Contacts of the helix formed by residues 237 - 256 (chain A) in PDB entry 1L9X
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 ALA 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A GLU* 5.6 1.3 - - - +
166A LEU* 3.8 18.8 - - + -
235A SER* 3.3 16.5 + - - +
236A HIS* 1.3 80.1 - - - +
238A PRO* 1.3 76.7 - - + +
239A ASN* 4.4 2.2 - - + +
240A ALA* 2.8 12.1 + - - +
241A VAL* 3.0 10.6 + - - +
7B ALA 5.4 5.2 - - - +
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Residues in contact with PRO 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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236A HIS 3.6 3.1 - - - +
237A ALA* 1.3 85.3 - - + +
239A ASN* 1.3 61.0 + - - +
241A VAL* 3.2 7.4 + - + +
242A LYS* 2.9 29.4 + - - +
249B GLU* 4.4 16.7 - - + +
253B ASN* 4.8 7.4 - - + +
256B ARG* 3.6 38.4 - - - +
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Residues in contact with ASN 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 3.8 19.5 - - + +
160A SER* 3.4 18.1 + - - -
164A GLU* 3.2 23.8 + - - +
166A LEU* 3.5 21.1 - - + -
237A ALA* 3.2 1.4 - - - +
238A PRO* 1.3 80.6 - - - +
240A ALA* 1.3 57.1 + - - +
242A LYS* 3.8 14.0 + - - +
243A THR* 2.8 33.8 + - - -
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.5 32.8 - - + +
221A PRO* 4.8 0.7 - - - +
224A ALA* 3.5 12.0 - - + +
235A SER* 3.4 37.7 - - - +
237A ALA 2.8 10.0 + - - +
239A ASN* 1.3 78.1 - - - +
241A VAL* 1.3 63.6 + - - +
243A THR* 3.4 6.1 + - - +
244A ALA* 3.2 17.2 + - - +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ALA* 3.6 27.8 - - - +
225A PRO* 4.0 10.3 - - + +
236A HIS* 3.8 12.6 - - - +
237A ALA 3.0 12.5 + - - +
238A PRO* 3.5 9.6 - - + +
240A ALA* 1.3 78.4 - - - +
242A LYS* 1.3 62.1 + - - +
244A ALA* 3.2 5.9 + - - +
245A PHE* 3.1 19.2 + - - +
42B SER 3.4 24.9 - - - +
43B ALA* 3.7 19.7 - - - +
44B GLY* 4.0 10.3 - - - +
245B PHE* 4.0 8.0 - - + -
256B ARG* 4.8 1.1 - - - +
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Residues in contact with LYS 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 PRO* 4.4 13.7 - - - +
157A LEU* 3.9 18.1 - - + +
238A PRO 2.9 15.8 + - - +
239A ASN* 3.9 13.7 + - - +
241A VAL* 1.3 75.7 - - - +
243A THR* 1.3 64.4 + - - +
245A PHE* 3.2 1.9 + - - +
246A TYR* 3.0 45.0 + - + -
152B ASN* 4.7 6.1 + - - +
154B PRO* 5.7 0.6 - - - +
245B PHE* 3.7 16.8 - - + -
246B TYR* 2.9 41.4 + - - -
249B GLU* 3.8 17.2 + - - +
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Residues in contact with THR 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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150A PHE* 5.8 0.4 - - + -
153A PHE* 4.3 7.6 - - + -
157A LEU* 3.7 13.6 - - - +
161A LEU* 3.5 42.1 - - + +
166A LEU* 5.8 0.7 - - - -
219A TRP* 3.8 32.3 - - + -
239A ASN 2.8 24.6 + - - -
240A ALA* 3.6 7.2 - - - -
242A LYS* 1.3 74.9 - - - +
244A ALA* 1.3 64.5 + - - +
246A TYR* 3.3 2.6 + - - +
247A LEU* 3.0 25.7 + - + +
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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 TYR* 3.3 21.8 - - + -
221A PRO* 3.3 35.6 - - - +
225A PRO* 3.6 18.8 - - + -
240A ALA 3.2 6.6 + - - +
241A VAL 3.3 9.9 - - - +
242A LYS 3.2 0.2 - - - -
