Contacts of the helix formed by residues 222 - 240 (chain A) in PDB entry 5LLU
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ASN* 3.1 49.5 + - - +
185A PRO* 4.0 16.4 - - - +
191A ALA* 2.9 16.1 + - + +
194A ARG 3.3 19.0 + - - +
195A SER* 3.4 8.0 + - - +
221A MET* 1.3 70.5 - - - +
223A ILE* 1.4 62.0 + - - +
224A LEU* 3.8 4.2 + - - +
225A GLY* 2.9 26.3 + - - -
226A LEU* 3.2 22.2 + - - +
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Residues in contact with ILE 223 (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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96A ILE* 3.8 11.7 - - + -
100A ILE* 3.8 21.5 - - + +
221A MET* 3.4 37.4 + - + +
222A ASN* 1.4 69.2 - - - +
224A LEU* 1.3 51.9 + - - +
226A LEU* 3.1 5.4 + - - +
227A VAL* 2.8 49.0 + - + +
346A SER* 3.8 32.3 - - - +
372A PRO 5.5 2.0 - - - +
375A ALA* 6.2 2.7 - - + -
376A THR* 4.7 13.0 - - - +
421A ALA* 6.1 1.3 - - + -
422A GLY 5.4 4.5 - - - +
423A ILE* 3.9 18.4 - - + -
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Residues in contact with LEU 224 (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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179A LEU* 3.8 29.8 - - + +
182A ASN* 4.6 7.2 - - + -
183A ILE* 3.6 37.2 - - + +
222A ASN* 3.4 4.0 + - - +
223A ILE* 1.3 75.1 - - - +
225A GLY* 1.3 58.2 + - - +
227A VAL* 3.3 8.7 + - + +
228A VAL* 2.9 44.0 + - + +
376A THR* 4.2 25.4 + - + +
377A ILE* 5.2 9.6 - - + -
418A ILE 6.2 0.2 - - - +
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Residues in contact with GLY 225 (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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182A ASN 3.1 24.3 + - - -
183A ILE 4.3 3.8 - - - -
185A PRO* 3.9 18.4 - - - +
222A ASN* 2.9 22.9 + - - -
224A LEU* 1.3 72.3 - - - +
226A LEU* 1.3 58.9 + - - +
228A VAL* 4.0 1.0 - - - +
229A PHE* 3.2 26.9 + - - +
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Residues in contact with LEU 226 (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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97A LEU* 3.7 18.6 - - + -
100A ILE* 4.6 7.2 - - + -
101A VAL* 4.5 19.1 - - + -
185A PRO* 6.0 0.2 - - + -
188A LEU* 4.3 21.3 - - + +
191A ALA* 3.8 31.4 - - + +
192A ALA* 3.9 5.2 - - + +
221A MET* 3.5 28.5 - - + -
222A ASN 3.2 12.7 + - - +
223A ILE* 3.1 8.1 + - - +
225A GLY* 1.3 75.3 - - - +
227A VAL* 1.4 55.7 + - - +
228A VAL 3.4 0.2 - - - -
229A PHE* 4.1 6.8 - - + +
230A SER* 2.7 41.8 + - - -
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Residues in contact with VAL 227 (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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100A ILE* 3.7 19.3 - - + -
104A LEU* 3.8 18.2 - - + +
223A ILE* 2.8 37.0 + - + +
224A LEU* 3.3 8.9 + - + +
226A LEU* 1.4 69.1 - - - +
228A VAL* 1.4 68.7 + - + +
231A ILE* 3.1 44.5 + - + +
372A PRO 4.1 13.5 - - - +
373A VAL* 4.1 13.9 - - + -
376A THR* 4.2 15.3 - - + -
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Residues in contact with VAL 228 (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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183A ILE* 3.5 46.0 - - + +
184A PHE* 5.5 6.3 - - + -
224A LEU* 2.9 33.9 + - + +
225A GLY 4.0 0.9 - - - +
227A VAL* 1.4 73.8 - - + +
229A PHE* 1.4 65.2 + - - +
231A ILE* 3.0 21.0 + - - +
232A VAL* 3.1 25.6 + - + +
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Residues in contact with PHE 229 (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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101A VAL* 6.5 1.6 - - + -
105A ILE* 5.5 4.5 - - + -
185A PRO* 5.4 3.1 - - + -
188A LEU* 3.6 45.5 - - + -
225A GLY 3.2 16.6 + - - +
226A LEU* 4.1 9.0 - - + +
227A VAL 3.6 0.2 - - - -
228A VAL* 1.4 78.4 - - - +
230A SER* 1.3 63.3 + - - +
232A VAL* 3.4 10.3 + - + +
233A PHE* 2.8 65.3 + + + +
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE 4.6 0.2 - - - -
101A VAL* 3.4 37.4 + - - +
104A LEU* 3.7 25.7 - - - -
105A ILE* 3.6 15.8 + - - +
226A LEU* 2.7 28.0 + - - +
227A VAL 3.8 2.2 - - - -
229A PHE* 1.3 76.4 - - - +
231A ILE* 1.4 52.8 + - - +
233A PHE* 3.3 1.3 + - - -
234A GLY* 2.8 32.2 + - - -
