Contacts of the helix formed by residues 129 - 142 (chain J) in PDB entry 3TDD
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 TYR 129 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1J MET* 4.8 20.9 - - + +
1J ASP 5.6 0.6 + - - -
127J HIS 3.7 0.2 + - - -
128J GLY* 1.3 75.3 - - - -
130J SER* 1.3 66.2 + - - +
131J GLY 3.2 2.7 - - - -
132J PHE* 2.9 37.5 + + - +
133J TYR* 3.5 24.0 - - + +
166J MET* 5.3 6.1 - - - -
24X ILE* 4.1 28.3 - - + -
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Residues in contact with SER 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1J ASP 3.8 2.8 + - - -
2J ILE* 3.5 32.9 - - - +
3J ILE 3.6 2.6 + - - -
4J LEU* 3.9 12.1 - - - -
126J ALA* 3.8 13.5 - - - -
127J HIS 3.3 17.9 + - - -
128J GLY 3.3 0.4 - - - -
129J TYR* 1.3 77.6 - - - +
131J GLY* 1.3 61.4 + - - +
133J TYR* 3.4 2.4 + - - -
134J THR* 2.9 28.8 + - - +
162J LEU* 4.2 13.4 - - - +
166J MET* 5.8 1.2 - - - -
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Residues in contact with GLY 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I LEU* 5.0 3.8 - - - -
126J ALA* 3.7 6.3 - - - +
128J GLY 4.4 3.4 + - - -
129J TYR 3.0 1.8 + - - -
130J SER* 1.3 79.2 - - - +
132J PHE* 1.3 60.1 + - - +
134J THR* 3.8 6.3 - - - -
135J PHE* 2.8 67.4 + - - +
133Y PHE* 4.0 0.6 - - - -
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Residues in contact with PHE 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I SER 5.4 1.6 - - - -
24I SER* 4.1 17.7 - - - -
25I LEU* 3.8 31.2 - - + +
128J GLY 4.1 11.4 - - - -
129J TYR* 2.9 39.1 + + - +
131J GLY* 1.3 77.6 - - - +
133J TYR* 1.3 59.2 + - + +
24X ILE* 4.5 13.7 - - + -
129Y SER 5.0 7.4 - - - -
132Y THR* 2.8 50.0 + - + +
133Y PHE* 3.5 36.2 - + - -
166Y ASP* 6.1 0.2 - - - -
999Y BFO 5.7 4.5 - - - -
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Residues in contact with TYR 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J TYR* 3.5 27.3 - - + +
130J SER 3.4 0.4 + - - -
131J GLY 3.2 0.4 - - - -
132J PHE* 1.3 79.1 - - + +
134J THR* 1.3 61.5 + - - +
135J PHE 3.8 0.2 - - - -
136J SER* 4.2 11.2 + - - -
137J LEU* 4.4 1.7 - - - +
161J GLU* 3.4 29.0 - - + +
162J LEU* 3.5 31.4 - - + -
165J ARG* 3.9 29.2 - - + -
166J MET* 3.2 30.8 - - + +
167J PRO* 4.1 1.7 - - - +
24X ILE* 2.6 44.2 + - + +
25X SER* 4.4 2.5 - - - -
132Y THR* 3.7 29.5 - - + +
135Y TYR* 6.4 0.2 - - + -
136Y GLY* 4.3 4.9 - - - -
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Residues in contact with THR 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 3.7 15.0 - - + +
130J SER 2.9 24.5 + - - +
131J GLY* 3.8 2.6 - - - -
133J TYR* 1.3 80.8 - - - +
135J PHE* 1.3 70.3 + - - +
136J SER 3.3 3.1 - - - -
137J LEU* 3.0 17.2 + - - +
138J LEU* 3.0 16.8 + - - +
158J CYS* 3.6 38.8 - - + +
162J LEU* 3.7 27.8 - - + +
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Residues in contact with PHE 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I LEU* 3.9 26.7 - - + -
26I GLY 4.6 0.9 - - - -
27I VAL* 5.6 5.2 - - + -
112J GLN* 4.8 4.0 - - - -
122J LEU* 5.9 1.6 - - + -
124J TYR* 4.2 10.8 - + - -
125J GLY* 4.1 20.0 - - - -
126J ALA* 3.8 24.2 - - + -
131J GLY* 2.8 41.9 + - - +
133J TYR 3.8 0.2 - - - -
134J THR* 1.3 73.5 + - - +
136J SER* 1.3 57.3 + - - +
138J LEU* 4.0 16.2 - - + +
139J ASP* 2.7 36.6 + - - +
133Y PHE* 4.3 4.9 - - + -
165Y ARG* 3.5 47.1 - - - +
