Contacts of the helix formed by residues 244 - 258 (chain A) in PDB entry 5L0P
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 SER 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A GLU 5.0 0.5 + - - -
155A ARG* 4.3 2.7 - - - +
214A LEU* 3.4 44.9 - - - +
215A ARG 4.1 5.4 + - - -
217A ILE* 5.0 4.9 - - - +
241A SER* 3.3 11.7 + - - -
243A HIS* 1.3 91.1 + - - +
245A GLY* 1.3 66.2 + - - +
246A ASP* 3.3 4.0 - - - -
247A VAL* 3.2 8.8 + - - +
248A LEU* 2.9 28.6 + - - +
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Residues in contact with GLY 245 (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 PHE* 3.4 37.7 - - - +
238A ARG* 4.1 1.1 - - - -
241A SER* 2.7 29.4 + - - -
242A PRO 4.7 0.4 + - - -
243A HIS 3.9 0.2 - - - -
244A SER* 1.3 70.9 - - - +
246A ASP* 1.3 58.0 + - - +
248A LEU* 3.2 5.2 + - - -
249A TYR* 2.8 26.9 + - - +
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Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.4 15.6 - - - +
151A ASP* 3.7 33.1 - - - +
154A TYR* 5.4 0.7 - - - -
155A ARG* 2.9 45.7 + - - +
234A LYS* 3.9 12.3 - - - +
238A ARG* 4.0 23.0 + - - +
242A PRO 6.0 0.4 - - - -
244A SER 3.9 1.7 - - - -
245A GLY* 1.3 69.9 + - - +
247A VAL* 1.3 71.9 + - - +
249A TYR* 3.4 2.1 + - - +
250A GLU* 2.9 27.4 + - - +
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Residues in contact with VAL 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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139A MET* 3.6 38.1 - - + -
143A ALA* 4.1 21.8 - - + +
146A LEU* 4.1 16.3 - - + +
147A LEU* 3.8 12.5 - - + +
155A ARG* 4.7 0.7 - - - +
212A PHE* 4.5 10.3 - - + -
214A LEU* 4.4 21.1 - - + -
244A SER* 3.2 8.9 + - - +
246A ASP* 1.3 85.9 + - - +
248A LEU* 1.3 55.4 + - + +
250A GLU* 3.2 4.5 + - - +
251A LEU* 2.7 33.7 + - + +
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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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204A TRP* 3.4 19.9 - - + -
205A LEU* 3.7 30.5 - - + -
208A ALA* 3.7 29.6 - - + -
214A LEU* 4.1 13.5 - - + -
217A ILE* 4.2 14.4 - - + -
222A PHE* 4.1 16.6 - - + -
237A PHE* 4.0 10.3 - - + -
241A SER* 4.4 8.1 - - - +
244A SER* 2.9 27.5 + - - +
245A GLY* 3.2 4.9 + - - +
247A VAL* 1.3 78.1 - - + +
249A TYR* 1.3 56.5 + - - +
251A LEU* 3.2 9.2 + - + +
252A LEU* 2.9 24.6 + - - +
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Residues in contact with TYR 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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232A LEU 4.0 9.4 - - - -
233A THR* 4.0 4.7 - - - -
234A LYS* 3.6 45.7 + - + -
237A PHE* 3.4 37.1 - + + -
245A GLY 2.8 20.1 + - - +
246A ASP 3.7 2.9 - - - +
248A LEU* 1.3 67.9 - - - +
250A GLU* 1.3 79.4 + - - +
252A LEU* 3.3 3.9 + - + +
253A GLN* 2.9 71.4 + - + +
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Residues in contact with GLU 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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146A LEU* 3.4 36.1 - - + +
147A LEU* 4.7 0.4 - - - -
148A THR* 3.7 15.8 - - + +
151A ASP* 4.0 4.0 - - - +
234A LYS* 2.8 33.8 + - - +
246A ASP 2.9 23.9 + - - +
247A VAL* 3.9 3.1 - - - +
249A TYR* 1.3 83.8 - - - +
251A LEU* 1.3 62.1 + - - +
253A GLN* 3.7 11.4 - - - +
254A HIS* 2.8 29.3 + - - +