243A THR* 1.3 79.9 - - - +
245A PHE* 1.3 64.4 + - - +
247A LEU* 3.3 0.7 + - - -
248A ALA* 3.0 20.0 + - - +
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Residues in contact with PHE 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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42A SER* 3.4 39.7 - - - +
43A ALA* 4.3 4.3 - - + -
225A PRO* 5.5 0.2 - - - +
241A VAL 3.1 5.0 + - - +
242A LYS 3.2 6.2 + - - +
244A ALA* 1.3 78.2 - - - +
246A TYR* 1.3 70.6 + + - +
248A ALA* 3.2 6.0 + - - +
249A GLU* 2.8 50.3 + - + +
42B SER 5.8 0.2 - - - +
241B VAL* 4.0 11.0 - - + -
242B LYS* 3.7 46.0 - - + -
245B PHE* 3.7 51.8 - + + -
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Residues in contact with TYR 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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152A ASN* 3.3 28.9 - - + -
153A PHE* 3.5 30.3 - + + -
154A PRO* 3.6 20.0 - - + +
157A LEU* 4.0 6.7 - - + -
242A LYS* 3.0 44.5 + - + +
243A THR 3.3 0.4 + - - +
245A PHE* 1.3 89.7 - + - +
247A LEU* 1.3 55.9 + - - +
249A GLU* 3.6 14.5 - - - +
250A PHE* 3.0 27.4 + - - +
154B PRO* 4.3 4.3 - - - +
242B LYS* 3.7 28.4 + - - +
246B TYR* 2.6 39.3 + + - -
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Residues in contact with LEU 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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39A TYR* 3.3 14.4 + - - +
107A TRP* 4.2 19.5 - - + -
149A MET* 3.6 35.9 - - + +
150A PHE* 4.3 4.5 - - + -
153A PHE* 3.6 22.2 - - + -
217A VAL* 4.6 2.0 - - + -
219A TRP* 3.4 38.8 - - + -
221A PRO* 4.1 11.7 - - + -
243A THR* 3.0 19.1 + - + +
244A ALA 3.9 1.8 - - - +
246A TYR* 1.3 73.9 - - - +
248A ALA* 1.3 65.4 + - - +
250A PHE* 3.3 5.7 + - + +
251A PHE* 3.1 23.2 + - - +
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Residues in contact with ALA 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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39A TYR* 3.4 46.1 + - + +
40A LEU* 4.9 3.1 - - - -
42A SER* 4.2 4.9 - - - +
43A ALA* 3.5 10.8 - - + -
244A ALA 3.0 17.0 + - - +
245A PHE 3.5 3.8 - - - +
247A LEU* 1.3 77.4 - - - +
249A GLU* 1.3 62.2 + - - +
251A PHE* 3.2 5.3 + - - +
252A VAL* 2.9 28.5 + - - +
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Residues in contact with GLU 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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43A ALA* 3.6 13.3 - - + +
152A ASN* 4.7 9.7 + - - +
245A PHE* 2.8 34.4 + - + +
246A TYR* 3.6 19.0 - - - +
248A ALA* 1.3 77.1 - - - +
250A PHE* 1.3 62.3 + - - +
252A VAL* 3.4 1.8 + - - +
253A ASN* 3.0 25.2 + - + +
256A ARG* 4.9 5.3 + - - +
238B PRO* 4.2 18.2 - - + +
241B VAL* 6.4 0.9 - - + -
242B LYS* 2.8 47.6 + - - +
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Residues in contact with PHE 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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107A TRP* 4.1 9.4 - + - -
148A ARG* 3.3 32.8 - - + -
149A MET* 3.6 37.2 - - + +
152A ASN* 5.8 8.1 - - - +
153A PHE* 5.7 0.2 - - + -
215A TYR* 3.5 53.8 - + - -
246A TYR 3.0 18.0 + - - +
247A LEU* 3.5 6.3 - - - +
248A ALA 3.2 0.2 - - - -
