Contacts of the helix formed by residues 239 - 253 (chain A) in PDB entry 1SHL
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 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ASP* 3.0 20.4 + - - -
184A GLN* 2.6 34.9 + - - -
226A VAL* 4.0 18.8 - - - -
238A GLY* 1.3 73.3 - - - +
240A TRP* 1.3 65.4 + - - +
241A PHE 4.3 0.7 - - - -
242A VAL* 3.2 10.7 + - - +
243A GLN* 3.0 21.1 + - - +
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Residues in contact with TRP 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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226A VAL* 4.8 20.6 - - + +
238A GLY 3.6 1.7 + - - -
239A SER* 1.3 72.8 - - - +
241A PHE* 1.3 56.6 - - - +
243A GLN* 3.6 15.7 + - - +
244A ALA* 3.0 30.7 + - - +
269A VAL* 4.2 19.3 - - + +
272A HIS* 2.9 64.7 + + + +
273A PHE* 4.1 35.9 - + - -
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Residues in contact with PHE 241 (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 PHE* 5.1 4.0 - + + -
183A ILE 4.3 12.6 - - - -
184A GLN* 3.7 22.2 - - + +
222A ALA* 4.1 32.1 - - + -
224A SER* 3.5 33.9 - - - +
226A VAL* 5.0 4.5 - - + +
239A SER* 3.2 1.3 - - - -
240A TRP* 1.3 75.0 - - - +
242A VAL* 1.3 73.8 + - + +
244A ALA* 3.1 4.5 + - - +
245A LEU* 2.9 46.8 + - + +
262A LEU* 5.4 2.5 - - + -
265A VAL* 3.7 24.7 - - + -
269A VAL* 4.1 11.9 - - + +
289A PRO* 3.8 22.9 - - + -
290A CYS 5.9 0.2 - - - -
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Residues in contact with VAL 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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93A ASP* 3.5 48.9 - - + +
96A ALA* 4.5 4.7 - - + -
97A LEU* 3.9 27.8 - - + -
142A LEU* 4.4 9.4 - - + -
184A GLN* 3.8 7.9 - - + +
239A SER* 3.2 18.0 + - - +
241A PHE* 1.3 85.7 - - + +
243A GLN* 1.3 60.8 + - - +
245A LEU* 3.0 9.5 + - + +
246A CYS* 2.8 36.1 + - - +
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Residues in contact with GLN 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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92A LYS* 5.9 0.9 - - - +
93A ASP* 5.1 0.2 + - - -
96A ALA* 6.2 1.3 - - - -
237A ARG* 3.5 39.9 + - + +
238A GLY 3.3 22.3 + - - +
239A SER 3.0 13.1 + - - +
240A TRP* 3.8 17.6 - - - +
242A VAL* 1.3 77.9 - - - +
244A ALA* 1.3 57.5 + - - +
246A CYS* 3.7 4.7 + - - +
247A SER* 3.2 28.9 + - - -
272A HIS* 5.8 3.9 - - - -
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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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240A TRP 3.0 18.8 + - - +
241A PHE 3.1 3.8 + - - +
243A GLN* 1.3 72.5 - - - +
245A LEU* 1.3 66.6 + - - +
247A SER* 3.3 1.3 + - - -
248A ILE* 3.0 31.9 + - - +
265A VAL* 4.1 16.2 - - + +
268A ARG* 4.0 37.7 - - + +
269A VAL* 4.5 2.9 - - + +
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Residues in contact with LEU 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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97A LEU* 3.9 26.0 - - + -
101A PHE* 4.4 2.5 - - + -
182A PHE* 3.8 30.5 - - + -
241A PHE* 2.9 30.0 + - + +
242A VAL* 3.5 7.4 - - - +
244A ALA* 1.3 76.0 - - - +
246A CYS* 1.3 59.6 + - - +
248A ILE* 4.3 0.7 - - - +
249A LEU* 3.1 60.5 + - + +
258A ILE* 6.3 0.4 - - + -
261A ILE* 4.8 1.6 - - + -
262A LEU* 4.0 27.6 - - + -
265A VAL* 3.7 17.2 - - + +
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Residues in contact with CYS 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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96A ALA* 3.4 47.6 - - + +