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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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146A LEU* 4.1 12.7 - - + +
183A ILE* 4.5 14.4 - - + -
204A TRP* 3.7 26.2 - - + +
207A TRP* 4.1 9.2 - - + -
208A ALA* 3.7 29.8 - - + -
212A PHE* 3.8 30.7 - - + -
247A VAL* 2.7 16.4 + - + +
248A LEU* 3.3 12.1 - - + +
250A GLU* 1.3 77.8 - - - +
252A LEU* 1.3 64.4 + - - +
254A HIS* 3.0 6.9 + - + +
255A ILE* 2.9 38.7 + - + +
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Residues in contact with LEU 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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193A PRO* 3.9 32.8 - - + -
196A TRP* 4.6 16.2 - - + -
204A TRP* 4.0 9.4 - - + -
229A LEU* 4.2 22.2 - - + +
230A LEU* 4.3 19.7 - - + -
237A PHE* 3.9 25.6 - - + -
248A LEU 2.9 13.8 + - - +
249A TYR* 3.5 8.5 - - + +
251A LEU* 1.3 76.6 - - - +
253A GLN* 1.3 74.3 + - - +
255A ILE* 3.3 4.7 + - + +
256A LEU* 3.1 24.1 + - + +
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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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230A LEU* 5.9 0.6 - - - +
249A TYR* 2.9 74.9 + - + +
250A GLU* 3.8 15.0 - - - +
251A LEU 3.2 0.2 - - - -
252A LEU* 1.3 88.9 - - - +
254A HIS* 1.3 68.0 + - - +
256A LEU* 3.4 20.1 + - - +
257A LYS* 3.2 19.9 + - - +
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Residues in contact with HIS 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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146A LEU* 4.4 17.3 - - + +
183A ILE* 3.0 44.2 + - + +
250A GLU 2.8 14.0 + - - +
251A LEU* 3.4 9.2 - - + +
253A GLN* 1.3 75.9 - - - +
255A ILE* 1.3 65.7 + - - +
257A LYS* 2.9 17.7 + - - +
258A GLN* 2.9 32.7 + - + +
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Residues in contact with ILE 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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183A ILE* 4.8 8.7 - - + -
185A LEU* 3.8 39.0 - - + -
191A LEU 5.7 0.7 - - - +
193A PRO* 3.8 30.4 - - + +
196A TRP* 4.4 5.4 - - + -
204A TRP* 3.5 29.8 - - + +
251A LEU* 2.9 32.8 + - + +
252A LEU* 3.3 6.3 + - + +
254A HIS* 1.3 80.7 - - - +
256A LEU* 1.3 62.2 + - - +
258A GLN* 3.5 17.8 - - - +
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Residues in contact with LEU 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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193A PRO* 4.1 27.1 - - + -
194A ILE 5.8 0.2 - - - +
230A LEU* 4.1 29.6 - - + -
252A LEU* 3.1 20.9 + - + +
253A GLN* 3.8 27.8 - - - +
254A HIS 3.1 1.0 - - - -
255A ILE* 1.3 78.5 - - - +
257A LYS* 1.3 63.1 - - - +
258A GLN 4.5 1.6 - - - +
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Residues in contact with LYS 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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253A GLN 3.2 11.7 + - - +
254A HIS* 2.9 8.7 + - - +
256A LEU* 1.3 79.5 - - - +
258A GLN* 1.3 64.9 + - - +
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Residues in contact with GLN 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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254A HIS* 2.9 38.3 + - + +
255A ILE* 3.5 17.3 - - - +
256A LEU 4.5 1.9 - - - +
257A LYS* 1.3 83.0 - - - +
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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