Contacts of the helix formed by residues 168 - 176 (chain B) in PDB entry 3UMO
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 SER 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B GLY 5.7 0.2 - - - -
139B SER* 5.7 5.4 - - - -
167B SER* 1.3 82.2 + - - +
169B GLY* 1.3 70.7 + - - +
171B ALA* 3.3 10.2 + - - +
172B LEU* 3.2 18.1 + - - -
190B GLU* 3.9 23.6 - - - -
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Residues in contact with GLY 169 (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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168B SER* 1.3 79.3 - - - +
170B GLU* 1.3 63.6 + - - -
172B LEU* 3.2 9.3 + - - +
173B SER* 3.3 12.9 + - - -
190B GLU* 5.6 1.0 - - - +
193B ALA* 5.5 12.8 - - - +
194B LEU* 5.8 0.2 - - - +
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Residues in contact with GLU 170 (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 LEU* 3.6 32.9 - - + +
168B SER 3.6 0.2 + - - -
169B GLY* 1.3 72.5 - - - -
171B ALA* 1.3 57.5 + - - +
173B SER* 3.4 7.1 + - - -
174B ALA* 2.9 31.2 + - - +
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Residues in contact with ALA 171 (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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138B GLY 5.3 0.2 - - - +
139B SER* 5.7 0.2 - - - -
140B LEU* 4.1 28.7 - - + +
146B LEU* 3.9 11.5 - - + +
149B LEU* 3.7 14.6 - - + +
167B SER* 3.5 18.8 - - - +
168B SER 3.3 5.5 + - - +
169B GLY 3.2 0.8 - - - -
170B GLU* 1.3 79.2 - - - +
172B LEU* 1.3 57.9 + - - +
174B ALA* 3.3 2.4 + - - +
175B ALA* 2.8 30.9 + - - +
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Residues in contact with LEU 172 (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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165B VAL* 3.7 25.8 - - + -
167B SER* 3.6 25.5 + - - +
168B SER* 3.2 22.6 + - - +
169B GLY 3.7 7.6 - - - +
171B ALA* 1.3 77.3 - - - +
173B SER* 1.3 63.4 + - - +
175B ALA* 3.3 3.1 + - - +
176B LEU* 3.1 25.3 + - + +
184B VAL* 3.8 17.5 - - + -
186B PRO* 4.6 9.0 - - + -
190B GLU* 4.3 25.1 - - + +
194B LEU* 4.1 22.4 - - + -
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Residues in contact with SER 173 (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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169B GLY 3.3 10.5 + - - -
170B GLU* 3.8 10.5 - - - -
172B LEU* 1.3 78.6 - - - +
174B ALA* 1.3 57.7 + - - +
176B LEU* 3.2 5.0 + - - +
177B ALA* 3.0 25.6 + - - +
194B LEU* 3.9 22.2 + - - +
217B LYS* 5.0 6.8 + - - +
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Residues in contact with ALA 174 (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 LEU* 4.0 29.4 - - + +
149B LEU* 4.8 3.1 - - + -
150B THR* 2.8 32.5 + - - +
170B GLU 2.9 19.0 + - - +
171B ALA* 3.6 4.9 - - - +
173B SER* 1.3 74.5 - - - +
175B ALA* 1.3 62.7 - - - +
177B ALA* 3.1 17.3 + - - +
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Residues in contact with ALA 175 (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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136B ILE* 6.1 1.3 - - + -
149B LEU* 4.2 9.4 - - + +
153B ILE* 3.6 29.7 - - + +
165B VAL* 3.8 25.8 - - + -
167B SER* 5.7 1.1 - - - -
171B ALA 2.8 20.6 + - - +
172B LEU* 3.3 6.7 + - - +
174B ALA* 1.3 73.7 - - - +
176B LEU* 1.3 58.5 + - - +
177B ALA 3.8 0.3 + - - -
178B ILE* 4.4 7.3 - - - +
181B ILE* 3.6 22.7 - - - +
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Residues in contact with LEU 176 (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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165B VAL* 5.6 1.1 - - + -
172B LEU* 3.1 19.3 + - + +
173B SER* 3.6 5.8 - - - +
174B ALA 3.1 0.6 - - - -
175B ALA* 1.3 75.7 - - + +
177B ALA* 1.3 64.3 + - - +
178B ILE 3.3 3.7 + - - -
179B GLY* 3.4 9.3 + - - -
181B ILE* 3.5 22.9 - - + -
184B VAL* 4.4 17.0 - - + -
194B LEU* 3.5 37.9 - - + -
212B ILE* 4.5 13.0 - - + -
217B LYS* 3.2 58.7 - - + +
218B ALA* 4.1 6.3 - - + -
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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