Contacts of the helix formed by residues 136 - 151 (chain V) in PDB entry 5XTE
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 136 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63V PHE* 5.1 0.2 - - - -
134V PRO* 3.5 2.2 - - - +
135V TRP* 1.3 77.6 - - - +
137V GLN* 1.3 62.7 + - - -
138V MET 3.7 1.3 - - - -
139V SER* 3.5 9.7 + - - -
140V PHE* 3.4 8.3 + - - +
255V ASN* 3.3 29.4 - - - -
257V THR 3.4 8.7 - - - -
259V ALA* 3.2 22.5 - - - +
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Residues in contact with GLN 137 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136V GLY* 1.3 70.5 - - - +
138V MET* 1.3 61.8 + - - +
140V PHE 3.4 1.2 + - - -
141V TRP* 2.5 68.2 + - - +
254V ASP* 3.3 31.6 + - + +
255V ASN* 3.9 0.4 - - - +
257V THR* 3.4 10.4 + - - +
258V LEU 2.8 21.8 - - - +
259V ALA* 4.1 0.2 - - - +
260V ASN* 3.2 30.4 + - - +
263V ASN* 4.0 5.4 + - - -
265V PRO* 3.5 31.3 - - + +
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Residues in contact with MET 138 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131V TYR* 3.5 20.5 - - + +
137V GLN* 1.3 77.1 - - - +
139V SER* 1.3 58.9 + - - +
141V TRP* 4.6 1.8 - - - +
142V GLY* 2.9 26.0 + - - -
252V ASP* 3.8 12.8 - - - +
254V ASP* 4.1 17.3 - - + +
255V ASN* 3.2 20.9 - - - +
265V PRO* 3.6 32.8 - - + -
267V HIS* 3.4 24.9 - - + -
268V ILE* 3.6 25.3 - - + +
269V LYS 3.5 25.1 - - - +
270V PRO* 6.2 0.4 - - + +
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Residues in contact with SER 139 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131V TYR* 2.8 35.1 + - - -
132V VAL* 3.8 14.6 - - - +
134V PRO* 4.1 5.9 - - - +
135V TRP* 3.8 11.6 + - - -
136V GLY 3.5 20.5 + - - -
137V GLN 3.2 1.0 - - - -
138V MET* 1.3 78.3 - - - +
140V PHE* 1.3 65.4 + - - +
142V GLY* 4.0 0.3 - - - -
143V ALA* 3.1 23.0 + - - +
255V ASN* 3.3 14.2 + - - +
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Residues in contact with PHE 140 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132V VAL* 5.8 0.7 - - - -
135V TRP* 3.5 42.3 - + + +
136V GLY 3.4 17.3 + - - +
137V GLN 3.4 3.0 + - - +
139V SER* 1.3 79.0 - - - +
141V TRP* 1.3 97.2 + + + +
143V ALA* 3.3 7.8 + - - +
144V THR* 3.1 34.9 + - - -
169V SER* 5.0 5.6 - - - -
170V VAL* 4.1 25.3 - - + +
259V ALA* 3.6 17.5 - - + -
260V ASN 4.9 0.7 - - - -
261V PRO* 4.0 33.0 - - + -
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Residues in contact with TRP 141 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137V GLN* 2.5 60.2 + - - +
138V MET 4.5 0.4 - - - +
140V PHE* 1.3 94.3 - + + +
142V GLY* 1.3 64.6 + - - +
144V THR* 3.3 20.5 + - + -
145V VAL* 3.0 33.5 + - + +
260V ASN 2.7 24.1 + - - -
261V PRO* 3.5 19.1 - - + -
262V LEU 4.8 0.2 - - - -
263V ASN 2.8 13.9 - - - -
264V THR* 3.7 19.3 - - + -
265V PRO* 3.2 21.9 - - + +
268V ILE* 3.3 26.0 - - + -
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Residues in contact with GLY 142 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128V PHE* 4.6 4.0 - - - -
131V TYR* 6.1 1.8 - - - -
138V MET 2.9 19.2 + - - -
139V SER 4.0 0.7 - - - -
141V TRP* 1.3 76.6 - - - +
143V ALA* 1.3 58.4 + - - +
145V VAL* 3.3 4.4 + - - -
146V ILE* 2.8 41.2 + - - +
268V ILE* 4.9 2.1 - - - +
270V PRO* 6.2 5.2 - - - -
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Residues in contact with ALA 143 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128V PHE* 4.1 11.4 - - - -
132V VAL* 4.1 23.7 - - + +
139V SER 3.1 14.1 + - - +
140V PHE* 3.5 10.8 - - - +
