Contacts of the helix formed by residues 18 - 23 (chain B) in PDB entry 2WSF
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 THR 18 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 1.3 75.4 + - - +
19B ARG* 1.3 51.5 + - - -
20B ARG 2.9 2.7 - - - -
21B ILE* 2.4 40.5 + - - +
22B TRP* 3.6 5.0 + - - -
695B ASP* 3.6 29.2 - - + +
696B LYS 3.5 4.9 + - - +
698B VAL* 3.0 22.9 + - - +
840B CLA 3.1 64.6 - - + +
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Residues in contact with ARG 19 (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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11B GLY 5.1 0.2 + - - -
12B ILE* 4.6 19.6 - - - +
15B ASP* 2.8 28.5 + - - +
17B THR* 2.9 13.5 + - - +
18B THR* 1.3 78.1 + - - +
20B ARG* 1.3 64.2 + - - +
21B ILE 2.8 1.7 + - - -
22B TRP* 4.4 10.0 - - + -
23B PHE* 3.1 74.6 + - + +
698B VAL* 4.3 8.0 - - + +
700B LEU* 6.4 0.4 - - - -
701B SER* 4.7 10.7 + - - +
704B GLN* 5.4 2.5 - - - +
70C TRP* 3.8 24.7 + - - -
72C GLU* 3.4 31.1 + - - +
77C MET* 5.0 11.7 - - + -
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Residues in contact with ARG 20 (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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5B ILE* 3.3 33.0 - - - +
6B PRO* 3.5 16.2 - - - +
12B ILE* 3.4 32.1 - - - +
13B ALA 3.8 8.0 + - - -
14B GLN 5.2 0.2 - - - -
15B ASP* 2.6 36.5 + - - +
17B THR 3.4 11.2 - - - +
19B ARG* 1.3 76.0 - - - +
21B ILE* 1.3 68.5 + - - +
24B GLY* 3.6 11.8 + - - -
694B ARG 5.0 0.8 + - - -
695B ASP* 2.6 39.5 + - - +
27I HIS* 2.9 37.4 + - - -
28I VAL* 3.8 9.1 + - - +
29I GLU* 5.0 0.2 + - - -
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Residues in contact with ILE 21 (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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830A CLA 3.8 17.9 - - + -
18B THR* 2.4 35.2 + - - +
20B ARG* 1.3 71.5 - - - +
22B TRP* 1.3 70.9 + - - +
24B GLY* 2.7 15.1 + - - -
25B ILE* 3.0 15.0 + - + +
695B ASP* 3.3 40.8 - - + +
840B CLA 4.3 24.9 - - + -
27I HIS* 4.2 20.6 + - + -
28I VAL* 6.0 1.1 - - + -
211L BCR 3.8 29.2 - - + -
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Residues in contact with TRP 22 (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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830A CLA 3.7 24.7 - - + -
18B THR 4.0 14.1 - - - -
19B ARG* 3.4 6.8 + - + +
21B ILE* 1.3 73.8 - - + +
23B PHE* 1.3 60.5 + - + +
25B ILE* 2.6 59.5 + - + +
26B ALA* 4.1 1.2 - - - +
700B LEU* 4.1 5.0 - - + +
704B GLN* 3.3 36.6 - - - +
840B CLA 2.8 57.9 - + + +
841B CLA 3.6 38.1 - + + -
843B PQN 4.1 30.1 - - + -
848B LMG 4.0 13.7 - - + -
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Residues in contact with PHE 23 (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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12B ILE* 4.1 19.8 - - + +
19B ARG* 3.1 50.7 + - + +
22B TRP* 1.3 83.4 - - + +
24B GLY* 1.3 60.4 + - - +
26B ALA* 4.3 2.0 - - - +
27B THR* 2.9 32.7 + - + +
701B SER* 3.1 40.6 - - - -
703B VAL* 4.9 4.7 - - + -
704B GLN* 3.6 20.4 - - + -
848B LMG 3.2 37.0 - - + -
70C TRP* 4.9 21.8 - + - -
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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