Contacts of the helix formed by residues 39 - 51 (chain 1) in PDB entry 2WSC
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 TYR 39 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311 GLU* 5.1 5.8 - - - -
351 ASN* 2.6 63.4 + - + +
361 LEU* 3.4 14.4 - - + +
381 ARG* 1.3 89.8 - - - +
401 LYS* 1.3 53.2 + - - +
411 GLU 3.2 2.9 - - - -
421 SER* 2.7 31.5 + - - +
1121 ARG* 3.5 43.0 + - + +
1151 GLU* 3.8 17.9 + - - -
11951 CLA 4.4 4.5 - - + -
11961 CLA 2.3 58.8 - + + +
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Residues in contact with LYS 40 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361 LEU* 2.8 32.9 + - - +
371 GLU* 2.6 49.8 + - + +
391 TYR* 1.3 78.9 - - - +
411 GLU* 1.3 58.5 + - - +
421 SER 3.2 0.4 - - - -
431 GLU* 3.4 25.9 - - + +
441 LEU* 3.0 26.9 - - - +
1551 LEU* 4.4 20.9 - - + +
11901 CLA 3.1 36.3 + - - -
11961 CLA 5.1 7.0 - - + -
11991 CLA 4.3 13.1 - - - +
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Residues in contact with GLU 41 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371 GLU 2.8 14.9 + - - +
381 ARG* 3.1 36.3 - - - +
391 TYR 3.2 0.2 - - - -
401 LYS* 1.3 76.6 - - - +
421 SER* 1.3 58.4 + - - +
441 LEU* 3.5 16.4 + - + +
451 ILE* 3.1 34.3 + - + +
1391 LYS* 4.8 9.5 + - - +
1471 GLU* 3.0 34.0 - - + +
11951 CLA 3.8 11.8 - - + +
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Residues in contact with SER 42 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 TYR 2.7 21.3 + - - -
411 GLU* 1.3 76.3 - - - +
431 GLU* 1.3 57.9 + - - +
451 ILE* 3.0 13.1 + - - -
461 HIS* 2.5 58.5 + - - -
1121 ARG* 4.6 12.8 - - - -
11951 CLA 3.7 15.0 - - - +
11961 CLA 3.9 15.8 - - - +
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Residues in contact with GLU 43 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401 LYS* 3.4 31.0 - - + +
421 SER* 1.3 82.1 + - - +
441 LEU* 1.3 57.4 + - - +
461 HIS* 3.9 6.2 - - - +
471 CYS* 2.9 29.8 + - + +
1551 LEU* 3.6 24.9 - - + +
1581 PHE* 4.3 19.2 - - + -
11901 CLA 3.4 60.2 + - - +
11961 CLA 5.6 4.4 - - + +
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Residues in contact with LEU 44 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371 GLU 5.5 0.7 - - - +
401 LYS 3.0 20.2 - - - +
411 GLU* 3.8 20.2 - - + +
421 SER 3.1 0.6 - - - -
431 GLU* 1.3 77.7 - - + +
451 ILE* 1.3 53.6 + - + +
471 CYS* 3.2 8.9 - - - +
481 ARG* 2.5 42.4 + - + +
1471 GLU* 4.8 6.1 - - + +
1501 ASN 5.2 0.9 - - - -
1511 GLY* 3.5 31.0 - - - +
1541 ALA* 3.4 32.5 - - + -
1551 LEU* 3.9 13.2 - - + -
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Residues in contact with ILE 45 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411 GLU* 3.1 21.6 + - + +
421 SER* 3.0 14.8 + - - +
441 LEU* 1.3 73.7 - - + +
461 HIS* 1.3 58.3 + - + +
471 CYS 3.2 0.9 - - - -
481 ARG* 3.1 35.1 - - + +
491 TRP* 2.6 38.1 + - + +
11951 CLA 2.9 56.8 - - + -
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Residues in contact with HIS 46 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421 SER* 2.5 54.4 + - - +
431 GLU* 3.9 7.0 - - - +
451 ILE* 1.3 76.0 - - + +
471 CYS* 1.3 51.5 + - - +
491 TRP* 3.2 13.1 + - - +
501 ALA* 2.8 31.2 + - - +
1051 ILE* 6.3 2.7 - - + -
11901 CLA 6.2 4.0 - - + -
11951 CLA 6.0 3.6 - - + +
11961 CLA 4.2 35.1 - + + +
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Residues in contact with CYS 47 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431 GLU* 2.9 20.3 + - + +
441 LEU* 3.2 9.9 - - - +
461 HIS* 1.3 74.3 - - - +
481 ARG* 1.3 55.5 + - - +
501 ALA* 4.0 10.3 - - - -
511 MET* 2.6 38.8 + - - +
1541 ALA* 5.5 8.5 - - + -
1581 PHE* 4.4 32.3 - - + -
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Residues in contact with ARG 48 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441 LEU* 2.5 27.8 + - + +
451 ILE* 3.1 36.3 + - + +
471 CYS* 1.3 74.9 - - - +
491 TRP* 1.3 52.0 + - - +
511 MET* 3.1 4.8 - - - +
521 LEU* 2.6 44.5 + - + +
11881 CLA 2.9 52.4 + - - +
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Residues in contact with TRP 49 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451 ILE* 2.6 21.6 + - + +
461 HIS* 3.3 17.0 - - - +
481 ARG* 1.3 74.6 - - + +
501 ALA* 1.3 56.9 + - - +
521 LEU* 3.2 9.7 + - + +
531 ALA* 3.0 27.6 + - + +
11951 CLA 6.1 5.4 - - + +
11971 CLA 5.0 36.1 - + + -
11981 CLA 5.7 8.3 - - + +
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Residues in contact with ALA 50 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461 HIS 2.8 16.8 + - - +
471 CYS* 3.8 13.5 - - - +
491 TRP* 1.3 75.7 - - - +
511 MET* 1.3 59.6 + - - +
521 LEU 3.3 0.2 - - - -
531 ALA* 3.6 5.5 - - - +
541 VAL* 3.0 38.4 + - + +
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Residues in contact with MET 51 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471 CYS* 2.6 24.7 + - - +
481 ARG* 3.1 7.9 - - - -
501 ALA* 1.3 71.5 - - - +
521 LEU* 1.3 65.2 + - - +
531 ALA 3.5 1.6 - - - -
541 VAL* 3.6 33.4 - - + -
551 PRO* 3.3 23.3 - - + +
571 ILE* 6.1 0.9 - - + -
581 LEU* 3.9 28.5 - - + -
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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