Contacts of the helix formed by residues 133 - 139 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ALA* 3.7 31.2 - - + +
88B PHE* 4.1 14.4 - - + -
131B GLN* 3.5 15.0 - - + +
132B SER* 1.3 86.5 - - - +
134B GLU* 1.3 66.4 + - - +
135B ALA* 3.1 4.0 - - - -
136B HIS* 2.9 41.9 + - + +
137B PHE* 3.7 27.5 + - + -
171B LEU* 4.4 4.0 - - + -
139D HIS* 5.0 3.4 - - - +
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Residues in contact with GLU 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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119B SER* 5.3 0.2 + - - -
132B SER* 3.2 35.3 + - - +
133B PRO* 1.3 72.7 - - - +
135B ALA* 1.3 65.0 + - + +
137B PHE* 2.9 17.6 + - - +
138B VAL* 2.9 26.3 + - + +
145B VAL* 4.4 5.6 - - + -
147B ALA* 6.0 0.7 - - - -
171B LEU* 3.7 19.1 - - + +
210B TYR* 2.6 40.7 + - - +
239B LEU* 3.6 24.5 - - + -
261B SER* 3.9 1.4 + - - -
262B ASP* 4.8 1.0 - - - +
263B ALA* 3.7 9.0 - - + +
269B PHE* 4.7 6.5 - - + +
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Residues in contact with ALA 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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133B PRO 3.0 1.2 + - - -
134B GLU* 1.3 82.2 - - + +
136B HIS* 1.3 63.0 + - - +
138B VAL* 3.9 6.4 - - - +
139B HIS* 3.0 27.7 + - - +
267B ALA 3.7 20.9 - - - +
268B SER* 4.1 7.9 - - - -
269B PHE* 4.1 7.9 - - - +
139D HIS* 3.6 31.8 + - + +
267D ALA* 4.0 5.7 - - + +
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Residues in contact with HIS 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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88B PHE* 3.8 25.8 - + - -
91B PHE* 3.9 21.7 - + + -
133B PRO* 2.9 25.1 + - + +
135B ALA* 1.3 77.4 - - - +
137B PHE* 1.3 64.6 + - + +
139B HIS* 4.8 0.4 - - - -
140B THR* 2.9 23.6 + - - -
91D PHE* 3.8 17.0 - + - -
95D VAL* 5.5 0.4 - - - +
136D HIS* 3.0 59.0 + - - -
139D HIS* 3.7 24.4 - + + +
140D THR* 4.0 9.0 + - - -
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Residues in contact with PHE 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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87B ILE* 4.0 17.3 - - + -
91B PHE* 4.4 5.2 - + - -
94B LEU* 3.6 31.2 - - + -
95B VAL* 6.0 0.4 - - + -
117B MET* 3.8 24.2 - - + -
133B PRO* 3.8 31.6 - - + -
134B GLU* 2.9 19.2 + - - +
136B HIS* 1.3 84.1 - - + +
138B VAL* 1.3 60.6 + - - +
139B HIS 3.1 1.6 - - - -
140B THR* 2.9 29.0 + - - +
143B LEU* 4.0 18.3 - - + +
145B VAL* 3.6 18.5 - - + +
169B VAL* 3.5 26.9 - - + -
171B LEU* 4.4 8.5 - - + -
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Residues in contact with VAL 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 GLU 2.9 25.5 + - - +
135B ALA* 4.0 6.1 - - - +
137B PHE* 1.3 71.2 - - - +
139B HIS* 1.3 60.6 + - - +
140B THR 3.3 4.2 + - - +
141B ALA* 4.9 0.7 + - - -
145B VAL* 4.1 15.9 - - + -
239B LEU* 3.9 31.0 - - + +
240B MET* 4.1 19.2 - - + +
269B PHE* 4.0 22.0 - - + -
266D HIS* 3.7 37.8 - - + +
267D ALA* 4.5 7.2 - - + +
296D ASP* 5.3 0.5 - - - +
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Residues in contact with HIS 139 (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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135B ALA 3.0 17.8 + - - +
136B HIS* 4.0 5.2 - - - +
137B PHE 3.1 0.2 - - - -
138B VAL* 1.3 76.7 - - - +
140B THR* 1.3 58.7 + - - +
141B ALA 3.6 3.2 + - - -
132D SER 4.4 9.3 + - - -
133D PRO* 5.1 0.4 - - + +
135D ALA* 3.6 28.4 + - + +
136D HIS* 3.7 27.9 - + + -
263D ALA* 4.7 2.7 - - + -
264D PRO* 3.4 58.1 + - + +
266D HIS* 2.7 28.3 + - - +
267D ALA* 3.8 9.5 + - + +
268D SER* 4.0 5.6 - - - -
296D ASP* 5.4 1.4 - - - +
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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