Contacts of the helix formed by residues 130 - 142 (chain Y) 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 GLY 130 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1Y THR 3.0 8.1 + - - -
2Y THR* 3.1 23.2 - - - +
129Y SER* 1.3 79.6 - - - +
131Y GLN* 1.3 63.4 + - - +
132Y THR 3.3 2.9 - - - -
133Y PHE* 3.1 22.5 + - - +
134Y ALA 3.4 8.0 + - - -
162Y ALA* 3.5 4.6 - - - +
166Y ASP* 3.1 17.8 + - - -
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Residues in contact with GLN 131 (chain Y).
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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22X ARG 5.4 1.2 + - - -
24X ILE* 3.8 8.0 - - - +
25X SER* 2.7 41.6 + - - +
27X LEU* 5.1 3.4 - - - +
2Y THR* 4.3 4.9 - - - +
126Y CYS* 3.9 35.1 + - + +
127Y VAL* 4.0 2.5 - - - +
128Y GLY* 3.0 34.1 + - - +
129Y SER 5.0 0.9 - - - +
130Y GLY* 1.3 76.9 - - - +
132Y THR* 1.3 76.9 + - + +
134Y ALA* 3.1 6.1 + - - +
135Y TYR* 2.9 31.5 + - - -
999Y BFO 4.1 19.0 - - + +
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Residues in contact with THR 132 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J PHE* 2.8 48.1 + - + +
133J TYR* 3.7 27.6 - - + +
161J GLU* 4.6 1.0 - - - +
24X ILE* 3.6 30.5 - - + -
25X SER* 4.0 12.1 - - - +
129Y SER 5.1 1.6 + - - -
130Y GLY 4.8 0.5 - - - -
131Y GLN* 1.3 81.9 - - + +
133Y PHE* 1.3 67.6 + - - +
135Y TYR* 3.6 9.6 + - - +
136Y GLY* 3.3 17.0 + - - -
999Y BFO 6.1 0.4 - - + -
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Residues in contact with PHE 133 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I LEU* 3.7 15.9 - - + -
131J GLY 4.0 6.3 - - - -
132J PHE* 3.5 53.4 - + - -
135J PHE* 4.3 1.1 - - + -
136J SER* 2.9 40.1 + - - -
129Y SER 4.5 5.2 - - - -
130Y GLY* 3.1 19.9 + - - +
132Y THR* 1.3 77.4 - - - +
134Y ALA* 1.3 66.1 + - - +
136Y GLY 3.2 4.2 + - - -
137Y VAL* 3.5 4.9 + - - +
161Y ALA* 4.1 5.2 - - - -
162Y ALA* 3.6 21.3 - - - +
165Y ARG* 3.5 42.2 - - + -
166Y ASP* 4.0 15.9 - - + -
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Residues in contact with ALA 134 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y THR* 3.9 22.4 - - + -
4Y LEU* 4.5 4.9 - - + -
126Y CYS* 3.8 17.9 - - - -
130Y GLY 3.4 1.4 + - - -
131Y GLN 3.1 8.1 + - - +
133Y PHE* 1.3 79.3 - - - +
135Y TYR* 1.3 61.8 + - - +
137Y VAL* 3.2 4.9 + - - +
138Y LEU* 3.0 24.1 + - - +
158Y SER* 3.7 32.1 + - - +
162Y ALA* 4.4 0.2 - - - +
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Residues in contact with TYR 135 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161J GLU* 3.6 11.7 - - - +
165J ARG* 3.3 51.7 + - + +
25X SER* 4.1 24.0 - - - -
27X LEU* 3.9 15.1 + - + +
124Y ILE* 4.2 11.3 + - + -
125Y PHE* 3.6 14.3 - - - -
126Y CYS* 3.0 55.1 + - + -
131Y GLN* 2.9 28.4 + - - +
132Y THR* 3.8 8.3 - - - +
133Y PHE 3.3 0.2 - - - -
134Y ALA* 1.3 75.1 - - - +
136Y GLY* 1.3 59.1 + - - +
138Y LEU* 4.4 2.2 - - + -
139Y ASP* 2.7 37.5 + - - +
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Residues in contact with GLY 136 (chain Y).
