Contacts of the helix formed by residues 238 - 251 (chain A) in PDB entry 1SOT
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 PHE 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ILE* 4.8 12.3 - - + -
144A ASN 3.6 27.1 - - - -
145A ALA* 4.0 17.0 - - + -
147A ARG* 3.7 14.6 - - + -
149A PRO* 3.9 16.8 - - + -
212A LEU* 3.2 44.0 - - + +
213A MSE 2.9 36.3 + - - +
214A GLY* 4.2 1.6 - - - -
236A ILE 3.3 2.8 + - - -
237A PRO* 1.3 72.0 - - - +
239A GLN* 1.3 91.9 + - + +
241A ALA* 3.6 7.4 - - - +
242A THR* 2.8 39.6 + - - +
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Residues in contact with GLN 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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145A ALA 5.5 2.7 - - - +
147A ARG 4.8 0.9 - - - +
149A PRO* 3.7 24.7 - - - +
179A ILE* 3.6 36.5 - - + +
213A MSE 4.7 0.2 + - - -
237A PRO* 3.4 22.8 - - - +
238A PHE* 1.3 111.6 - - + +
240A LEU* 1.3 58.6 + - - +
242A THR* 3.7 5.3 + - - -
243A LYS* 3.3 31.6 + - - +
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Residues in contact with LEU 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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125A THR* 4.2 15.0 - - + -
178A ARG 4.1 10.8 - - - +
179A ILE* 3.3 31.9 - - - +
180A GLY 3.7 15.9 - - - +
181A LEU* 4.1 13.5 - - + -
189A PHE* 5.5 6.5 - - + -
236A ILE* 3.9 17.7 - - + -
237A PRO* 3.0 14.2 + - + +
239A GLN* 1.3 76.3 - - - +
241A ALA* 1.3 68.0 + - - +
242A THR 3.1 1.3 - - - -
243A LYS* 3.1 5.6 + - + +
244A ILE* 2.9 43.6 + - + +
256A ARG* 5.7 0.4 - - - +
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Residues in contact with ALA 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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85A MSE 6.0 0.9 - - + -
92A ILE* 3.9 11.6 - - + +
127A LEU* 3.8 22.1 - - + +
212A LEU* 5.9 1.8 - - + -
215A ILE* 3.8 28.7 - - + -
236A ILE* 3.7 4.6 - - + +
237A PRO 2.9 12.9 + - - +
238A PHE* 3.6 10.1 - - - +
240A LEU* 1.3 76.1 - - - +
242A THR* 1.3 63.4 + - - +
244A ILE* 3.5 1.6 + - - +
245A MSE 3.0 24.1 + - - +
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Residues in contact with THR 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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85A MSE 4.5 6.4 - - - +
92A ILE* 5.3 0.7 - - - -
143A ILE* 4.5 17.5 - - - +
238A PHE* 2.8 24.1 + - - +
239A GLN* 3.9 7.2 - - - +
241A ALA* 1.3 76.2 - - - +
243A LYS* 1.3 65.1 + - + +
245A MSE 3.3 16.5 + - + +
246A ASP* 3.1 38.3 + - - +
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Residues in contact with LYS 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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179A ILE* 3.4 42.6 + - - +
180A GLY* 4.4 5.0 - - - -
181A LEU* 5.1 5.8 - - + +
239A GLN* 3.3 17.9 + - - +
240A LEU* 3.1 14.2 + - + +
242A THR* 1.3 80.9 - - + +
244A ILE* 1.3 63.8 + - + +
246A ASP* 3.4 7.8 + - - +
247A LYS* 3.1 39.3 + - - +
324A GLU* 4.9 13.3 + - - +
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Residues in contact with ILE 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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122A ASP* 3.8 7.6 - - + +
125A THR* 3.2 46.4 - - + +
127A LEU* 4.4 16.2 - - + -
129A VAL* 5.8 0.4 - - + -
181A LEU* 4.3 10.3 - - + -
240A LEU* 2.9 37.7 + - + +
