Contacts of the helix formed by residues 283 - 294 (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 HIS 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B GLY* 4.7 15.0 - - - -
153B GLY 4.6 4.0 - - - -
156B ASP* 3.4 34.1 - - + +
157B LYS* 3.6 22.1 + - + +
160B SER* 3.8 3.8 - - - -
282B GLY* 1.3 83.4 + - - -
284B ALA* 1.3 68.9 + - - +
285B LEU* 3.1 3.2 - - - +
286B GLU* 3.0 12.3 + - - +
287B VAL* 3.2 16.3 + - - +
406B ALA* 3.2 34.6 + - + +
415B LEU* 3.5 9.4 - - + +
416B ARG 4.8 0.7 - - - -
417B LEU* 3.4 39.8 + - + +
419B VAL 4.0 4.2 + - - -
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Residues in contact with ALA 284 (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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160B SER* 2.9 24.7 + - - +
283B HIS* 1.3 72.7 - - - +
285B LEU* 1.3 64.8 + - + +
287B VAL* 3.3 12.5 + - - +
288B GLU* 3.3 9.9 + - - +
369B ARG* 6.0 0.2 - - - -
372B LEU* 3.5 15.1 - - + +
373B PRO* 3.3 35.4 - - + +
417B LEU 2.9 21.7 + - - +
418B GLY* 4.3 1.8 - - - -
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Residues in contact with LEU 285 (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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280B CYS* 3.8 20.9 - - + +
281B VAL 4.0 7.6 - - - +
283B HIS 3.1 3.5 - - - +
284B ALA* 1.3 78.1 - - + +
286B GLU* 1.3 65.2 + - - +
288B GLU* 3.1 14.7 + - - +
289B GLU 3.2 10.6 + - - -
369B ARG* 4.3 26.0 - - + +
373B PRO 5.9 1.1 - - - +
374B ARG* 6.6 0.2 - - - -
417B LEU 4.8 0.2 + - - -
418B GLY 4.5 9.0 - - - +
419B VAL 5.4 0.2 - - - +
420B GLY* 3.9 13.0 - - - +
421B ALA 3.7 33.7 - - - +
422B GLU* 4.7 4.9 - - + -
441B HIS* 4.0 37.9 - - + +
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Residues in contact with GLU 286 (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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122B GLY* 3.1 37.2 + - - -
124B LYS* 3.7 19.4 - - + +
127B LEU* 4.6 1.8 - - - -
157B LYS* 2.6 43.3 + - + +
280B CYS* 3.6 9.4 - - - +
281B VAL* 3.3 4.2 - - - +
282B GLY 2.9 44.3 + - - +
283B HIS 3.0 7.8 + - - +
285B LEU* 1.3 77.1 - - - +
287B VAL* 1.3 57.2 + - - +
289B GLU* 3.6 0.7 + - - +
290B ALA* 3.0 29.3 + - - +
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Residues in contact with VAL 287 (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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127B LEU* 4.3 11.4 - - + -
157B LYS 3.3 31.0 - - - +
158B LEU* 4.8 0.7 - - + +
160B SER* 3.8 5.8 - - - +
161B ILE* 3.8 30.7 - - + -
283B HIS 3.2 7.9 + - - +
284B ALA 3.5 8.3 - - - +
285B LEU 3.1 0.6 - - - -
286B GLU* 1.3 78.1 - - - +
288B GLU* 1.3 56.6 + - - +
290B ALA* 3.3 7.3 + - + +
291B LEU* 2.9 45.2 + - + +
343B PHE* 4.8 7.4 - - + -
360B LEU* 5.4 1.6 - - + -
372B LEU* 4.0 11.2 - - + -
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Residues in contact with GLU 288 (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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280B CYS* 5.4 2.1 - - - -
284B ALA 3.3 8.6 + - - +
285B LEU 3.1 9.5 + - - +
287B VAL* 1.3 77.5 - - - +
289B GLU* 1.3 72.2 + - - +
291B LEU* 3.1 10.0 + - - +
292B LEU* 2.9 29.3 + - - +
365B PRO* 3.6 28.7 - - - +
368B ARG* 3.7 24.3 + - + -