97A LEU* 3.6 22.7 - - - -
100A CYS* 3.8 18.1 - - + -
242A VAL* 2.8 19.0 + - - +
243A GLN* 4.1 4.5 - - - +
245A LEU* 1.3 75.4 - - - +
247A SER* 1.3 58.2 + - - +
249A LEU* 3.5 1.0 + - - +
250A GLU* 2.8 37.3 + - - +
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Residues in contact with SER 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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243A GLN 3.2 19.0 + - - -
244A ALA 3.8 3.6 - - - -
246A CYS* 1.3 77.1 - - - +
248A ILE* 1.3 61.9 + - - +
250A GLU* 3.5 6.3 + - - +
251A GLU* 3.3 23.9 + - - +
268A ARG* 3.3 23.9 + - - -
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Residues in contact with ILE 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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244A ALA 3.0 19.4 + - - +
245A LEU 4.3 0.9 - - - +
247A SER* 1.3 74.4 - - - +
249A LEU* 1.3 53.7 + - - +
251A GLU* 3.2 4.5 + - - +
252A HIS* 2.7 48.3 + - + +
261A ILE* 3.8 34.8 - - + +
264A ARG* 3.9 34.3 - - + -
265A VAL* 4.2 9.2 - - + +
268A ARG* 2.9 34.3 - - - +
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Residues in contact with LEU 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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100A CYS* 3.5 25.1 - - - -
101A PHE* 3.9 19.1 - - + -
104A LEU* 4.0 26.9 - - + +
182A PHE* 5.3 2.2 - - + -
245A LEU* 3.1 44.3 + - + +
248A ILE* 1.3 73.1 - - - +
250A GLU* 1.3 59.4 + - - +
251A GLU 3.0 4.9 - - - -
253A GLY* 2.9 40.6 + - - +
254A LYS* 6.1 0.3 - - - +
258A ILE* 5.2 2.2 - - + -
261A ILE* 3.9 24.5 - - + -
301A PHE* 4.0 14.6 - - + -
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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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96A ALA 5.2 0.9 - - - +
99A LYS* 4.5 20.8 + - - +
100A CYS* 3.8 25.2 + - - +
103A SER* 3.7 27.1 + - - -
246A CYS* 2.8 23.1 + - - +
247A SER* 3.6 7.6 - - - +
249A LEU* 1.3 76.0 - - - +
251A GLU* 1.3 58.9 + - + +
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Residues in contact with GLU 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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247A SER 3.3 15.0 - - - +
248A ILE* 3.7 3.8 - - - +
249A LEU 3.0 0.6 - - - -
250A GLU* 1.3 81.6 - - - +
252A HIS* 1.3 88.2 + - + +
253A GLY 3.7 0.7 - - - -
254A LYS 5.4 0.2 + - - -
255A ASP* 3.9 7.3 - - - +
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Residues in contact with HIS 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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248A ILE* 2.7 22.9 + - + +
251A GLU* 1.3 105.4 + - + +
253A GLY* 1.3 56.2 + - - +
254A LYS 2.8 16.9 + - - -
255A ASP* 2.7 38.6 + - - -
256A LEU* 3.0 35.3 + - + +
261A ILE* 3.7 8.1 - - + +
264A ARG* 3.7 26.1 + - - -
58B TYR* 5.3 2.0 + - - -
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Residues in contact with GLY 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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104A LEU* 3.9 13.9 - - - +
248A ILE 3.8 0.8 + - - -
249A LEU* 2.9 26.9 + - - -
251A GLU 3.7 0.6 - - - -
252A HIS* 1.3 75.4 - - - +
254A LYS* 1.3 61.2 + - - +
256A LEU 4.7 3.0 - - - +
261A ILE* 3.9 14.8 - - - -
301A PHE* 3.3 34.0 + - - +
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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