Contacts of the helix formed by residues 113 - 120 (chain D) in PDB entry 3SZ9
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 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107D THR* 3.6 0.2 + - - -
111D GLY 3.7 2.7 - - - +
112D LYS* 1.3 90.5 - - + +
114D TYR* 1.3 58.2 + - - +
115D VAL* 4.4 4.5 - - + +
116D ILE* 2.8 45.5 + - + +
117D SER 2.9 11.3 + - - -
297D ASN* 6.2 0.7 - - - -
298D GLN* 3.4 16.2 - - - +
334D PRO* 3.5 13.9 - - + +
339D THR* 4.2 17.0 - - + +
340D GLU 3.5 30.3 - - - +
342D GLY* 4.1 5.2 - - - +
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Residues in contact with TYR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 2.9 32.2 - - + +
9D PRO* 2.6 35.8 + - - +
10D ALA 4.1 0.2 - - - -
11D PRO* 3.7 39.0 - - + +
100D THR* 3.9 13.2 - - - +
103D ALA* 3.9 8.7 - - + -
104D ALA* 3.8 33.9 - - + -
107D THR* 3.0 18.1 + - - +
112D LYS 3.5 0.2 + - - -
113D PRO* 1.3 71.2 - - - +
115D VAL* 1.3 70.9 + - + +
117D SER* 3.4 1.2 + - - -
118D TYR* 2.9 27.7 + + + +
334D PRO 2.9 13.2 + - - +
335D PHE* 3.7 23.6 - + + -
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 4.4 17.3 - - + -
113D PRO* 3.1 4.5 - - + -
114D TYR* 1.3 87.7 - - + +
116D ILE* 1.3 69.0 + - + +
118D TYR* 3.4 0.7 + - - +
119D LEU* 2.8 50.7 + - + +
334D PRO 4.7 0.4 + - - -
336D ASP 5.6 0.9 - - - +
337D SER* 4.5 28.7 - - - +
339D THR 5.9 2.0 - - - +
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Residues in contact with ILE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LYS* 5.2 6.1 - - + -
113D PRO* 2.8 39.8 + - + +
115D VAL* 1.3 80.4 - - + +
117D SER* 1.3 59.3 + - - +
119D LEU* 5.0 0.9 - - + -
120D VAL* 2.8 56.1 + - + +
121D ASP* 3.3 7.7 + - - +
296D PHE* 3.7 33.7 - - + -
297D ASN* 5.8 1.3 - - - +
340D GLU* 5.3 2.5 - - - +
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Residues in contact with SER 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ALA* 3.5 27.8 + - - -
106D GLU* 3.9 6.4 - - - +
107D THR* 3.1 25.2 + - - -
112D LYS* 3.3 21.6 - - - +
113D PRO 2.9 5.7 + - - -
114D TYR 3.5 5.4 - - - -
116D ILE* 1.3 76.3 - - - +
118D TYR* 1.3 56.6 + - - +
121D ASP* 3.5 11.1 + - - +
122D LEU* 2.9 37.1 + - - +
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Residues in contact with TYR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ALA 5.0 2.0 - - - -
8D VAL* 3.9 18.6 - - + -
9D PRO* 3.3 23.1 - - + +
99D ARG* 2.7 84.0 + - + +
100D THR* 3.4 28.8 + - - -
103D ALA* 3.8 11.2 - - + -
114D TYR* 2.9 29.3 + - + +
115D VAL 3.9 2.7 - - - +
117D SER* 1.3 77.3 - - - +
119D LEU* 1.3 75.4 + - + +
120D VAL 3.6 0.3 + - - -
122D LEU* 3.8 5.4 - - - +
123D ASP 4.0 0.2 + - - -
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ALA 4.9 14.4 - - - +
8D VAL* 3.7 21.3 - - + -
99D ARG* 4.0 5.2 + - - +
115D VAL* 2.8 34.5 + - + +
116D ILE* 4.7 1.1 - - + +
118D TYR* 1.3 95.7 - - + +
120D VAL* 1.3 65.7 + - + +
123D ASP* 3.3 20.0 - - - +
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Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ILE* 2.8 36.5 + - + +
118D TYR 3.4 0.2 - - - -
119D LEU* 1.3 84.9 - - + +
121D ASP* 1.3 80.3 + - - +
122D LEU 3.4 0.2 - - - -
123D ASP* 3.1 4.0 + - - +
124D MET* 2.9 43.7 + - - +
170D PHE* 6.0 0.4 - - + -
296D PHE* 4.2 20.6 - - + -
8001D I3E 5.1 4.0 - - + -
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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