Contacts of the helix formed by residues 44 - 51 (chain 2) 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 ASN 44 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422 ARG* 2.5 24.5 + - + +
432 TRP* 1.3 70.3 - - - +
452 VAL* 1.3 54.8 + - - +
462 GLN* 2.8 8.3 - - - +
472 ALA* 2.9 28.4 + - + +
482 GLU* 3.6 8.8 + - - +
1262 PRO* 3.0 46.0 + - - +
1J MET* 3.6 49.5 + - - +
2J ARG* 3.7 11.4 - - - +
8J LEU* 5.8 0.2 - - - +
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Residues in contact with VAL 45 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412 LEU* 3.1 45.5 - - + +
422 ARG* 3.4 9.0 - - + +
432 TRP* 2.9 4.8 - - - +
442 ASN* 1.3 77.5 - - - +
462 GLN* 1.3 75.5 + - - +
472 ALA 3.3 0.4 - - - -
482 GLU* 4.1 12.5 + - - +
492 LEU* 3.6 13.0 - - - +
12152 CLA 3.6 25.7 - - + +
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Residues in contact with GLN 46 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432 TRP* 3.5 20.9 - - - +
442 ASN* 4.5 2.2 - - - +
452 VAL* 1.3 93.3 - - - +
472 ALA* 1.3 58.6 + - - +
492 LEU* 3.2 33.3 - - + +
502 VAL* 4.0 7.1 + - - +
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Residues in contact with ALA 47 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442 ASN* 2.9 21.8 + - + +
462 GLN* 1.3 76.6 - - - +
482 GLU* 1.3 66.6 + - + +
492 LEU 3.0 2.9 + - - -
502 VAL* 3.1 6.8 + - - +
512 HIS* 2.9 21.8 + - - +
1102 TRP* 3.5 35.3 - - + -
1J MET* 4.5 10.3 - - + -
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Residues in contact with GLU 48 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422 ARG* 4.3 15.1 - - - +
442 ASN 4.0 9.0 - - - +
452 VAL* 4.3 11.8 - - - +
472 ALA* 1.3 76.2 - - - +
492 LEU* 1.3 56.6 + - - +
512 HIS* 2.8 33.4 + - + +
522 SER* 2.9 13.7 + - - -
12152 CLA 3.3 37.5 - - + +
12162 CLA 4.5 31.5 - - + +
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Residues in contact with LEU 49 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452 VAL 3.6 14.8 - - - +
462 GLN* 3.2 32.8 - - + +
472 ALA 3.1 0.8 - - - -
482 GLU* 1.3 75.6 - - - +
502 VAL* 1.3 74.2 + - + +
512 HIS 3.0 4.7 - - - -
522 SER* 2.9 20.9 + - - -
532 ARG* 3.0 12.3 + - - +
1662 ASN* 5.2 4.8 - - - +
12152 CLA 3.2 32.7 - - + +
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Residues in contact with VAL 50 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462 GLN 4.4 5.4 - - - +
472 ALA* 3.1 8.6 + - - +
492 LEU* 1.3 94.2 - - + +
512 HIS* 1.3 57.2 + - - +
522 SER 3.4 0.2 - - - -
532 ARG* 4.1 33.2 - - + +
542 TRP* 3.0 27.0 + - + +
1102 TRP* 5.5 14.3 + - + +
1132 ILE* 6.0 4.9 - - + -
12222 CLA 4.8 1.9 - - - +
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Residues in contact with HIS 51 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472 ALA 2.9 11.3 + - - +
482 GLU* 2.8 28.2 + - + +
492 LEU 3.0 0.2 - - - -
502 VAL* 1.3 79.3 - - - +
522 SER* 1.3 60.5 + - - +
532 ARG 3.5 0.2 - - - -
542 TRP* 3.1 25.1 - - - +
552 ALA* 3.2 14.0 + - + +
562 MET* 6.2 1.6 - - + -
1102 TRP* 5.5 4.3 - - + -
12152 CLA 5.6 3.1 - - + +
12162 CLA 3.6 60.5 + + + -
12222 CLA 3.7 35.0 - + - +
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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