Contacts of the helix formed by residues 239 - 254 (chain A) in PDB entry 2WSK
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 THR 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLN* 5.2 1.1 - - - -
236A SER* 2.9 32.4 + - - +
237A PRO 2.7 2.8 + - - -
238A GLU* 1.3 95.6 - - - +
240A ALA* 1.3 62.0 + - - +
241A LEU* 3.4 2.5 - - - -
242A ASP* 2.9 34.1 + - - +
243A GLU* 3.6 9.0 + - - +
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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
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176A TYR* 4.3 2.0 - - + -
229A LEU* 3.8 21.2 - - + +
231A PRO* 4.6 9.6 - - + -
234A ALA* 3.2 29.6 - - + -
236A SER 2.8 5.7 + - - -
237A PRO* 3.2 10.8 + - + +
239A THR* 1.3 75.6 - - - +
241A LEU* 1.3 66.8 + - - +
243A GLU* 3.0 7.0 + - - +
244A PHE* 2.9 22.9 + - - +
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Residues in contact with LEU 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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98A ARG 5.8 2.9 - - - +
134A ASP* 5.3 2.7 - - - +
229A LEU* 4.0 26.2 - - + +
239A THR 3.4 1.0 - - - -
240A ALA* 1.3 78.1 - - - +
242A ASP* 1.3 63.5 + - - +
244A PHE* 3.4 1.0 + - + -
245A ARG* 3.0 44.4 + - - +
323A TYR* 3.3 28.5 - - + +
324A TRP* 5.0 3.4 - - + -
327A THR* 4.2 13.2 - - + -
328A CYS* 3.6 31.9 - - + -
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Residues in contact with ASP 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASP* 4.5 0.7 - - - +
136A TYR* 3.5 24.0 - - + +
239A THR* 2.9 26.1 + - + +
240A ALA 3.2 0.6 - - - -
241A LEU* 1.3 77.1 - - - +
243A GLU* 1.3 62.0 + - - +
245A ARG* 2.7 31.7 + - - -
246A ASP* 3.0 33.0 + - - +
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Residues in contact with GLU 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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175A THR* 3.6 0.3 - - - -
176A TYR* 3.5 10.8 + - + +
177A LYS* 3.1 41.0 + - + +
234A ALA* 3.7 6.9 - - - +
235A CYS* 2.7 45.9 + - - +
236A SER* 2.8 20.2 + - - -
239A THR 3.6 5.4 + - - +
240A ALA 3.0 10.7 + - - +
242A ASP* 1.3 79.7 - - - +
244A PHE* 1.3 61.7 + - - +
246A ASP* 3.2 11.5 + - - +
247A ALA* 3.2 20.4 + - - +
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Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 3.5 32.5 - + + +
179A LEU* 4.1 9.4 - - + -
198A LEU* 3.9 30.5 - - + -
201A VAL* 4.5 13.0 - - + -
229A LEU* 3.8 26.2 - - + -
240A ALA 2.9 14.3 + - - +
241A LEU 3.8 3.4 - - - +
243A GLU* 1.3 77.2 - - - +
245A ARG* 1.3 56.1 - - - +
247A ALA* 3.1 6.1 + - + +
248A ILE* 2.9 46.9 + - + +
251A LEU* 6.3 1.1 - - + -
258A VAL* 4.5 3.6 - - + -
260A LEU* 4.0 20.0 - - + -
324A TRP* 4.9 2.5 - + - -
328A CYS* 3.6 29.8 - - - -
330A VAL* 4.9 0.9 - - + -
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Residues in contact with ARG 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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134A ASP* 2.7 43.2 + - - -
136A TYR* 3.2 36.6 + - + +
138A TRP* 3.3 27.0 - - + +
241A LEU* 3.0 43.2 + - + +
242A ASP* 2.7 30.1 + - - +
244A PHE* 1.3 73.2 - - - +
246A ASP* 1.3 60.7 + - - +
248A ILE* 3.3 9.3 + - - +
249A LYS* 3.0 26.3 + - - +
327A THR* 3.1 34.2 + - - +
328A CYS* 3.8 10.1 - - - +
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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
----------------------------------------------------------
136A TYR* 2.5 34.1 + - - -
242A ASP* 3.0 20.7 + - - +
243A GLU* 3.4 11.0 - - - +
244A PHE 3.1 0.2 - - - -
245A ARG* 1.3 73.7 - - - +
247A ALA* 1.3 68.2 + - - +
249A LYS* 3.2 18.6 + - - +
