Contacts of the helix formed by residues 210 - 225 (chain B) in PDB entry 2WK6
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 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 4.0 6.2 + - - +
79B ARG* 4.2 18.2 - - - +
207B THR 4.2 1.3 - - - -
208B VAL 2.7 8.9 + - - -
209B ASP* 1.3 73.6 - - - +
211B LEU* 1.3 65.0 + - - +
212B PRO* 3.3 22.1 - - - +
213B LEU* 3.0 33.8 + - - +
214B ILE* 2.9 23.2 + - - +
242B PHE* 3.9 2.4 - - - -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B THR* 5.5 1.6 - - + +
210B SER* 1.3 68.9 - - - +
212B PRO* 1.3 72.9 - - + +
214B ILE* 3.4 3.4 + - - +
215B THR* 2.6 46.2 + - - +
242B PHE* 3.5 23.1 - - + -
247B GLN* 5.0 4.5 - - + +
250B GLU* 4.0 34.1 - - + +
251B LEU* 4.2 14.9 - - + +
254B THR* 3.5 32.1 - - + +
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Residues in contact with PRO 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 4.4 3.4 - - + -
82B GLY* 4.7 4.7 - - - -
83B MET* 3.1 53.1 - - + +
88B THR* 3.3 25.9 - - + +
210B SER* 3.3 16.6 - - - +
211B LEU* 1.3 100.8 - - + +
213B LEU* 1.3 55.4 + - - +
215B THR* 3.4 1.7 + - - -
216B ALA* 3.0 30.1 + - - +
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.5 42.2 - - + +
78B ILE* 4.0 24.9 - - + -
91B LEU* 4.0 23.6 - - + -
95B LEU* 5.6 0.3 - - - +
198B LEU* 5.0 7.2 - - + -
202B ARG* 3.6 18.5 + - - +
207B THR* 3.4 23.1 - - - +
210B SER* 3.0 24.1 + - - +
212B PRO* 1.3 75.8 - - - +
214B ILE* 1.3 60.9 + - - +
216B ALA* 4.1 0.9 - - - +
217B SER* 2.9 31.7 + - - -
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 5.1 0.4 - - + -
202B ARG* 3.6 4.9 - - - +
208B VAL 3.3 23.8 - - - +
210B SER 2.9 16.1 + - - +
211B LEU 3.8 2.7 - - - +
213B LEU* 1.3 75.8 - - - +
215B THR* 1.3 59.5 + - - +
217B SER* 3.2 0.9 + - - -
218B ILE* 2.8 55.2 + - + +
241B VAL* 3.8 16.6 - - + -
242B PHE* 3.5 32.5 - - + -
251B LEU* 4.0 20.9 - - + -
1482B IUR 3.3 26.5 - - + +
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Residues in contact with THR 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B THR* 3.4 24.5 - - + -
92B THR* 4.5 1.1 - - - +
211B LEU* 2.6 36.5 + - - +
212B PRO 3.4 4.9 - - - -
214B ILE* 1.3 77.5 - - - +
216B ALA* 1.3 62.2 + - - +
218B ILE* 4.0 0.3 - - - +
219B LEU* 3.0 48.3 + - + +
251B LEU* 3.7 8.1 - - - +
254B THR* 3.3 21.0 - - + +
255B LEU* 4.1 10.9 - - + +
258B VAL* 4.3 3.8 - - + -
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B THR 4.1 1.3 - - - +
91B LEU* 3.7 28.9 - - + -
92B THR* 3.0 39.2 - - - +
95B LEU* 3.9 7.2 - - + -
212B PRO 3.0 11.3 + - - +
213B LEU 4.2 0.9 - - - +
215B THR* 1.3 76.2 - - - +
217B SER* 1.3 51.0 + - - +
220B SER* 2.7 42.0 + - - -
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Residues in contact with SER 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.1 4.2 - - - +
195B ASP* 2.5 26.8 + - - -
199B TYR* 3.8 2.9 - - - -
202B ARG* 3.7 14.8 + - - -
213B LEU 2.9 19.5 + - - -
214B ILE 3.5 3.8 - - - -
216B ALA* 1.3 76.4 - - - +
218B ILE* 1.3 60.8 + - - +
220B SER* 2.7 17.2 + - - -
221B LYS* 3.1 22.1 + - - -
1482B IUR 3.0 21.0 + - - -
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B HIS* 3.8 29.8 - - + -
117B SER 4.5 2.7 - - - +
118B THR* 4.5 4.3 - - + -
214B ILE* 2.8 45.5 + - + +
217B SER* 1.3 75.1 - - - +
219B LEU* 1.3 63.4 + - + +