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Residues in contact with SER 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J TYR 4.2 4.7 + - - -
134J THR 4.9 0.2 - - - +
135J PHE* 1.3 77.7 - - - +
137J LEU* 1.3 63.4 + - - +
139J ASP* 3.8 9.0 - - - +
140J HIS* 3.3 21.0 + - - +
133Y PHE* 2.9 45.9 + - - -
136Y GLY* 3.7 15.6 - - - -
137Y VAL* 3.8 9.4 + - - +
157Y ARG* 5.0 2.1 + - - -
161Y ALA* 3.9 22.8 - - - +
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Residues in contact with LEU 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J TYR 4.4 5.4 - - - +
134J THR 3.0 8.1 + - - +
136J SER* 1.3 84.3 + - - +
138J LEU* 1.3 65.3 + - - +
140J HIS* 3.1 4.2 + - + +
141J HIS* 3.0 35.1 + - + +
154J LEU* 4.6 3.1 - - + -
157J LEU* 4.0 33.2 - - + +
158J CYS* 4.0 18.2 - - - -
161J GLU* 3.8 30.1 - - + -
136Y GLY* 3.5 30.1 - - - +
137Y VAL* 4.4 2.9 - - + +
140Y SER* 3.6 18.2 - - - +
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Residues in contact with LEU 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 5.5 6.1 - - + -
5J GLY 5.4 1.6 - - - +
6J ILE* 4.1 18.2 - - + -
124J TYR* 3.3 46.2 - - + -
125J GLY 5.4 1.1 - - - +
134J THR* 3.0 25.5 + - - +
135J PHE* 3.9 15.5 - - + +
137J LEU* 1.3 70.1 - - - +
139J ASP* 1.3 67.2 + - - +
140J HIS 2.9 2.0 - - - -
142J TYR* 2.9 30.1 + - - +
154J LEU* 3.7 33.0 - - + -
155J LEU* 5.8 4.3 - - + +
158J CYS* 3.8 15.7 - - - -
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Residues in contact with ASP 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J TYR* 2.5 28.9 + - - -
135J PHE 2.7 24.2 + - - +
136J SER* 3.8 7.9 - - - +
138J LEU* 1.3 73.2 - - - +
140J HIS* 1.3 59.1 + - - +
142J TYR* 4.8 1.8 + - - +
161Y ALA* 5.2 1.6 - - + +
164Y HIS* 3.5 21.8 + - - -
165Y ARG* 2.9 40.1 + - - +
206Y PHE* 2.8 50.6 + - + +
207Y ASN 4.3 1.6 + - - -
208Y ASN* 5.5 2.1 + - - +
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Residues in contact with HIS 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J SER 3.3 11.4 + - - +
137J LEU* 3.1 8.7 + - - +
138J LEU 2.9 2.0 - - - -
139J ASP* 1.3 81.2 - - - +
141J HIS* 1.3 82.9 + + + +
142J TYR 3.5 0.6 + - - +
143J ARG* 2.8 28.1 + - - -
137Y VAL* 6.1 4.5 - - + -
141Y ASN* 5.1 13.7 + - - -
157Y ARG* 3.0 28.7 + - + +
203Y GLU* 3.0 38.6 + - + -
205Y SER* 3.4 19.8 - - - -
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Residues in contact with HIS 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J LEU* 3.0 24.7 + - + -
140J HIS* 1.3 97.2 + + + +
142J TYR* 1.3 65.5 + - - +
143J ARG* 3.0 20.9 + - - +
146J MET* 4.3 8.3 - - + +
154J LEU* 3.8 26.2 - - + +
157J LEU* 4.1 24.1 - - + +
140Y SER* 5.0 5.8 - - - -
141Y ASN* 5.3 3.1 + - - -
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Residues in contact with TYR 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ILE* 3.9 24.5 - - + -
7J ARG* 2.5 46.9 + - - -
8J VAL* 4.4 2.0 - - - -
123J PRO* 3.6 21.2 - - + +
124J TYR* 3.6 28.9 - + + +
138J LEU 2.9 25.2 + - - +
139J ASP* 4.7 1.7 - - - +
140J HIS 3.5 1.7 - - - +
141J HIS* 1.3 71.6 - - - +
143J ARG* 1.3 88.0 + - - +
144J PRO* 3.7 32.2 + - + +
146J MET* 4.1 5.4 - - - -
154J LEU* 3.9 9.0 - - + +
207Y ASN* 3.5 25.0 + - + +
208Y ASN* 5.2 3.4 - - + -
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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