Contacts of the helix formed by residues 133 - 139 (chain D) in PDB entry 1UMD
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 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B HIS* 5.1 2.2 - - - +
84D ALA* 3.6 31.6 - - + +
87D ILE* 4.7 0.2 - - + -
88D PHE* 4.1 16.2 - - + -
131D GLN* 3.6 14.6 - - + +
132D SER* 1.3 85.2 - - - +
134D GLU* 1.3 66.8 + - - +
135D ALA* 3.2 3.6 - - - -
136D HIS* 3.0 41.1 + - + +
137D PHE* 3.7 27.6 + - + -
171D LEU* 4.4 4.0 - - + -
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Residues in contact with GLU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D SER* 5.3 0.2 + - - -
132D SER* 3.2 29.6 - - - -
133D PRO* 1.3 73.1 - - - +
135D ALA* 1.3 65.5 + - + +
137D PHE* 2.9 17.0 + - - +
138D VAL* 2.9 25.5 + - + +
145D VAL* 4.4 8.3 - - + -
171D LEU* 3.8 16.6 - - + +
210D TYR* 2.6 38.8 + - - +
239D LEU* 3.7 24.5 - - + -
261D SER* 3.9 1.2 + - - -
262D ASP* 4.8 1.4 - - - +
263D ALA* 3.6 15.1 - - + +
269D PHE* 4.7 5.6 - - + +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B HIS* 3.6 28.2 + - + +
267B ALA* 4.3 4.9 - - + +
132D SER 5.0 0.2 + - - -
133D PRO 3.0 1.2 + - - -
134D GLU* 1.3 82.7 - - + +
136D HIS* 1.3 62.9 + - - +
138D VAL* 3.8 7.4 - - - +
139D HIS* 2.9 28.9 + - - +
263D ALA* 6.1 0.9 - - + -
267D ALA 3.6 24.0 - - - +
268D SER* 4.1 7.9 - - - -
269D PHE* 4.1 8.3 - - - +
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Residues in contact with HIS 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PHE* 3.8 16.3 - + - -
95B VAL* 5.4 0.6 - - - +
136B HIS* 3.0 61.8 + - - -
139B HIS* 3.7 23.9 - + - -
140B THR* 4.1 8.7 + - - -
88D PHE* 3.9 24.8 - + - -
91D PHE* 3.8 22.5 - + + -
95D VAL* 5.0 0.2 - - - +
133D PRO* 3.0 25.4 + - + +
135D ALA* 1.3 77.1 - - - +
137D PHE* 1.3 63.2 + - + +
139D HIS* 3.9 0.6 + - - -
140D THR* 2.9 24.1 + - - -
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Residues in contact with PHE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ILE* 4.0 16.4 - - + -
91D PHE* 4.2 11.0 - + - -
94D LEU* 3.7 29.8 - - + -
95D VAL* 6.0 0.2 - - + -
117D MET* 3.9 20.4 - - + -
133D PRO* 3.7 36.8 - - + -
134D GLU* 2.9 18.7 + - - +
136D HIS* 1.3 79.5 - - + +
138D VAL* 1.3 64.7 + - - +
139D HIS 3.2 1.6 - - - -
140D THR* 3.0 23.9 + - - +
143D LEU* 4.0 18.7 - - + +
145D VAL* 3.6 18.7 - - + +
169D VAL* 3.6 28.9 - - + -
171D LEU* 4.4 7.9 - - + -
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B HIS* 3.8 38.9 - - + +
267B ALA* 4.5 6.7 - - + -
296B ASP* 5.3 0.2 - - - +
134D GLU 2.9 22.3 + - - +
135D ALA* 3.9 5.6 - - - +
137D PHE* 1.3 76.4 - - - +
139D HIS* 1.3 61.6 + - - +
140D THR 3.3 4.2 + - - +
141D ALA* 4.8 0.9 + - - -
145D VAL* 4.1 13.9 - - + -
239D LEU* 4.0 29.8 - - + +
240D MET* 4.2 17.6 - - + +
269D PHE* 3.9 24.2 - - + -
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Residues in contact with HIS 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B SER 4.4 8.5 + - - -
133B PRO* 5.0 0.6 - - - +
135B ALA* 3.6 32.0 + - + +
136B HIS* 3.7 28.8 - + + +
263B ALA* 4.8 2.4 - - + +
264B PRO* 3.3 59.9 + - + +
266B HIS* 2.8 27.6 + - - +
267B ALA* 3.9 7.0 + - + +
268B SER* 4.0 5.2 - - - -
296B ASP* 5.3 1.5 - - - +
135D ALA 2.9 18.2 + - - +
136D HIS 4.0 5.2 - - - +
138D VAL* 1.3 78.1 - - - +
140D THR* 1.3 58.2 + - - +
141D ALA 3.6 2.8 + - - -
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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