Contacts of the helix formed by residues 241 - 257 (chain A) in PDB entry 5A36
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 ASP 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TRP* 3.9 15.8 - - + +
39A GLN* 3.1 37.1 + - + +
40A GLN* 2.8 38.3 + - - +
239A LYS 4.7 0.2 - - - -
240A PRO* 1.3 70.1 - - - +
242A GLU* 1.3 61.4 + - - +
243A ARG* 3.1 8.9 + - - +
244A ALA* 2.8 30.1 + - + +
245A ILE* 3.1 23.8 + - - +
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Residues in contact with GLU 242 (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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154A LYS* 3.0 33.0 + - - -
176A PHE* 3.1 32.3 + - + +
177A HIS* 3.6 23.3 + - + -
239A LYS* 6.1 1.3 - - - -
240A PRO 3.3 4.6 + - - -
241A ASP* 1.3 71.7 + - - +
243A ARG* 1.3 71.2 + - + +
245A ILE* 4.0 0.3 - - - +
246A MET* 2.8 42.5 + - + +
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Residues in contact with ARG 243 (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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40A GLN* 3.8 21.9 + - - +
44A PHE* 3.9 9.4 - - + -
131A LEU 5.7 0.2 - - - -
132A GLY* 4.5 13.5 + - - -
135A TRP* 3.4 69.9 - - + +
241A ASP* 3.1 7.4 + - - +
242A GLU* 1.3 85.1 + - + +
244A ALA* 1.3 60.4 + - - +
246A MET* 4.1 5.8 - - + -
247A THR* 2.7 30.4 + - - -
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Residues in contact with ALA 244 (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 GLN* 3.9 21.3 - - + +
40A GLN* 4.5 2.5 - - - +
43A THR* 3.4 39.6 - - - +
44A PHE* 4.2 4.4 - - - -
229A LEU* 3.9 7.6 - - + +
234A ILE* 6.3 1.3 - - + -
241A ASP* 2.8 27.1 + - + +
242A GLU 3.3 0.2 - - - -
243A ARG* 1.3 73.7 - - - +
245A ILE* 1.4 62.0 + - + +
247A THR 3.3 1.0 + - - -
248A TYR 3.2 16.8 + - - -
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Residues in contact with ILE 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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176A PHE* 3.5 27.1 - - + +
177A HIS* 4.0 9.0 - - - +
180A TRP* 3.9 33.2 - - + +
186A LEU* 6.1 0.7 - - + -
229A LEU* 4.3 12.3 - - + -
234A ILE* 4.3 22.9 - - + -
240A PRO* 3.5 32.1 - - + -
241A ASP 3.1 12.3 + - - +
242A GLU 3.2 0.4 + - - -
244A ALA* 1.4 76.5 - - + +
246A MET* 1.3 58.4 + - - +
248A TYR* 3.1 3.8 + - - +
249A VAL* 2.9 41.2 + - + +
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Residues in contact with MET 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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135A TRP* 3.7 30.1 - - + -
139A LEU* 6.1 0.2 - - - -
143A ILE* 3.9 17.4 - - + +
154A LYS* 3.7 51.6 - - + +
157A LEU* 3.9 4.6 - - + +
176A PHE* 3.5 28.7 - - + -
242A GLU* 2.8 43.0 + - + +
243A ARG* 3.9 6.1 - - + +
245A ILE* 1.3 68.4 - - - +
247A THR* 1.3 61.5 + - - +
249A VAL* 4.6 4.9 - - - -
250A SER* 2.8 33.4 + - - -
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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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43A THR* 3.7 14.6 - - + +
44A PHE* 3.6 13.1 - - + -
47A TRP* 3.4 41.1 - - + -
135A TRP* 3.7 2.0 - - - -
138A ILE* 3.6 25.5 - - + +
228A MET* 4.4 2.0 - - - -
243A ARG 2.7 19.8 + - - -
244A ALA 3.5 8.5 - - - -
245A ILE 3.3 0.2 - - - -
246A MET* 1.3 75.4 - - - +
248A TYR* 1.3 63.0 + - - +
250A SER* 2.7 22.4 + - - -
251A CYS* 3.5 8.7 + - - -
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Residues in contact with TYR 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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43A THR* 4.5 0.2 - - - +
186A LEU* 4.0 19.1 - - + -
215A ALA* 5.8 0.4 - - + -
216A MET* 3.4 41.6 + - + +
219A ALA* 3.5 15.8 - - - +
225A ILE* 3.7 13.2 + - + -
226A PRO 3.5 22.8 + - - -
228A MET* 3.6 32.3 - - + -
229A LEU* 3.7 38.8 - - + -
244A ALA 3.2 2.4 + - - +
245A ILE 3.1 5.6 + - - +
247A THR* 1.3 79.4 - - - +
249A VAL* 1.3 62.8 + - + +
251A CYS* 3.0 21.2 + - - +
252A PHE* 3.2 32.0 - + - -
