Contacts of the helix formed by residues 14 - 24 (chain I) 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 LEU 14 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1770B CLA 3.5 33.2 - - + +
1781B BCR 3.7 13.7 - - + -
66H THR* 4.9 10.1 - - + -
1079H CLA 3.6 49.4 - - + -
9I VAL 3.2 1.4 + - - -
10I PRO* 2.9 23.5 + - + +
12I VAL 2.7 4.4 + - - -
13I GLY* 1.4 71.2 - - - +
15I LEU* 1.3 56.2 + - - +
17I PRO* 2.7 25.1 - - - +
18I ALA* 3.1 12.0 + - - +
1170L BCR 4.1 23.3 - - + -
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Residues in contact with LEU 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H ILE* 4.1 24.9 - - + +
59H LEU* 5.0 12.1 - - + +
62H GLY* 3.0 34.1 - - - +
63H SER* 4.9 4.3 - - - -
66H THR* 5.1 4.0 - - + +
10I PRO* 2.4 27.1 + - + +
11I LEU* 3.8 25.8 - - + +
14I LEU* 1.3 65.6 - - - +
16I PHE* 1.3 66.4 + - - +
17I PRO 3.1 1.3 - - - -
18I ALA* 2.9 28.0 + - + -
19I VAL* 3.0 20.3 + - + +
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Residues in contact with PHE 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1740B CLA 3.6 31.2 - - + -
1781B BCR 4.3 29.8 - - + -
11I LEU* 2.6 25.9 + - + +
12I VAL* 3.4 13.0 - - + +
15I LEU* 1.3 71.9 - - - +
17I PRO* 1.4 82.6 - - + +
19I VAL* 3.2 24.6 + - + +
20I ALA* 3.5 12.5 + - + +
1032I BCR 3.3 70.9 - - + -
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Residues in contact with PRO 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1740B CLA 5.6 3.8 - - + -
1770B CLA 5.0 1.3 - - + -
1781B BCR 4.2 21.5 - - + -
12I VAL 2.4 32.3 - - - +
13I GLY* 3.4 17.7 - - - +
14I LEU 2.7 20.0 - - - +
16I PHE* 1.4 84.1 - - + +
18I ALA* 1.3 71.8 + - - +
20I ALA* 2.8 14.4 + - + +
21I MET* 3.1 36.8 + - + +
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Residues in contact with ALA 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1770B CLA 4.9 8.0 - - + +
1771B CLA 3.4 24.2 - - + +
58H ILE* 5.1 7.2 - - + -
14I LEU 3.1 7.4 + - - +
15I LEU* 2.9 31.9 + - + +
17I PRO* 1.3 74.8 - - - +
19I VAL* 1.3 66.9 + - - +
21I MET* 4.5 0.8 - - - +
22I ALA* 2.8 25.0 + - - +
94L ILE* 5.9 4.0 - - + -
97L MET* 5.6 5.2 - - + -
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Residues in contact with VAL 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H ILE* 5.5 7.6 - - + -
15I LEU* 3.0 24.9 + - + +
16I PHE* 3.2 17.3 - - + +
17I PRO 2.9 1.2 + - - -
18I ALA* 1.3 76.4 - - - +
20I ALA* 1.3 53.3 + - + +
22I ALA* 3.2 2.7 - - - +
23I SER* 2.4 48.3 + - - -
1032I BCR 5.0 17.7 - - + -
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Residues in contact with ALA 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1740B CLA 5.3 5.8 - - + -
16I PHE* 3.5 17.2 + - + +
17I PRO* 2.8 13.3 + - + +
19I VAL* 1.3 72.4 - - + +
21I MET* 1.3 59.2 + - - +
22I ALA 3.3 1.3 - - - -
23I SER* 3.9 7.6 - - - -
24I LEU* 2.5 41.7 + - + +
1032I BCR 3.7 33.7 - - + -
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Residues in contact with MET 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1740B CLA 5.4 8.3 - - + -
1770B CLA 3.0 30.5 - - + -
1771B CLA 2.8 77.2 - - + -
1781B BCR 4.8 9.0 - - + -
17I PRO* 3.1 34.7 + - + +
20I ALA* 1.3 70.9 - - - +
22I ALA* 1.3 64.5 + - - +
25I PHE* 3.5 14.7 + - - +
1169L BCR 3.8 47.6 - - + +
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Residues in contact with ALA 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1771B CLA 3.6 18.3 - - + +
54H LEU* 6.5 1.1 - - + -
58H ILE* 5.1 11.2 - - + -
18I ALA 2.8 17.8 + - - +
19I VAL* 3.1 9.0 - - - +
21I MET* 1.3 74.0 - - - +
23I SER* 1.3 72.2 + - - +
24I LEU 2.7 0.2 + - - -
25I PHE* 2.6 23.7 + - - +
97L MET* 5.7 1.8 - - - +
101L MET* 5.2 14.8 - - + -
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Residues in contact with SER 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I VAL* 2.4 42.0 + - - +
20I ALA* 3.9 4.3 - - - -
22I ALA* 1.3 74.5 - - - +
24I LEU* 1.3 50.6 + - - -
25I PHE* 2.8 10.0 + - - +
26I LEU* 2.7 40.1 + - - +
1032I BCR 6.2 0.7 - - - +
101L MET* 4.2 1.7 - - - +
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Residues in contact with LEU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1740B CLA 6.5 0.9 - - + -
20I ALA* 2.5 29.8 + - + +
23I SER* 1.3 69.6 + - - +
25I PHE* 1.3 48.7 + - - -
26I LEU* 2.5 23.2 + - + +
27I HIS* 2.7 31.0 + - - +
1032I BCR 4.1 36.8 - - + -
1169L BCR 3.6 68.5 - - + +
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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