Contacts of the helix formed by residues 34 - 39 (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 ALA 34 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321 VAL 2.7 2.9 + - - -
331 PRO* 1.3 79.8 - - - +
351 ASN* 1.3 61.3 + - - +
371 GLU* 2.7 10.4 + - - -
381 ARG* 2.4 39.5 + - + +
1371 PRO* 3.6 12.1 - - + -
1391 LYS 3.5 24.2 - - - +
1401 LEU* 4.2 11.7 - - - -
1411 GLU* 4.5 4.5 - - + +
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Residues in contact with ASN 35 (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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301 GLY 3.4 19.4 + - - +
311 GLU* 3.3 15.3 + - - +
341 ALA* 1.3 75.6 - - - +
361 LEU* 1.3 52.8 + - - +
381 ARG* 2.9 7.8 + - - -
391 TYR* 2.6 72.8 + - + -
1151 GLU* 4.4 12.0 + - - +
1171 ASP* 5.8 1.4 + - - -
1371 PRO* 3.3 30.5 + - - +
1391 LYS 4.9 0.5 - - - +
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Residues in contact with LEU 36 (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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311 GLU* 2.9 55.7 + - + +
321 VAL* 3.8 18.5 + - + -
341 ALA 3.1 1.8 + - - -
351 ASN* 1.3 70.5 - - - +
371 GLU* 1.3 66.4 + - - +
391 TYR* 3.4 10.2 - - + +
401 LYS* 2.8 42.8 + - - +
11901 CLA 4.0 30.3 - - + -
11961 CLA 4.2 22.8 - - + +
11991 CLA 6.4 0.7 - - + -
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Residues in contact with GLU 37 (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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321 VAL* 3.0 24.2 - - - +
331 PRO 5.6 0.7 - - - +
341 ALA* 2.7 13.6 + - - +
361 LEU* 1.3 79.2 - - - +
381 ARG* 1.3 53.3 + - - +
401 LYS* 2.6 47.8 + - + +
411 GLU* 2.8 29.0 + - - +
441 LEU* 5.5 0.7 - - - +
1481 ILE* 5.4 12.1 - - + -
1551 LEU* 5.1 6.5 - - + -
11991 CLA 3.6 39.2 + - + +
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Residues in contact with ARG 38 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341 ALA* 2.4 39.8 + - + +
351 ASN* 3.4 7.7 + - - +
371 GLU* 1.3 67.2 - - - +
391 TYR* 1.3 72.9 + - - +
401 LYS 3.1 1.6 - - - -
411 GLU* 3.1 43.8 + - - +
1121 ARG* 5.4 3.0 - - - +
1151 GLU* 4.2 7.3 + - - -
1371 PRO 4.8 1.4 + - - -
1381 LYS* 3.5 23.0 - - - +
1391 LYS* 3.2 52.4 - - + +
11951 CLA 3.2 63.2 - - + +
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Residues in contact with TYR 39 (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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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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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