Contacts of the helix formed by residues 110 - 120 (chain O) in PDB entry 3J0S
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 PRO 110 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78O LYS* 2.7 32.1 - - - +
79O ASP* 4.6 6.5 - - - +
80O CYS 5.7 0.4 - - - +
108O SER 4.5 0.4 - - - +
109O ALA* 1.4 77.8 - - + +
111O LEU* 1.3 67.1 + - - +
112O LYS* 3.3 6.1 + - + +
113O SER* 3.5 12.8 + - - +
114O LYS* 3.1 23.0 + - - +
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Residues in contact with LEU 111 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ASP* 4.2 25.8 - - + +
144B ALA 6.1 0.4 - - - +
334B GLU* 4.1 34.3 - - + +
341B ILE* 5.5 4.0 - - + -
345B ILE* 6.5 0.2 - - + -
107O GLU* 5.9 4.3 - - - +
109O ALA 3.1 6.6 + - - +
110O PRO* 1.3 73.0 - - - +
112O LYS* 1.3 68.2 + - + +
114O LYS* 4.4 10.5 - - + -
115O MET* 2.9 69.7 + - + +
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Residues in contact with LYS 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLY 5.3 6.7 - - - +
25B ASP* 3.7 27.1 + - - +
345B ILE* 5.8 1.6 - - + +
44O LYS* 4.4 1.7 - - - -
110O PRO* 3.3 3.9 - - + -
111O LEU* 1.3 89.2 - - + +
113O SER* 1.3 62.3 + - - +
115O MET* 4.0 4.4 + - - +
116O ILE* 3.9 17.8 + - - +
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Residues in contact with SER 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O LEU* 5.7 1.9 - - - +
44O LYS* 3.8 29.6 + - - +
80O CYS* 4.5 17.7 + - - +
110O PRO* 3.5 16.3 + - - +
111O LEU 3.4 0.2 - - - -
112O LYS* 1.3 76.7 - - - +
114O LYS* 1.3 66.7 + - - +
115O MET 3.5 0.2 + - - -
116O ILE 3.5 2.6 + - - -
117O TYR* 3.3 18.4 + - - +
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Residues in contact with LYS 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ALA 3.1 24.9 - - - -
145B SER* 3.2 22.8 + - - +
146B GLY* 3.4 12.9 - - - -
80O CYS* 4.0 20.4 - - + +
105O ALA* 3.6 16.8 + - - +
106O PRO 3.2 22.4 + - - +
107O GLU* 4.2 14.8 - - - +
109O ALA* 4.0 10.1 - - + +
110O PRO 3.1 21.7 + - - +
111O LEU* 4.0 11.2 - - + +
113O SER* 1.3 78.8 - - - +
115O MET* 1.3 58.8 + - - +
117O TYR* 3.1 4.3 + - - +
118O ALA* 2.9 31.4 + - - +
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Residues in contact with MET 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ALA* 4.5 25.1 - - + +
341B ILE* 3.1 33.7 - - + +
342B GLY* 4.7 4.3 - - - +
345B ILE* 3.4 49.6 - - + -
111O LEU* 2.9 42.5 + - + +
112O LYS* 4.4 3.8 - - - +
113O SER 3.3 0.2 - - - -
114O LYS* 1.3 80.7 - - - +
116O ILE* 1.3 61.1 + - - +
118O ALA* 3.5 6.5 + - + +
119O SER* 3.1 31.3 + - - +
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Residues in contact with ILE 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B ILE* 3.3 30.7 - - + +
346B LEU* 4.9 6.2 - - + +
349B LEU* 3.9 36.6 - - + -
4O GLY* 6.0 1.1 - - - -
5O VAL* 4.8 3.6 - - + -
40O LEU* 3.6 14.4 - - + -
44O LYS* 3.3 43.1 - - + -
112O LYS 3.9 12.0 + - - +
113O SER 3.5 1.4 + - - -
114O LYS 3.3 0.4 - - - -
115O MET* 1.3 75.6 - - - +
117O TYR* 1.3 58.1 + - - +
119O SER* 3.4 5.2 + - - -
120O SER* 2.9 35.1 + - - -
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Residues in contact with TYR 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLY 4.9 1.8 - - - -
40O LEU* 4.6 7.3 - - + +
80O CYS* 3.1 29.4 - - + +
81O ARG 2.9 19.9 + - - -
82O TYR* 3.0 70.5 + + - -
103O PHE* 3.2 24.5 - + + -
104O TRP 2.9 37.6 + - - -
105O ALA* 3.4 20.0 - - + -
113O SER 3.3 10.6 + - - +
114O LYS 3.1 8.9 + - - +
116O ILE* 1.3 79.1 - - - +
118O ALA* 1.3 66.9 + - - +
120O SER* 3.2 5.4 + - - -
121O LYS* 3.5 6.0 + - + +
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Residues in contact with ALA 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B TYR* 2.8 50.8 - - - +
144B ALA* 3.8 4.5 - - - +
146B GLY* 3.3 27.7 - - - +
148B THR* 5.1 0.3 + - - -
114O LYS* 2.9 24.7 + - - +
115O MET* 3.8 5.6 - - - +
117O TYR* 1.3 80.9 - - - +
119O SER* 1.3 52.6 + - - +
120O SER 3.3 0.3 + - - -
121O LYS* 3.5 10.5 + - - +
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Residues in contact with SER 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B TYR* 3.1 32.9 + - - -
144B ALA* 5.8 1.0 - - - -
342B GLY* 4.9 0.9 + - - -
345B ILE* 5.5 1.3 - - - +
346B LEU* 3.4 31.3 - - - +
1O MET* 3.4 25.2 - - - +
2O ALA 4.7 1.7 - - - +
3O SER* 4.8 0.2 - - - -
4O GLY 3.8 11.1 + - - -
115O MET* 3.1 22.0 + - - +
116O ILE* 3.8 3.8 - - - -
118O ALA* 1.3 77.0 - - - +
120O SER* 1.3 56.4 + - - +
122O ASP 4.5 0.2 + - - -
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Residues in contact with SER 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O GLY* 4.3 9.9 - - - +
5O VAL* 3.2 35.7 - - - +
40O LEU* 5.0 1.1 - - - +
47O ILE* 4.3 3.6 - - - +
82O TYR* 3.0 24.3 + - - -
116O ILE* 2.9 16.5 + - - -
117O TYR 3.2 0.8 + - - -
119O SER* 1.3 77.1 - - - +
121O LYS* 1.3 58.6 + - - +
122O ASP 3.3 2.9 - - - -
123O ALA* 3.1 5.2 + - - +
124O ILE* 2.7 26.0 + - - +
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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