221B LYS* 3.3 5.6 + - - +
222B LYS* 3.3 25.1 + - + +
232B VAL* 4.1 20.0 - - + -
255B LEU* 4.0 30.1 - - + -
1482B IUR 3.5 33.0 - - + +
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 3.5 15.5 - - + -
215B THR* 3.0 26.3 + - + +
218B ILE* 1.3 76.6 - - + +
220B SER* 1.3 59.8 + - - +
222B LYS* 3.2 3.5 + - - +
223B LEU* 2.8 38.9 + - + +
230B LEU* 4.2 21.5 - - + -
232B VAL* 5.5 0.2 - - + -
255B LEU* 3.7 32.3 - - + +
258B VAL* 3.8 22.4 - - + -
259B GLY* 3.7 30.7 - - - +
262B LEU* 4.8 0.7 - - + -
264B LEU* 5.0 3.8 - - + -
266B VAL* 4.5 4.0 - - + -
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Residues in contact with SER 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 3.6 16.1 - - - +
95B LEU* 3.5 30.0 - - - +
96B ALA* 3.7 10.1 - - - +
192B VAL* 4.0 3.3 - - - +
195B ASP* 4.1 7.6 - - - +
216B ALA 2.7 29.3 + - - -
217B SER* 2.7 18.2 + - - -
219B LEU* 1.3 73.9 - - - +
221B LYS* 1.3 64.6 + - - +
224B VAL* 3.1 28.2 + - - +
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Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B HIS* 4.1 7.9 - - - -
143B ILE* 3.2 49.2 - - + +
144B SER 3.4 15.9 - - - +
187B GLN* 4.0 8.1 - - + +
192B VAL* 3.8 20.9 - - + -
195B ASP* 2.8 26.2 + - - +
199B TYR* 4.0 1.0 - - - -
217B SER* 3.1 18.1 + - - +
218B ILE* 3.3 6.4 + - - +
219B LEU 3.3 0.6 - - - -
220B SER* 1.3 83.6 + - - +
222B LYS* 1.3 63.7 + - - +
224B VAL* 3.6 4.7 + - - +
225B GLU* 3.2 25.6 + - - +
1482B IUR 2.7 30.4 + - - -
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Residues in contact with LYS 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASP* 2.6 30.1 + - - +
115B LYS 4.5 0.6 + - - -
116B HIS* 3.4 35.6 + - - -
142B MET* 4.2 3.2 - - - +
143B ILE 3.1 23.6 + - - +
218B ILE* 3.3 15.9 + - + +
219B LEU 3.2 6.6 + - - +
221B LYS* 1.3 76.3 - - - +
223B LEU* 1.3 64.8 + - - +
225B GLU* 3.0 35.6 + - - +
226B GLY 3.8 0.9 + - - -
227B LEU* 3.8 12.1 + - + +
230B LEU* 3.3 43.3 - - + -
264B LEU* 4.0 8.2 - - + +
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR* 3.7 16.4 - - + +
93B GLN* 5.3 3.4 - - + +
96B ALA* 4.4 14.4 - - + -
101B GLN* 3.1 12.6 + - - +
219B LEU* 2.8 27.0 + - + +
220B SER 4.0 3.6 - - - +
221B LYS 3.5 0.2 - - - -
222B LYS* 1.3 72.3 - - - +
224B VAL* 1.3 62.7 + - - +
225B GLU 3.3 0.7 + - - -
226B GLY* 3.3 9.7 + - - -
259B GLY* 5.6 1.3 - - - -
262B LEU* 3.5 48.7 - - + +
264B LEU* 3.4 37.7 - - + -
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 3.2 35.9 - - + +
100B GLN 2.8 26.2 - - - +
101B GLN* 3.4 11.8 - - - +
102B LEU* 2.9 38.2 + - + +
143B ILE* 6.4 1.1 - - + -
191B LEU* 4.7 7.9 - - + -
192B VAL* 3.9 13.2 - - + +
220B SER 3.1 19.0 + - - +
221B LYS 3.8 5.8 - - - +
222B LYS 3.2 0.2 - - - -
223B LEU* 1.3 76.0 - - - +
225B GLU* 1.3 59.7 + - + +
226B GLY 3.3 0.4 - - - -
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Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 4.1 8.5 - - + -
104B TRP* 2.8 26.8 + - - -
112B LEU* 4.7 0.5 - - - +
114B ASP* 2.6 32.6 - - - +
141B PRO* 3.0 20.2 - - + +
143B ILE* 3.0 45.6 + - + +
221B LYS 3.2 11.5 - - - +
222B LYS* 3.0 26.5 + - - +
224B VAL* 1.3 79.0 - - - +
226B GLY* 1.3 62.1 + - - +
227B LEU* 3.5 18.6 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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