Contacts of the helix formed by residues 393 - 404 (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 ARG 393 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ASP 3.6 7.2 - - - +
391B LEU* 3.8 21.3 - - + -
392B VAL* 1.3 70.0 - - - +
394B ALA* 1.3 64.2 + - - +
395B LEU* 5.4 6.1 - - - +
396B PRO* 3.2 47.2 - - + +
397B LEU* 3.6 11.8 + - - +
454B ALA 5.3 0.2 + - - -
457B GLU* 3.6 28.5 + - - +
458B ALA* 2.8 28.1 + - - +
460B VAL* 4.2 10.3 - - + +
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 3.9 13.4 - - + +
239B ALA* 3.6 19.1 - - + -
273B MET* 3.9 2.5 - - + +
274B ASP 2.9 20.1 + - - +
275B LYS 3.7 19.5 - - - -
276B PRO* 3.7 16.6 - - + -
392B VAL 3.0 2.2 + - - -
393B ARG* 1.3 69.6 - - - +
395B LEU* 1.3 66.7 + - - +
397B LEU* 3.0 6.3 + - - +
398B ALA* 2.9 22.2 + - - +
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Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B HIS* 3.8 40.6 - - + +
238B GLY 3.5 27.8 - - - +
239B ALA* 3.5 7.8 - - + +
274B ASP 4.8 0.4 + - - -
393B ARG* 5.4 6.7 - - - +
394B ALA* 1.3 77.0 - - - +
396B PRO* 1.3 71.8 - - + +
397B LEU 3.0 0.5 + - - -
398B ALA* 3.0 3.6 + - - +
399B LEU* 2.9 46.8 + - + +
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Residues in contact with PRO 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ARG* 3.2 61.7 - - + +
395B LEU* 1.3 94.5 - - + +
397B LEU* 1.3 60.4 + - - +
399B LEU* 3.6 10.8 + - + +
400B VAL* 3.1 31.0 + - - +
454B ALA* 3.7 25.1 - - + +
455B LEU* 4.5 1.8 - - - -
458B ALA* 3.9 8.7 - - + -
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 5.2 4.0 - - + -
276B PRO* 3.9 25.8 - - + -
281B VAL* 4.6 13.5 - - + -
392B VAL* 4.0 18.4 - - + -
393B ARG 3.6 6.6 + - - +
394B ALA* 3.0 11.8 + - - +
396B PRO* 1.3 79.0 - - - +
398B ALA* 1.3 64.8 + - - +
400B VAL* 3.4 0.3 + - - -
401B LEU* 2.8 57.5 + - + +
421B ALA* 4.0 13.7 - - + -
423B LEU* 4.5 10.3 - - + -
437B TRP* 5.7 0.9 - - + -
438B LEU* 4.3 13.7 - - + -
455B LEU* 3.8 18.1 - - + +
458B ALA* 4.9 4.7 - - + +
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 3.8 20.8 - - + +
150B HIS* 3.4 36.1 - - + +
281B VAL* 5.5 2.9 - - - -
394B ALA 2.9 12.0 + - - +
395B LEU 3.6 6.3 - - - +
397B LEU* 1.3 75.7 - - - +
399B LEU* 1.3 55.2 + - - +
401B LEU* 3.2 5.7 + - - +
402B HIS* 2.6 38.9 + - - +
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B HIS* 4.2 19.7 - - + +
395B LEU* 2.9 38.9 + - + +
396B PRO* 3.7 9.6 - - + +
398B ALA* 1.3 75.7 - - - +
400B VAL* 1.3 61.0 + - + +
402B HIS* 2.9 28.2 - - + +
403B GLU* 3.1 13.5 + - - +
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Residues in contact with VAL 400 (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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396B PRO 3.1 18.3 + - - +
399B LEU* 1.3 72.4 - - + +
401B LEU* 1.3 69.1 + - + +
402B HIS 3.0 1.3 - - - -
403B GLU* 3.0 21.3 + - + +
404B LEU* 3.2 32.7 + - + +
447B LEU* 4.4 0.7 - - + -
451B GLN* 4.1 26.7 - - + +
454B ALA* 3.8 24.0 - - + -
455B LEU* 3.7 36.1 - - + -
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B VAL* 4.9 11.7 - - + -
282B GLY* 6.3 0.4 - - - -
397B LEU* 2.8 54.9 + - + +
398B ALA* 3.7 5.4 - - - +
400B VAL* 1.3 80.4 - - + +
402B HIS* 1.3 62.4 + - - +
404B LEU* 3.0 27.2 + - + +
406B ALA* 3.0 27.4 + - + +
419B VAL* 3.9 7.5 - - + +
420B GLY* 3.0 49.4 - - - +
421B ALA* 4.0 6.1 - - + +
440B VAL* 4.5 4.7 - - + -
455B LEU* 4.7 3.6 - - + -
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Residues in contact with HIS 402 (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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35A GLN* 6.1 4.9 - - + +
37A PRO* 6.2 1.0 - - - +
149B GLY 3.9 22.1 + - - -
150B HIS* 4.6 8.3 - - - +
203B ASP* 5.7 0.2 - - - -
398B ALA 2.6 18.2 + - - +
399B LEU* 2.9 24.0 - - + +
401B LEU* 1.3 72.2 - - - +
403B GLU* 1.3 66.0 + - + +
405B GLY* 3.2 12.3 + - - -
406B ALA* 4.0 2.0 - - - +
407B GLY* 3.2 45.2 + - - +
408B ARG 3.1 29.1 + - - -
409B SER* 5.0 6.1 + - - -
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Residues in contact with GLU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN* 6.3 3.6 - - + -
399B LEU 3.6 10.4 - - - +
400B VAL* 3.0 25.3 + - - +
402B HIS* 1.3 86.4 - - + +
404B LEU* 1.3 59.3 + - - +
405B GLY 3.2 2.8 + - - -
451B GLN* 3.2 35.3 + - - +
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B VAL* 3.2 21.8 - - + +
401B LEU* 3.0 20.4 + - + +
403B GLU* 1.3 77.1 - - - +
405B GLY* 1.3 57.4 + - - +
406B ALA 3.6 0.9 - - - -
416B ARG* 3.4 17.5 + - - -
419B VAL* 3.5 19.5 - - + +
440B VAL* 3.9 28.3 - - + -
442B ARG* 4.6 16.6 - - + -
443B ASP 5.1 1.7 + - - -
444B GLY 5.7 1.4 + - - -
445B PRO* 5.3 6.7 - - + +
447B LEU* 4.0 15.7 - - + -
451B GLN* 3.4 29.8 - - - +
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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