141V TRP 3.2 0.4 - - - -
142V GLY* 1.3 76.8 - - - +
144V THR* 1.3 58.4 + - - +
147V THR* 1.9 39.7 + - - +
170V VAL* 4.6 16.2 - - + -
178V PHE* 4.6 8.1 - - + -
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Residues in contact with THR 144 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140V PHE* 3.1 31.5 + - - -
141V TRP* 3.3 24.9 + - + -
143V ALA* 1.3 75.0 - - - +
145V VAL* 1.3 66.0 + - + +
147V THR* 3.9 3.2 + - - -
148V ASN* 3.2 41.4 + - - +
165V TRP* 5.1 6.7 - - + -
169V SER* 5.6 0.5 + - - -
170V VAL* 3.7 16.3 - - + +
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Residues in contact with VAL 145 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141V TRP* 3.0 22.1 + - + +
142V GLY* 3.9 5.6 - - - +
144V THR* 1.3 83.6 - - + +
146V ILE* 1.3 68.0 + - + +
148V ASN* 3.6 9.7 + - - +
149V LEU* 3.3 23.6 + - + +
268V ILE* 4.9 15.7 - - + -
278V TYR* 4.6 23.8 - - + +
281V LEU* 5.8 2.0 - - + -
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Residues in contact with ILE 146 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128V PHE* 3.3 42.0 - - + -
142V GLY* 2.8 26.2 + - - +
145V VAL* 1.3 82.2 - - + +
147V THR* 1.3 63.2 + - - +
149V LEU* 3.1 37.9 + - + +
150V LEU* 4.0 5.2 + - + +
270V PRO* 6.2 4.5 - - + -
274V PHE* 6.4 1.6 - - + -
278V TYR* 5.3 9.4 - - + -
281V LEU* 5.2 4.9 - - + -
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Residues in contact with THR 147 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128V PHE* 5.2 2.3 - - + -
143V ALA* 1.9 36.9 + - - +
144V THR 4.0 1.8 - - - -
146V ILE* 1.3 77.7 - - - +
148V ASN* 1.3 63.4 + - - +
150V LEU* 3.0 29.9 + - + +
151V SER 3.7 1.6 + - - -
161V VAL* 3.8 9.3 - - + +
164V ILE* 3.7 24.7 - - + -
165V TRP* 3.1 39.3 + - + +
170V VAL* 4.7 0.3 - - - +
178V PHE* 5.3 7.1 - - + -
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Residues in contact with ASN 148 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144V THR* 3.2 28.4 + - - +
145V VAL* 3.8 8.0 - - - +
146V ILE 3.3 0.4 - - - -
147V THR* 1.3 73.4 - - - +
149V LEU* 1.3 57.3 + - + +
151V SER* 2.7 39.2 + - - -
161V VAL* 4.7 1.7 - - - +
165V TRP* 3.3 30.2 - - - -
287V LYS* 3.4 17.6 + - - +
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Residues in contact with LEU 149 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145V VAL* 3.3 17.9 - - + +
146V ILE* 3.1 31.9 + - + +
147V THR 3.1 0.2 - - - -
148V ASN* 1.3 77.9 - - + +
150V LEU* 1.3 57.9 + - + +
152V ALA* 2.7 33.9 + - - +
153V ILE* 4.2 1.2 + - - +
281V LEU* 3.3 35.7 - - + -
287V LYS* 4.2 14.6 - - + +
291V VAL* 3.8 24.8 - - + +
294V LEU* 4.4 16.6 - - + -
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Residues in contact with LEU 150 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146V ILE* 5.0 5.2 - - + +
147V THR* 3.0 18.7 + - + +
149V LEU* 1.3 82.1 - - + +
151V SER* 1.3 62.0 + - - +
152V ALA 3.0 1.2 + - - -
153V ILE* 3.1 29.4 + - + +
157V GLY* 4.1 4.5 - - - +
160V LEU* 3.4 17.4 - - + +
161V VAL* 3.6 10.3 - - + +
164V ILE* 3.0 39.5 - - + -
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Residues in contact with SER 151 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148V ASN* 2.7 21.7 + - - -
150V LEU* 1.3 76.3 - - - +
152V ALA* 1.3 61.6 + - - +
153V ILE 3.2 8.3 + - - +
157V GLY* 3.8 11.2 - - - -
158V THR* 4.6 8.8 + - - -
161V VAL* 3.1 26.3 - - - +
287V LYS* 4.2 8.0 - - - -
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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