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 4.3 2.0 - - - -
136J SER* 3.7 12.3 - - - -
137J LEU* 3.5 15.5 - - - +
161J GLU* 3.4 21.6 + - - +
132Y THR 3.3 6.3 + - - -
133Y PHE 3.2 4.9 + - - -
135Y TYR* 1.3 81.7 - - - +
137Y VAL* 1.3 63.6 + - - +
139Y ASP* 4.0 1.7 - - - +
140Y SER* 3.3 20.3 + - - -
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Residues in contact with VAL 137 (chain Y).
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* 3.8 12.7 + - - +
137J LEU* 4.8 2.5 - - + -
140J HIS* 6.1 3.6 - - + -
133Y PHE 3.5 5.7 + - - +
134Y ALA 3.2 3.5 + - - +
136Y GLY* 1.3 75.7 - - - +
138Y LEU* 1.3 62.6 + - - +
140Y SER* 4.3 2.7 - - - -
141Y ASN* 3.3 30.9 + - - +
154Y LEU* 3.8 13.9 - - + -
157Y ARG* 4.3 19.3 - - + +
158Y SER* 2.9 31.0 - - - +
161Y ALA* 3.4 33.0 - - + -
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Residues in contact with LEU 138 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y LEU* 4.0 17.0 - - + -
5Y ALA 5.5 0.2 - - - +
6Y PHE* 4.3 20.0 - - + -
124Y ILE* 3.5 35.0 - - + -
126Y CYS* 3.7 24.5 - - - -
134Y ALA 3.0 11.5 + - - +
135Y TYR* 3.8 4.3 - - + +
137Y VAL* 1.3 77.2 - - - +
139Y ASP* 1.3 58.3 + - - +
141Y ASN 3.1 0.3 + - - -
142Y TYR* 2.8 37.4 + - + +
154Y LEU* 3.8 26.2 - - + +
158Y SER* 2.8 32.7 + - - +
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Residues in contact with ASP 139 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161J GLU* 3.0 28.5 - - - +
164J LYS* 3.4 19.0 - - + +
165J ARG* 2.9 45.4 + - - +
124Y ILE* 4.8 8.3 - - - +
135Y TYR* 2.7 23.9 + - - +
136Y GLY 4.0 1.1 - - - +
138Y LEU* 1.3 74.8 - - - +
140Y SER* 1.3 60.9 + - - +
141Y ASN 3.6 0.2 + - - -
142Y TYR* 4.2 9.2 + - - +
143Y LYS* 5.8 0.2 + - - -
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Residues in contact with SER 140 (chain Y).
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* 3.6 14.8 - - - +
141J HIS* 5.0 3.8 - - - -
157J LEU* 4.3 27.0 - - - +
136Y GLY 3.3 15.3 + - - -
137Y VAL* 3.3 2.1 + - - -
138Y LEU 3.2 0.2 - - - -
139Y ASP* 1.3 79.4 - - - +
141Y ASN* 1.3 74.0 + - - +
143Y LYS* 3.9 14.6 + - - -
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Residues in contact with ASN 141 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J HIS* 5.1 12.2 + - - -
141J HIS* 5.3 5.5 - - - -
137Y VAL* 3.3 10.1 + - - +
138Y LEU 3.1 1.8 + - - -
140Y SER* 1.3 96.0 + - - +
142Y TYR* 1.3 66.7 + - - +
143Y LYS* 3.5 12.4 + - - +
146Y LEU* 3.9 9.0 - - - +
154Y LEU* 3.6 31.3 - - + +
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Residues in contact with TYR 142 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y PHE* 3.6 30.7 - + + -
7Y ARG* 2.5 31.4 + - - +
8Y PHE* 4.5 1.3 - - + -
123Y ASP* 4.9 8.0 - - + +
124Y ILE* 3.6 32.1 - - + -
138Y LEU* 2.8 19.2 + - + +
139Y ASP* 4.2 6.7 + - - +
140Y SER 3.7 0.2 - - - -
141Y ASN* 1.3 78.4 - - - +
143Y LYS* 1.3 97.4 + - - +
144Y TRP* 3.5 23.3 - - + +
146Y LEU* 4.9 1.8 - - + -
154Y LEU* 3.9 10.1 - - + +
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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