250A ALA* 3.3 12.6 + - - +
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Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR 3.1 28.0 - - - +
177A LYS* 4.7 2.9 - - - +
179A LEU* 4.3 6.7 - - + -
180A GLY* 3.7 22.3 - - - +
243A GLU 3.2 5.6 + - - +
244A PHE* 3.1 13.8 + - + +
246A ASP* 1.3 80.0 - - - +
248A ILE* 1.3 62.1 + - - +
250A ALA* 3.3 4.8 + - - +
251A LEU* 3.0 29.9 + - + +
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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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138A TRP* 4.4 5.4 - - + -
244A PHE* 2.9 43.5 + - + +
245A ARG* 3.6 11.0 - - - +
246A ASP 3.2 0.2 - - - -
247A ALA* 1.3 74.6 - - + +
249A LYS* 1.3 65.6 + - - +
251A LEU* 3.8 7.8 - - + +
252A HIS* 2.9 53.0 + - + +
258A VAL* 4.4 15.7 - - + -
328A CYS* 3.4 45.5 - - - +
329A HIS 4.2 2.5 - - - +
330A VAL* 4.8 7.0 - - + -
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Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 3.1 30.6 + - - +
137A ASP 2.7 29.1 + - - -
138A TRP* 3.5 29.6 - - + +
139A GLU* 3.0 28.2 + - + +
141A ASP* 3.4 15.6 - - + +
245A ARG 3.0 13.0 + - - +
246A ASP* 3.2 12.1 + - - +
248A ILE* 1.3 75.2 - - - +
250A ALA* 1.3 59.5 + - - +
252A HIS* 3.1 4.2 + - - +
253A LYS* 2.8 36.9 + - + +
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Residues in contact with ALA 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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180A GLY* 3.8 12.3 - - - +
185A ILE* 3.3 28.5 - - + +
246A ASP 3.3 8.3 + - - +
247A ALA* 3.4 8.5 - - - +
248A ILE 3.3 0.2 - - - -
249A LYS* 1.3 79.4 - - - +
251A LEU* 1.3 63.5 + - - +
253A LYS* 2.9 20.8 + - - +
254A ALA* 3.1 9.9 + - - +
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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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179A LEU* 3.8 33.4 - - + +
185A ILE* 4.0 11.4 - - + +
188A LEU* 4.1 23.6 - - + -
196A LEU* 4.2 14.8 - - + -
244A PHE* 6.3 0.9 - - + -
247A ALA* 3.0 26.1 + - + +
248A ILE* 3.8 4.7 - - + +
250A ALA* 1.3 78.5 - - - +
252A HIS* 1.3 61.0 + - - +
254A ALA* 3.1 9.4 + - - -
256A ILE* 2.8 55.9 + - + +
258A VAL* 4.1 23.1 - - + -
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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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141A ASP* 2.9 41.8 + - - +
142A ALA 3.9 17.4 + - - +
143A PRO* 5.1 1.2 - - - +
144A PRO* 3.4 14.8 - - + +
248A ILE* 2.9 30.2 + - + +
249A LYS 3.5 1.1 - - - +
251A LEU* 1.3 76.2 - - - +
253A LYS* 1.3 58.9 + - - +
255A GLY* 2.9 18.7 + - - -
256A ILE 3.3 14.9 + - - -
257A GLU* 4.4 0.4 - - - -
258A VAL* 4.5 3.3 - - + +
329A HIS* 3.2 20.4 + - - +
331A ASP* 2.8 40.3 + - - -
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Residues in contact with LYS 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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140A ASP* 2.6 43.2 + - - -
141A ASP* 5.8 3.1 - - - +
249A LYS* 2.8 22.6 + - + +
250A ALA* 2.9 12.5 + - - +
252A HIS* 1.3 77.9 - - + +
254A ALA* 1.3 56.4 + - - +
255A GLY 3.3 2.9 + - - -
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Residues in contact with ALA 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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185A ILE* 3.5 31.6 - - + -
189A LYS* 3.0 40.9 + - + +
250A ALA 3.1 7.5 + - - +
251A LEU 3.1 8.0 + - - +
253A LYS* 1.3 75.7 - - - +
255A GLY* 1.3 59.1 + - - +
256A ILE* 3.3 4.3 - - + -
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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