Contacts of the helix formed by residues 139 - 151 (chain B) in PDB entry 5DTM
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 THR 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B PHE* 4.1 21.1 - - + -
135B VAL 4.2 1.6 + - - -
138B GLU* 1.3 83.1 + - - +
140B SER* 1.4 61.3 + - - +
141B PHE 3.3 2.0 - - - -
142B ASP* 3.2 9.6 + - - +
143B LEU* 3.0 26.6 + - + +
305B TRP* 4.5 8.3 - - + -
308B LYS* 3.6 34.0 + - + +
310B VAL* 3.9 34.5 - - + -
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Residues in contact with SER 140 (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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131B PHE* 3.4 32.4 + - - +
135B VAL 4.9 2.0 + - - -
136B TYR* 3.3 39.4 + - - -
139B THR* 1.4 74.0 - - - +
141B PHE* 1.3 56.6 + - - +
143B LEU 3.3 0.2 + - - -
144B VAL* 2.8 41.1 + - - +
401B 5F4 3.5 18.3 - - - +
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Residues in contact with PHE 141 (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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104B THR* 3.5 43.3 - - + -
107B LEU* 4.0 10.1 - - + -
108B ARG* 3.6 55.2 - - + +
111B LEU* 3.7 20.0 - - + -
136B TYR* 3.1 22.2 + + + +
137B GLY* 4.3 15.5 - - - +
139B THR 3.3 0.4 - - - -
140B SER* 1.3 74.4 - - - +
142B ASP* 1.3 60.3 + - - +
145B ALA* 3.0 14.8 + - + +
172B GLN* 2.9 55.6 + - - -
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Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A THR* 4.7 0.2 + - - -
104B THR* 6.0 0.2 - - - +
108B ARG* 2.8 40.8 + - - -
137B GLY 4.9 0.8 + - - +
138B GLU 4.1 14.6 - - - +
139B THR* 3.2 6.0 + - - +
141B PHE* 1.3 78.3 - - - +
143B LEU* 1.3 57.6 + - - +
145B ALA* 3.4 6.8 + - - +
146B GLN* 3.1 27.0 + - - +
305B TRP* 3.7 28.1 - - + -
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Residues in contact with LEU 143 (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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131B PHE* 5.1 2.0 - - + -
139B THR 3.0 17.2 + - - +
140B SER 4.0 1.3 - - - +
142B ASP* 1.3 72.1 - - - +
144B VAL* 1.3 60.6 + - - +
146B GLN* 3.3 6.9 + - + +
147B MET* 2.9 28.1 + - - +
298B PRO* 3.8 37.0 - - + -
305B TRP* 3.9 5.8 - - + -
310B VAL* 3.9 23.8 - - + +
311B SER 4.3 9.0 - - - +
312B TYR* 4.0 15.4 - - + -
401B 5F4 3.5 53.6 - - + -
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TYR* 3.5 15.5 - - + +
140B SER 2.8 25.2 + - - +
143B LEU* 1.3 72.2 - - - +
145B ALA* 1.4 50.3 + - - +
147B MET* 3.2 10.2 + - + +
148B ILE* 2.8 44.3 + - + +
169B VAL* 4.4 10.1 - - + -
172B GLN* 3.5 30.1 - - + +
173B VAL* 4.1 15.5 - - + -
239B PHE* 4.3 11.0 - - + -
401B 5F4 3.6 23.8 - - + -
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Residues in contact with ALA 145 (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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104B THR* 4.7 20.2 - - + +
141B PHE* 3.0 19.4 + - + +
142B ASP* 3.5 10.1 - - - +
144B VAL* 1.4 74.8 - - - +
146B GLN* 1.4 59.8 + - - +
148B ILE* 3.3 10.1 + - - +
149B ASP* 3.1 29.8 + - - +
172B GLN* 3.5 11.8 - - - +
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Residues in contact with GLN 146 (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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142B ASP 3.1 14.3 + - - +
143B LEU* 3.5 14.6 - - + +
145B ALA* 1.4 74.1 - - - +
147B MET* 1.4 57.0 + - - +
149B ASP* 3.3 16.0 + - - +
150B GLU* 3.0 67.6 + - - +
298B PRO* 4.0 31.9 - - + +
305B TRP* 4.8 8.3 - - + -
312B TYR* 4.9 1.1 - - + -
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Residues in contact with MET 147 (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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143B LEU 2.9 13.9 + - - +
144B VAL* 3.3 27.4 - - + +
146B GLN* 1.4 72.7 - - - +
148B ILE* 1.3 61.1 + - + +
150B GLU 3.2 0.9 + - - -
151B ILE* 2.9 50.7 + - + +
153B MET* 4.6 11.9 - - - -
159B PHE* 4.6 6.3 - - + -
173B VAL* 4.4 13.5 - - + -
237B VAL* 5.9 0.4 - - - -
239B PHE* 3.5 35.2 - - + -
267B VAL* 4.0 16.4 - - + -
312B TYR* 3.3 36.7 + - + +
401B 5F4 4.1 3.1 - - + -
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Residues in contact with ILE 148 (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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107B LEU* 6.0 0.2 - - + -
144B VAL* 2.8 37.7 + - + +
145B ALA* 3.3 11.4 + - - +
147B MET* 1.3 76.8 - - + +
149B ASP* 1.4 64.6 + - - +
151B ILE 3.1 21.9 - - - +
152B LYS* 5.1 0.9 - - - +
153B MET* 4.9 4.6 - - + +
172B GLN* 4.1 11.2 - - + +
173B VAL* 4.1 25.1 - - + -
176B ALA* 3.9 35.2 - - + +
177B THR* 4.1 19.3 - - + +
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Residues in contact with ASP 149 (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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145B ALA* 3.1 18.2 + - - +
146B GLN* 3.3 16.8 + - - +
148B ILE* 1.4 79.7 - - - +
150B GLU* 1.3 60.1 + - + +
152B LYS* 3.2 28.2 + - - -
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Residues in contact with GLU 150 (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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146B GLN* 3.0 45.0 + - - +
147B MET 3.2 0.4 + - - +
149B ASP* 1.3 76.9 - - + +
151B ILE* 1.3 68.7 + - + +
152B LYS* 3.5 14.1 + - - +
296B LEU* 4.1 22.8 - - + +
297B SER 5.5 4.5 + - - +
298B PRO* 5.7 1.8 - - - +
312B TYR* 2.5 38.3 + - - +
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Residues in contact with ILE 151 (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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147B MET* 2.9 38.9 + - + +
148B ILE 3.1 16.4 - - - +
150B GLU* 1.3 75.0 - - + +
152B LYS* 1.3 64.0 + - - +
153B MET* 3.4 28.1 + - + +
237B VAL* 4.5 12.6 - - + -
265B ARG* 3.4 33.0 - - - +
267B VAL* 4.1 8.1 - - + -
296B LEU* 4.0 7.4 - - + -
312B TYR* 4.0 15.5 - - + +
314B LEU* 3.7 35.2 - - + -
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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