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Residues in contact with VAL 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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157A LEU* 4.1 14.8 - - + -
160A TRP* 4.6 1.3 - - + -
161A CYS* 3.4 31.6 - - - -
176A PHE* 4.4 3.4 - - + -
180A TRP* 4.2 21.5 - - + -
186A LEU* 4.2 13.7 - - + -
189A LEU* 4.3 10.3 - - + -
245A ILE* 2.9 39.1 + - + +
246A MET* 4.2 2.9 - - - +
248A TYR* 1.3 72.1 - - + +
250A SER* 1.3 62.6 + - - +
252A PHE* 2.9 20.7 + - - +
253A TYR* 3.1 10.9 + - - +
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Residues in contact with SER 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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47A TRP* 4.9 2.4 + - - -
138A ILE* 5.0 0.2 - - - +
142A ALA* 4.0 22.4 - - - +
143A ILE* 3.5 24.5 - - - +
146A ILE* 4.8 1.1 - - - -
157A LEU* 3.9 12.5 - - - +
246A MET 2.8 17.7 + - - -
247A THR* 2.7 22.0 + - - -
249A VAL* 1.3 77.0 - - - +
251A CYS* 1.4 56.8 + - - +
253A TYR* 3.3 3.0 + - - +
254A HIS* 2.9 36.1 + - - -
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Residues in contact with CYS 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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47A TRP* 4.3 14.8 - - - -
50A SER* 5.2 3.4 - - - -
51A HIS* 6.0 1.3 - - - -
225A ILE* 3.8 27.2 - - + +
228A MET* 3.7 27.6 - - + -
247A THR 4.2 7.4 - - - -
248A TYR 3.0 11.5 + - - +
250A SER* 1.4 78.5 + - - +
252A PHE* 1.3 60.8 + - - +
254A HIS* 3.5 7.3 + - - +
255A ALA* 2.9 30.1 + - - +
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Residues in contact with PHE 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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160A TRP* 4.2 1.8 - - + -
186A LEU* 4.6 11.9 - - + -
189A LEU* 4.6 19.1 - - + -
190A ILE* 3.6 31.0 - - + -
215A ALA* 4.8 2.2 - - + -
219A ALA* 3.6 17.7 - - + -
223A LEU* 4.2 7.0 - - + -
225A ILE* 4.2 10.1 - - + -
248A TYR* 3.2 59.5 - + - -
249A VAL* 2.9 14.8 + - - +
251A CYS* 1.3 75.4 - - - +
253A TYR* 1.3 58.1 + - - +
255A ALA* 3.3 2.1 + - - +
256A PHE* 2.9 64.5 + + + -
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Residues in contact with TYR 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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146A ILE* 3.8 43.5 - - + +
147A SER 4.0 15.8 + - - -
148A VAL* 4.1 6.1 - - + +
157A LEU* 3.9 20.6 - - + -
160A TRP* 3.5 55.5 - + + -
249A VAL 3.1 6.0 + - - +
250A SER 3.6 7.9 - - - +
251A CYS 3.3 0.2 - - - -
252A PHE* 1.3 75.4 - - - +
254A HIS* 1.3 77.7 + + - +
256A PHE* 3.2 1.2 + - - +
257A ALA* 2.9 47.7 + - + +
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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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141A PHE 5.1 2.2 + - - -
142A ALA* 2.6 43.7 + - + -
146A ILE* 4.3 6.4 - - + +
250A SER 2.9 27.7 + - - +
251A CYS* 4.0 7.0 - - - +
253A TYR* 1.3 94.2 - + - +
255A ALA* 1.3 62.1 + - - +
257A ALA* 3.6 15.0 - - - +
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A LEU* 4.7 16.8 - - + +
225A ILE* 4.1 19.1 - - + -
251A CYS 2.9 18.7 + - - +
252A PHE* 3.7 4.7 - - - +
254A HIS* 1.3 76.8 - - - +
256A PHE* 1.3 70.8 + - + +
257A ALA 4.5 1.7 - - - +
89B ARG* 5.9 1.9 + - - +
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Residues in contact with PHE 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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160A TRP* 4.0 8.5 - + + -
189A LEU* 3.5 13.0 - - + -
190A ILE* 4.1 9.4 - - + -
193A HIS* 3.1 67.2 - + + +
194A ARG* 4.7 7.6 - - + -
223A LEU* 3.7 40.6 - - + -
252A PHE* 2.9 44.3 + + + +
253A TYR 4.1 1.1 - - - +
255A ALA* 1.3 82.6 - - + +
257A ALA* 1.3 63.8 + - - +
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Residues in contact with ALA 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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160A TRP* 5.9 2.2 - - + +
253A TYR* 2.9 43.8 + - + +
254A HIS* 3.6 12.7 - - - +
255A ALA 3.6 2.3 - - - +
256A PHE* 1.3 81.6 - - - +
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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