369B ARG* 3.2 51.7 + - - +
372B LEU* 4.4 4.9 - - + +
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Residues in contact with GLU 289 (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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124B LYS* 2.7 29.2 + - - +
278B GLY* 3.0 7.8 - - - -
279B ARG* 2.9 38.3 + - - +
280B CYS* 3.3 26.5 + - + -
285B LEU 3.2 11.9 + - - +
286B GLU 4.1 3.4 - - - +
288B GLU* 1.3 85.9 + - - +
290B ALA* 1.3 61.9 + - - +
292B LEU* 3.3 9.7 + - + +
293B CYS* 3.1 21.3 + - - +
299B PRO* 4.0 16.0 - - + +
302B LEU* 3.7 13.2 - - + +
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Residues in contact with ALA 290 (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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124B LYS* 4.0 8.9 - - + +
127B LEU* 4.1 17.3 - - + -
128B VAL* 3.5 26.4 - - + +
286B GLU 3.0 19.3 + - - +
287B VAL* 3.4 8.7 - - + +
288B GLU 3.1 0.2 - - - -
289B GLU* 1.3 78.0 - - - +
291B LEU* 1.3 62.5 + - - +
293B CYS* 3.0 14.7 + - - +
294B MET* 3.0 18.7 + - + +
302B LEU* 4.3 3.4 - - - -
343B PHE* 6.2 0.9 - - + -
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Residues in contact with LEU 291 (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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287B VAL* 2.9 36.9 + - + +
288B GLU* 3.1 6.5 + - - +
290B ALA* 1.3 75.1 - - - +
292B LEU* 1.3 61.1 + - - +
294B MET* 3.1 9.4 + - + +
295B ASP* 3.0 24.6 + - - +
340B LEU* 3.5 25.5 - - + +
343B PHE* 3.7 26.7 - - + -
360B LEU* 4.0 25.4 - - + +
368B ARG* 3.4 45.3 - - + +
372B LEU* 5.2 0.2 - - + -
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Residues in contact with LEU 292 (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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288B GLU* 2.9 24.7 + - - +
289B GLU* 3.4 14.4 - - + +
290B ALA 3.2 0.2 - - - -
291B LEU* 1.3 76.9 - - - +
293B CYS* 1.3 59.0 + - - +
295B ASP* 2.9 34.2 + - + +
297B ALA* 3.0 25.6 + - + -
298B GLY* 3.8 24.0 - - - +
299B PRO* 5.4 2.2 - - + -
365B PRO* 3.9 28.0 - - + -
368B ARG* 3.9 2.8 - - - +
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Residues in contact with CYS 293 (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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128B VAL* 3.7 16.6 - - + -
289B GLU 3.1 5.0 + - - +
290B ALA 3.0 10.2 + - - +
292B LEU* 1.3 73.1 - - - +
294B MET* 1.3 56.1 + - - +
295B ASP 3.0 5.2 - - - -
296B GLY* 3.0 19.1 + - - -
297B ALA 3.3 13.4 + - - +
298B GLY* 4.7 1.5 - - - +
299B PRO 5.5 0.2 - - - -
302B LEU* 3.4 46.4 - - + -
303B ARG* 3.9 25.7 + - - -
334B LEU* 4.1 16.4 - - - +
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Residues in contact with MET 294 (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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127B LEU 3.9 14.4 - - - +
128B VAL* 4.1 20.2 - - + +
131B PRO* 3.7 23.8 - - - -
290B ALA* 3.0 33.9 + - + +
291B LEU* 3.1 10.5 + - + +
293B CYS* 1.3 75.0 - - - +
295B ASP* 1.3 56.0 + - - +
296B GLY 3.2 2.5 - - - -
334B LEU* 3.1 21.3 - - + +
339B ALA* 4.0 10.5 + - + +
340B LEU* 3.2 43.5 + - + +
343B PHE* 3.8 33.9 - - + -
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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