241A ALA 3.9 2.9 - - - +
243A LYS* 1.3 74.3 - - - +
245A MSE 1.3 67.3 + - - +
247A LYS* 3.2 7.7 + - - +
248A LEU* 2.9 36.3 + - + +
254A VAL* 3.8 21.3 - - + -
256A ARG* 4.2 4.3 - - - +
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Residues in contact with MSE 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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85A MSE 3.6 50.7 - - + -
86A ASP* 5.2 5.4 - - - +
88A ARG* 5.8 2.0 - - - +
90A TYR* 4.2 16.4 - - - -
92A ILE* 4.0 9.2 - - + -
129A VAL* 3.7 26.5 - - + -
241A ALA 3.0 15.9 + - - +
242A THR* 3.3 15.5 + - + +
244A ILE* 1.3 77.7 - - - +
246A ASP* 1.3 69.2 + - - +
248A LEU* 3.2 2.4 + - - +
249A ILE* 2.9 44.8 + - + +
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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
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88A ARG* 5.3 4.2 + - - -
242A THR* 3.1 32.1 + - - +
243A LYS* 3.8 8.1 - - - +
244A ILE 3.3 0.2 - - - -
245A MSE 1.3 86.7 - - - +
247A LYS* 1.3 57.9 + - + +
249A ILE* 3.2 10.5 + - - +
250A ARG* 3.0 36.3 + - - +
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Residues in contact with LYS 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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181A LEU* 3.5 27.6 - - + +
243A LYS* 3.1 24.9 + - - +
244A ILE* 3.6 4.7 - - - +
246A ASP* 1.3 76.7 - - + +
248A LEU* 1.3 57.5 + - - +
250A ARG* 4.2 30.0 - - - +
251A ASP* 2.8 39.8 + - - +
253A ARG 3.6 6.6 - - - +
254A VAL* 4.1 29.2 - - + -
255A ILE 4.7 8.6 + - - +
324A GLU* 2.7 31.5 + - - +
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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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119A VAL* 3.5 18.6 - - + +
120A GLY* 3.7 22.4 - - - +
121A SER* 3.6 29.6 - - - +
127A LEU* 4.6 4.0 - - + +
128A ALA 4.6 0.7 - - - -
129A VAL* 3.7 26.0 - - + +
244A ILE* 2.9 33.1 + - + +
245A MSE 3.6 4.0 - - - +
247A LYS* 1.3 71.4 - - - +
249A ILE* 1.3 59.0 + - - +
251A ASP 2.3 23.7 - - - +
252A GLY* 3.5 6.4 - - - -
253A ARG* 3.5 32.3 - - - +
254A VAL* 3.7 8.5 - - + -
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Residues in contact with ILE 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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88A ARG* 4.3 15.9 - - - +
90A TYR* 3.8 55.4 - - + +
119A VAL* 4.1 10.0 - - + +
129A VAL* 4.7 0.9 - - + -
245A MSE 2.9 41.5 + - + +
246A ASP* 3.8 11.4 - - - +
248A LEU* 1.3 77.5 - - - +
250A ARG* 1.3 71.0 + - - +
251A ASP 3.6 0.9 - - - +
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Residues in contact with ARG 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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246A ASP* 3.0 21.0 + - - +
247A LYS* 4.0 35.8 - - - +
249A ILE* 1.3 83.6 - - - +
251A ASP* 1.3 92.3 + - - +
255A ILE* 6.1 0.6 - - - +
326A ARG* 3.6 17.3 - - - +
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Residues in contact with ASP 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 LYS* 2.8 12.3 + - - +
248A LEU 2.3 33.4 - - - +
249A ILE 4.3 0.9 - - - -
250A ARG* 1.3 111.2 + - - +
252A GLY* 1.3 52.7 + - - +
253A ARG* 3.2 20.7 - - + +
255A ILE* 4.1 17.2 + - + +
326A ARG* 3.2 23.8 + - - -
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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