Contacts of the strand formed by residues 117 - 125 (chain D) in PDB entry 3RT0
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 SER 117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93D GLU* 4.3 4.9 - - - -
104D ILE 3.3 13.0 - - - -
105D ARG* 3.7 31.8 + - - -
115D ASN 3.6 1.3 + - - -
116D TYR* 1.3 78.6 - - - +
118D SER* 1.3 61.3 + - - +
139D PHE* 3.2 3.1 - - - +
140D VAL* 2.9 53.2 + - - +
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Residues in contact with SER 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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102D LEU 4.7 0.2 - - - -
103D GLY* 3.4 3.5 - - - -
104D ILE* 3.0 40.8 + - - +
116D TYR* 3.6 27.1 - - - -
117D SER* 1.3 74.6 - - - +
119D THR* 1.3 63.4 + - - +
137D GLU* 3.9 17.0 + - - -
138D SER 3.0 17.7 - - - -
139D PHE* 4.0 2.0 - - - +
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Residues in contact with THR 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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94D ILE* 5.0 8.9 - - + +
101D ILE* 3.9 24.7 - - + -
102D LEU 3.4 5.4 - - - +
103D GLY* 4.7 3.8 - - - -
118D SER* 1.3 76.7 + - - +
120D ILE* 1.3 64.9 + - - +
121D SER* 4.6 3.8 - - - +
136D ILE 3.7 1.0 - - - +
137D GLU* 3.3 4.7 - - - -
138D SER* 2.9 45.1 + - - +
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Residues in contact with ILE 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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43D TRP* 5.1 0.5 - - - -
46D VAL* 3.9 25.4 - - + -
55D TYR* 5.3 6.7 - - + +
100D HIS 4.1 0.3 - - - +
101D ILE* 3.3 4.3 - - - +
102D LEU* 2.9 64.0 + - + +
119D THR* 1.3 77.2 - - - +
121D SER* 1.3 61.0 + - - +
122D LEU* 4.0 26.5 - - + -
135D ALA* 4.4 2.9 - - + -
136D ILE 3.2 11.7 - - - +
137D GLU* 4.2 24.0 - - + +
164D LEU* 4.4 17.7 - - + -
167D LEU* 4.8 2.0 - - + -
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Residues in contact with SER 121 (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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100D HIS 3.5 4.7 - - - -
101D ILE* 3.9 22.7 - - - -
119D THR* 4.2 4.6 - - - +
120D ILE* 1.3 74.4 - - - +
122D LEU* 1.3 67.0 + - - +
123D HIS* 2.9 31.5 + - - -
134D LEU 3.8 1.0 - - - +
135D ALA* 3.8 0.3 - - - -
136D ILE* 2.9 42.9 + - - +
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Residues in contact with LEU 122 (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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39D LEU* 3.3 18.4 - - + +
42D VAL* 3.6 24.5 - - + -
43D TRP* 3.6 50.5 - - + +
46D VAL* 4.1 6.3 - - + -
99D GLU 4.1 5.5 - - - +
100D HIS* 3.0 21.8 + - + +
120D ILE* 4.0 16.6 - - + -
121D SER* 1.3 80.9 - - - +
123D HIS* 1.3 71.8 + - - +
133D THR* 4.1 3.4 - - + -
134D LEU 3.5 1.8 - - - +
135D ALA* 3.7 26.5 - - + -
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Residues in contact with HIS 123 (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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39D LEU* 4.1 2.4 - - - +
99D GLU 5.8 1.6 - - - -
101D ILE* 6.2 0.9 - - + -
121D SER* 2.9 31.1 + - - -
122D LEU* 1.3 85.5 + - - +
124D SER* 1.3 66.6 + - - +
125D GLU* 6.0 0.2 - - + -
133D THR* 3.6 4.2 - - - +
134D LEU* 2.7 56.5 + - + +
136D ILE* 3.7 27.1 - - + +
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Residues in contact with SER 124 (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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39D LEU* 4.1 29.3 + - - +
123D HIS* 1.3 77.6 - - - +
125D GLU* 1.3 59.6 + - - +
131D THR* 4.0 14.9 - - - +
132D GLY 3.5 11.9 + - - -
133D THR* 4.5 1.1 - - - +
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Residues in contact with GLU 125 (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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34D HIS* 2.7 47.5 + - - +
35D ILE 4.7 0.9 + - - +
123D HIS* 4.2 2.7 - - + +
124D SER* 1.3 76.8 + - - +
126D THR* 1.3 65.4 + - - +
127D ILE* 3.0 21.6 - - + +
131D THR* 2.9 7.1 - - - +
132D GLY* 2.3 45.4 + - - +
133D THR 4.1 2.1 + - - +
134D LEU* 3.4 30.7 - - + +
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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