Contacts of the helix formed by residues 245 - 256 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B PRO* 3.5 43.4 - - + +
182B LEU* 5.2 0.2 - - - +
243B ILE* 3.4 15.6 - - + +
244B ASN* 1.3 82.6 + - - +
246B LYS* 1.3 59.3 + - - +
247B THR* 3.5 3.1 - - - +
248B LEU* 3.1 18.2 + - + +
249B GLN* 2.9 27.2 + - - +
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Residues in contact with LYS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU* 3.1 46.4 - - + +
309A ARG* 5.0 16.1 - - - +
244B ASN 2.9 15.2 + - - +
245B GLU* 1.3 70.1 - - - +
247B THR* 1.3 66.7 + - + +
249B GLN* 3.3 11.8 + - - +
250B GLN* 3.1 37.0 + - - +
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Residues in contact with THR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ASP* 2.8 23.4 + - - +
79B ALA* 3.5 32.5 - - + +
80B ARG* 3.7 41.7 + - + +
245B GLU* 3.5 2.5 - - - +
246B LYS* 1.3 81.5 - - + +
248B LEU* 1.3 58.3 + - - +
250B GLN* 3.4 3.5 + - - +
251B GLY* 2.8 24.4 + - - -
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B VAL* 3.9 24.9 - - + -
76B ASP* 3.1 16.9 + - + +
177B ARG 3.6 25.6 - - - +
178B VAL* 4.3 11.4 - - + +
181B PRO* 3.7 23.8 - - + -
182B LEU* 3.7 27.8 - - + -
243B ILE* 4.2 9.4 - - + -
245B GLU* 3.1 16.4 + - + +
247B THR* 1.3 75.2 + - - +
249B GLN* 1.3 67.2 + - - +
251B GLY* 3.1 0.7 + - - -
252B ILE* 2.9 32.3 + - + +
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Residues in contact with GLN 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU* 3.7 26.3 - - - +
249A GLN* 3.9 6.6 - - - +
240B PRO* 3.1 24.9 - - + +
241B LEU* 2.9 49.0 + - + +
243B ILE* 3.1 22.6 + - - +
245B GLU 2.9 12.7 + - - +
246B LYS* 3.4 13.0 - - - +
248B LEU* 1.3 79.2 - - - +
250B GLN* 1.3 63.5 + - + +
252B ILE* 3.4 4.7 + - - +
253B GLN* 3.3 27.6 + - - +
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Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU* 4.2 20.2 - - + +
253A GLN* 3.6 26.5 + - - +
306A PRO* 5.9 4.4 - - - +
307A ALA 6.0 0.2 + - - -
79B ALA* 3.1 33.3 + - + +
246B LYS* 3.1 23.5 + - - +
247B THR* 3.8 5.9 - - - +
249B GLN* 1.3 76.8 - - + +
251B GLY* 1.3 59.1 + - - +
253B GLN* 3.2 10.6 + - - +
254B LEU* 2.9 39.2 + - + +
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Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B VAL* 4.2 7.4 - - - -
75B GLY* 3.4 34.9 + - - -
76B ASP* 3.6 3.4 - - - -
247B THR 2.8 13.9 + - - -
248B LEU 3.1 3.9 + - - -
250B GLN* 1.3 76.8 - - - +
252B ILE* 1.3 61.5 + - - +
254B LEU* 3.2 3.7 + - - +
255B ALA* 3.0 23.2 + - - +
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B VAL* 3.7 27.3 - - + +
182B LEU* 4.8 6.5 - - + -
233B TRP* 5.2 0.4 - - + -
236B SER* 3.6 30.1 - - - +
237B ASN* 3.4 33.2 - - - +
240B PRO* 3.8 17.5 - - + -
243B ILE* 4.4 14.6 - - + -
248B LEU* 2.9 27.0 + - + +
249B GLN 3.8 4.7 - - - +
250B GLN 3.3 0.2 - - - -
251B GLY* 1.3 75.3 - - - +
253B GLN* 1.3 64.1 + - - +
255B ALA* 3.3 11.1 + - - +
256B GLN* 3.4 20.9 + - - +
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Residues in contact with GLN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLN* 4.5 26.7 + - - +
253A GLN* 5.2 5.4 + - - -
240B PRO* 4.0 18.0 - - + +
241B LEU* 3.3 31.0 - - - +
249B GLN* 3.3 17.0 + - - +
250B GLN* 3.2 13.5 + - - +
251B GLY 3.2 0.2 - - - -
252B ILE* 1.3 79.5 - - - +
254B LEU* 1.3 63.5 + - + +
256B GLN* 3.1 14.6 + - - +
257B SER* 3.3 13.7 + - - -
306B PRO* 6.2 2.0 - - - +
307B ALA* 4.0 18.4 + - + +
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A PRO* 4.1 21.1 - - + -
75B GLY* 3.6 28.3 - - - +
78B ILE* 3.9 26.9 - - + -
79B ALA* 4.5 5.8 - - + +
250B GLN* 2.9 23.5 + - + +
251B GLY 3.2 4.9 + - - +
253B GLN* 1.3 77.4 - - + +
255B ALA* 1.3 62.2 + - - +
257B SER* 3.2 19.0 + - - +
259B TYR* 2.8 32.2 + - - +
269B LEU* 3.9 4.8 - - + +
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Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLY 4.2 5.6 - - - -
72B VAL* 3.8 22.4 - - + -
251B GLY 3.0 15.7 + - - +
252B ILE 3.7 6.5 - - - +
253B GLN 3.2 0.4 - - - -
254B LEU* 1.3 76.0 - - - +
256B GLN* 1.3 59.3 + - - +
257B SER 3.4 0.2 - - - -
268B GLY* 3.5 5.4 - - - -
269B LEU* 2.9 52.5 + - + +
271B TRP* 4.0 13.4 - - + +
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Residues in contact with GLN 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ASN* 2.9 39.6 + - - +
240B PRO* 5.4 1.6 - - - +
252B ILE* 3.4 14.5 + - - +
253B GLN* 3.1 6.7 + - - +
254B LEU 3.1 0.6 - - - -
255B ALA* 1.3 79.5 - - - +
257B SER* 1.3 64.0 + - - +
258B ARG* 3.7 2.9 + - - +
271B TRP* 4.2 14.4 - - + -
273B MET* 3.5 18.8 - - + +
307B ALA* 3.5 35.2 - - + +
308B VAL 4.6 2.4 + - - +
313B VAL* 4.0 17.6 - - + +
328B PHE* 3.7 24.8 - - - -
330B PRO* 4.1 8.7 - - - +
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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