249A GLU* 1.3 76.9 - - - +
251A PHE* 1.3 67.9 + - - +
253A ASN* 3.2 10.5 + - + +
254A GLU* 3.0 42.4 + - + +
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Residues in contact with PHE 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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12A ILE* 3.7 28.3 - - + -
39A TYR* 5.7 2.0 - + + +
40A LEU* 3.7 24.2 - - + -
68A GLY 4.6 0.9 - - - -
69A ILE 3.4 32.5 - - - -
70A LEU* 4.3 5.4 - - + -
105A PRO* 3.7 35.2 - - + -
106A VAL 4.2 0.9 - - - -
107A TRP* 3.6 44.2 - + + -
215A TYR* 4.8 4.3 - + - -
247A LEU 3.1 12.7 + - - +
248A ALA* 3.8 4.7 - - - +
250A PHE* 1.3 84.1 - - - +
252A VAL* 1.3 62.2 + - - +
254A GLU* 3.0 8.5 + - + +
255A ALA* 3.0 19.4 + - - +
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Residues in contact with VAL 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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10A PRO* 3.6 26.0 - - + -
12A ILE* 4.0 9.2 - - + -
40A LEU* 4.0 9.0 - - + +
43A ALA* 3.4 34.8 - - + +
44A GLY 4.2 1.1 - - - +
45A ALA* 3.7 23.1 - - + -
248A ALA 2.9 20.5 + - - +
249A GLU* 3.9 3.8 - - - +
251A PHE* 1.3 76.1 - - - +
253A ASN* 1.3 63.4 + - - +
255A ALA* 3.1 16.8 + - - +
256A ARG* 3.2 24.2 + - - +
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Residues in contact with ASN 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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152A ASN* 5.6 6.6 - - - +
249A GLU* 3.0 16.0 + - + +
250A PHE* 3.2 12.5 + - + +
252A VAL* 1.3 76.5 - - - +
254A GLU* 1.3 65.1 + - - +
256A ARG* 3.1 45.9 + - - +
257A LYS* 3.7 25.0 - - - +
238B PRO* 4.9 4.8 - - - +
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Residues in contact with GLU 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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103A TYR* 2.6 32.2 + - + -
105A PRO* 3.7 20.2 - - + +
148A ARG* 4.9 2.0 - - - +
215A TYR* 2.5 31.8 + - + +
250A PHE* 3.0 46.1 + - + +
251A PHE* 3.0 10.7 + - - +
253A ASN* 1.3 79.2 + - - +
255A ALA* 1.3 57.6 + - - +
257A LYS* 2.7 58.4 + - - +
258A ASN* 4.7 0.2 + - - -
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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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10A PRO* 4.1 8.2 - - + +
12A ILE* 4.1 23.6 - - + -
67A ASN* 3.4 49.4 + - + +
105A PRO* 3.7 6.3 - - + +
251A PHE 3.0 11.5 + - - +
252A VAL 3.1 10.3 + - - +
254A GLU* 1.3 77.6 - - - +
256A ARG* 1.3 57.1 - - - +
257A LYS 3.1 2.1 + - - -
258A ASN* 3.6 9.5 + - - +
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Residues in contact with ARG 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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8A LYS* 3.2 52.0 + - + +
10A PRO* 4.2 18.3 - - + +
43A ALA 3.9 10.9 + - - -
44A GLY* 4.9 4.2 + - - -
249A GLU* 4.9 5.3 + - - +
252A VAL* 3.4 30.2 - - - +
253A ASN* 3.1 51.1 + - - +
255A ALA* 1.3 75.9 - - - +
257A LYS* 1.3 57.7 + - + +
258A ASN 3.3 8.1 + - - -
236B HIS 4.4 10.9 + - - -
238B PRO* 3.6 38.9 - - - +
241B VAL* 5.3 1.2 - - - +
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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