Contacts of the helix formed by residues 127 - 138 (chain B) in PDB entry 5TTE
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 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B GLN 4.6 0.7 - - - +
126B ASN* 1.3 86.6 - - + +
128B ALA* 1.3 59.0 + - - +
129B THR* 3.0 6.3 - - + +
130B ILE* 2.7 40.2 + - + +
131B THR 3.2 6.1 + - - -
165B ASN* 3.5 26.7 - - - +
166B PRO* 4.0 21.5 - - + -
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL* 6.1 4.5 - - + -
117B ILE* 4.1 12.1 - - + +
121B ASN* 3.7 15.2 - - - +
126B ASN 3.3 2.0 + - - -
127B PRO* 1.3 70.8 - - - +
129B THR* 1.3 64.2 + - + +
131B THR 3.8 0.4 + - - -
132B ARG* 3.2 30.6 + - - +
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B PRO* 2.9 4.0 + - + +
128B ALA* 1.3 78.9 - - + +
130B ILE* 1.3 83.8 + - - +
132B ARG* 3.3 30.3 + - - +
133B ILE* 3.5 11.3 + - - +
227B GLN* 5.0 0.5 - - - +
238B ILE* 4.9 2.1 - - - +
239B LEU* 3.3 26.8 + - + +
240B VAL 4.3 2.0 - - - +
241B ASP* 3.6 40.2 - - + +
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ASN* 3.9 27.1 - - + +
127B PRO* 2.7 27.7 + - + +
129B THR* 1.3 89.8 + - - +
131B THR* 1.3 58.8 + - - +
133B ILE* 2.8 23.7 + - - +
134B LEU* 3.1 28.5 + - + +
158B PHE* 4.1 8.3 - - + -
163B VAL* 3.4 22.7 - - + -
164B ILE 4.2 2.7 - - - +
165B ASN* 3.2 22.2 - - - +
238B ILE* 4.2 14.1 - - + -
239B LEU* 3.8 13.7 - - + -
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ILE* 4.2 12.6 - - + +
120B VAL* 3.9 17.3 - - + -
121B ASN* 2.9 34.3 + - + +
124B ILE* 4.7 5.4 - - + +
126B ASN* 3.4 18.0 + - - +
127B PRO 3.2 2.3 + - - -
128B ALA 4.3 0.2 - - - -
130B ILE* 1.3 78.3 - - - +
132B ARG* 1.3 61.3 + - - +
134B LEU* 3.9 7.8 - - + +
135B LEU* 3.2 44.1 + - + +
145B LEU* 4.7 6.7 - - + -
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 6.3 0.4 - - - -
113B MET* 4.2 7.9 - - + +
114B VAL* 6.5 0.4 - - - -
117B ILE* 3.5 30.5 - - + +
128B ALA* 3.2 23.6 + - - +
129B THR* 3.3 19.7 + - - +
130B ILE 3.1 0.2 + - - -
131B THR* 1.3 77.8 - - - +
133B ILE* 1.3 59.5 + - - +
136B SER* 3.0 30.1 + - - -
140B TRP* 4.3 4.7 - - - -
227B GLN* 2.4 46.9 + - - +
240B VAL 4.5 3.7 + - - -
241B ASP* 4.2 5.7 - - - +
242B ASP* 3.3 34.9 - - - +
258B TYR* 3.3 21.8 + - - -
262B ILE* 3.6 23.4 - - - +
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B THR 3.7 13.9 - - - +
130B ILE* 2.8 15.8 + - - +
132B ARG* 1.3 69.2 - - - +
134B LEU* 1.3 55.4 + - + +
136B SER* 3.0 7.5 + - - -
137B HIS* 2.7 34.4 + - + +
161B CYS* 4.0 35.2 - - + +
163B VAL* 4.5 10.3 - - + -
227B GLN* 3.5 29.4 - - + +
228B THR* 3.6 25.6 - - + -
239B LEU* 4.7 14.1 - - + -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ILE* 5.3 1.6 - - + -
126B ASN* 4.2 3.6 - - - +
130B ILE* 3.1 39.2 + - + +
131B THR* 4.1 6.5 - - - +
132B ARG 3.5 0.2 - - - -
133B ILE* 1.3 79.9 - - + +
135B LEU* 1.3 58.5 + - - +
137B HIS* 3.1 7.3 + - - +
138B PHE* 2.9 34.1 + - - -
145B LEU* 3.8 22.0 - - + -
149B TYR* 3.8 28.9 - - + -
157B LEU* 4.2 18.2 - - + -
158B PHE* 4.2 14.1 - - + -
161B CYS* 4.8 6.5 - - + -
163B VAL* 4.3 21.3 - - + -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B CYS* 4.9 1.6 - - - -
117B ILE* 4.4 10.5 - - + -
120B VAL* 3.8 30.7 - - + -
131B THR* 3.2 24.2 + - + +
134B LEU* 1.3 75.7 - - - +
136B SER* 1.3 61.3 + - - +
138B PHE* 3.1 4.2 + - + +
139B ASN 3.1 4.9 + - - -
140B TRP* 2.7 66.3 + - + -
141B ASP 4.6 3.8 - - - +
142B LYS* 4.1 29.4 - - + +
145B LEU* 3.8 24.5 - - + -
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG 3.0 19.4 + - - -
133B ILE* 3.0 7.9 + - - -
135B LEU* 1.3 76.0 - - - +
137B HIS* 1.3 59.8 + - - +
139B ASN* 3.7 12.1 + - - -
140B TRP* 3.2 21.2 + - - +
227B GLN* 4.0 9.1 + - - -
265B SER* 2.8 33.0 + - - -
269B CYS* 5.5 1.0 - - - -
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Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 2.7 17.2 + - + +
134B LEU 3.3 8.3 - - - +
135B LEU 3.0 0.2 - - - -
136B SER* 1.3 72.1 - - - +
138B PHE* 1.3 80.3 + + - +
139B ASN* 3.1 18.3 + - - +
157B LEU* 4.0 4.7 - - + +
160B GLU* 3.6 31.3 + - + -
161B CYS* 3.3 34.2 - - - -
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Residues in contact with PHE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU 2.9 21.7 + - - +
135B LEU* 3.1 4.9 + - - +
137B HIS* 1.3 84.8 - + - +
139B ASN* 1.3 71.8 + - - +
140B TRP 3.1 1.6 - - - -
141B ASP* 3.1 28.4 + - - +
144B LYS* 3.4 29.6 - - + +
145B LEU* 3.5 34.1 - - + -
148B ARG* 3.8 34.1 - - + -
157B LEU* 3.7 25.6 - - + -
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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