Contacts of the helix formed by residues 118 - 123 (chain C) in PDB entry 3S52
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 TRP 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B GLY 3.1 29.3 + - - -
116B GLN* 3.8 3.0 - - + -
117B PRO* 3.4 50.2 - - + +
119B GLU* 5.5 0.9 - - - +
23C GLY* 5.4 0.4 - - - -
42C VAL* 4.6 8.5 - - + -
44C PHE* 4.3 14.1 - + + -
108C GLN* 3.1 34.8 - - + -
111C PHE* 4.2 14.1 - - + -
112C LYS* 3.8 24.2 - - + +
116C GLN 3.6 14.6 + - - -
117C PRO* 1.3 72.6 - - - +
119C GLU* 1.3 69.0 + - - +
120C LYS 3.2 2.9 - - - -
121C ALA* 2.8 8.9 + - - +
122C LYS* 2.8 43.1 + - + -
219C SO4 3.5 23.1 - - - -
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Residues in contact with GLU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU 4.1 9.4 + - - +
44B PHE* 3.4 11.4 - - - +
45B ILE* 2.9 49.4 + - + +
118B TRP* 5.4 1.1 + - - +
119B GLU* 3.5 32.6 + - - +
179B PHE* 3.5 17.7 - - + -
45C ILE 4.9 2.2 - - - +
117C PRO* 3.3 21.2 - - - +
118C TRP* 1.3 74.5 + - - +
120C LYS* 1.3 61.0 + - - +
122C LYS* 5.0 0.9 - - - -
123C ALA* 2.6 46.2 + - + +
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Residues in contact with LYS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLU* 4.2 10.5 + - - +
41B PRO 2.9 22.9 + - - -
42B VAL* 4.9 1.5 - - - +
43B LEU* 3.9 26.4 + - + +
174B TYR* 2.5 25.2 + - - -
178B PHE* 3.5 45.1 - - + -
179B PHE* 4.0 12.8 - - + -
104C LEU* 3.5 17.5 - - - +
107C LEU* 4.8 2.7 - - + -
111C PHE* 3.6 33.3 - - + -
117C PRO 4.8 1.2 + - - +
118C TRP 3.2 1.0 - - - -
119C GLU* 1.3 78.7 - - - +
121C ALA* 1.3 60.6 + - - +
124C PHE* 3.6 12.3 - - - +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C THR* 3.6 4.4 - - + -
104C LEU* 3.1 49.3 + - - +
107C LEU* 4.1 2.2 - - + -
108C GLN* 3.8 27.8 - - + +
111C PHE* 3.8 9.5 - - + -
118C TRP 2.8 8.2 + - - +
120C LYS* 1.3 81.4 - - - +
122C LYS* 1.3 59.6 + - + +
124C PHE* 3.2 11.7 - - - -
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Residues in contact with LYS 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C PHE* 3.6 39.0 - - + -
45C ILE 5.6 0.9 - - - +
46C LYS* 2.8 32.8 + - + +
70C GLU* 3.1 12.5 + - - -
101C ASP* 2.7 31.4 + - - +
102C LEU 4.4 0.7 - - - -
103C THR* 2.9 26.3 + - + +
108C GLN* 3.6 23.6 - - - +
118C TRP* 2.8 35.1 + - + +
119C GLU* 5.0 0.9 - - - -
121C ALA* 1.3 77.6 - - + +
123C ALA* 1.3 58.0 + - + +
124C PHE 3.6 2.0 - - - -
127C SER* 2.9 8.3 + - - -
219C SO4 3.2 13.8 + - - -
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Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 4.3 2.7 - - + -
179B PHE* 3.5 19.8 - - + -
45C ILE 4.2 8.1 - - - +
46C LYS* 4.7 0.9 - - - -
47C PRO* 3.6 36.2 - - + +
49C THR* 5.0 1.4 + - - -
50C ALA* 4.4 1.0 - - - +
119C GLU* 2.6 40.3 + - + +
122C LYS* 1.3 72.7 - - + +
124C PHE* 1.3 66.8 + - - +
125C ASP 3.9 0.3 + - - -
127C SER* 3.7 2.9 - - - -
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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