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Residues in contact with ILE 231 (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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104A LEU* 3.7 19.1 - - + -
108A LEU* 3.8 28.7 - - + +
227A VAL* 3.1 39.3 + - + +
228A VAL* 3.0 11.2 + - + +
230A SER* 1.4 74.1 - - - +
232A VAL* 1.4 59.7 + - + +
234A GLY* 3.3 2.1 + - - -
235A ILE* 3.1 38.3 + - + +
369A PHE* 4.5 7.4 - - + -
373A VAL* 3.9 17.5 - - + -
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Residues in contact with VAL 232 (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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228A VAL* 3.1 31.4 + - + +
229A PHE* 4.0 9.0 - - + +
231A ILE* 1.4 72.8 - - + +
233A PHE* 1.3 59.8 + - - +
235A ILE* 3.5 15.9 + - + +
236A ALA* 3.0 27.4 + - - +
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Residues in contact with PHE 233 (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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105A ILE* 3.8 29.8 - - + -
229A PHE* 2.8 50.1 + + + +
230A SER* 3.7 4.7 - - - +
232A VAL* 1.3 72.8 - - - +
234A GLY* 1.3 63.7 + - - +
236A ALA* 3.3 10.4 + - + +
237A LEU* 3.1 45.3 + - + +
247A LEU* 4.2 20.9 - - + -
251A PHE* 4.6 8.7 - + - -
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Residues in contact with GLY 234 (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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105A ILE* 3.4 28.5 - - - +
108A LEU* 4.1 6.3 - - - -
109A ALA* 3.3 18.8 - - - +
230A SER 2.8 16.5 + - - -
231A ILE 3.3 3.1 + - - -
232A VAL 3.3 0.2 - - - -
233A PHE* 1.3 73.4 - - - +
235A ILE* 1.3 56.8 + - - +
237A LEU* 3.3 2.5 + - - -
238A GLY 3.0 22.3 + - - -
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Residues in contact with ILE 235 (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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108A LEU* 3.8 28.2 - - + +
116A SER* 5.7 4.5 - - - -
231A ILE* 3.1 30.7 + - + +
232A VAL* 3.6 18.4 - - + +
234A GLY* 1.3 75.5 - - - +
236A ALA* 1.3 51.7 + - - +
238A GLY* 3.2 3.7 + - - -
239A LYS* 2.8 37.3 + - + +
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Residues in contact with ALA 236 (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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232A VAL 3.0 13.5 + - - +
233A PHE* 3.5 18.8 - - + +
234A GLY 3.3 0.4 - - - -
235A ILE* 1.3 77.9 - - - +
237A LEU* 1.4 60.2 + - + +
239A LYS* 3.5 11.0 + - - +
240A MET* 3.3 36.3 + - + +
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Residues in contact with LEU 237 (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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105A ILE* 3.7 31.2 - - + +
109A ALA* 4.1 9.2 - - + -
233A PHE* 3.1 30.6 + - + +
234A GLY 3.3 6.9 + - - +
236A ALA* 1.4 74.2 - - + +
238A GLY* 1.3 59.7 + - - +
240A MET* 3.0 48.5 - - + +
241A GLY 4.5 0.7 - - - +
244A GLY* 3.9 16.4 - - - +
247A LEU* 3.7 37.7 - - + -
248A VAL* 4.2 17.1 - - + +
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Residues in contact with GLY 238 (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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108A LEU 5.1 1.3 - - - -
109A ALA* 4.0 20.3 - - - +
111A LEU 5.7 2.0 - - - -
234A GLY 3.0 12.9 + - - -
235A ILE* 3.2 5.6 + - - -
237A LEU* 1.3 77.5 - - - +
239A LYS* 1.4 60.5 + - - +
240A MET 3.3 6.8 - - - +
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Residues in contact with LYS 239 (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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235A ILE* 2.8 16.8 + - + +
236A ALA* 3.5 14.8 - - - +
237A LEU 3.3 0.2 - - - -
238A GLY* 1.4 76.8 - - - +
240A MET* 1.3 60.0 + - - +
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Residues in contact with MET 240 (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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236A ALA* 3.3 23.5 + - + +
237A LEU* 3.0 48.8 - - + +
238A GLY 3.3 6.8 - - - +
239A LYS* 1.3 80.3 - - - +
241A GLY* 1.3 62.2 + - - +
243A GLN* 4.6 16.2 - - + -
244A GLY* 3.7 18.6 - - - +
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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