - -
330A PRO* 4.1 8.3 - - - +
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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