Contacts of the helix formed by residues 173 - 181 (chain B) in PDB entry 6UZA
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 TYR 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B VAL 3.3 26.0 - - - -
142B ALA 4.1 7.2 + - - -
143B ASN 4.8 1.0 - - - -
144B GLU* 3.8 28.1 + - + +
168B ALA* 3.1 14.0 + - + +
171B LYS* 3.7 44.6 + - + +
172B GLY* 1.3 76.2 - - - +
174B VAL* 1.3 64.1 + - - +
175B ARG 3.4 2.0 - - - +
176B ILE* 3.9 25.5 - - + +
177B VAL* 3.1 27.0 + - - +
234B ILE* 4.9 0.7 - - - -
882B GLY 5.1 4.9 + - - -
885B LYS* 4.9 3.3 + - - -
886B GLU* 3.7 32.9 - - - +
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Residues in contact with VAL 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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172B GLY 3.4 12.8 + - - +
173B TYR* 1.3 71.4 - - - +
175B ARG* 1.3 60.9 + - + +
177B VAL* 3.4 6.2 + - + +
178B GLU* 2.9 31.1 + - + +
231B GLU* 5.6 2.0 - - - +
233B GLU* 3.6 46.4 - - + +
234B ILE* 4.4 20.4 - - + -
237B THR* 5.6 2.7 - - - +
108C TYR* 5.1 9.4 - - - +
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Residues in contact with ARG 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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144B GLU* 5.2 9.9 + - - +
146B LEU* 3.5 38.4 - - + +
173B TYR 3.4 0.2 - - - -
174B VAL* 1.3 75.0 - - + +
176B ILE* 1.3 63.3 + - + +
178B GLU* 3.4 6.0 + - - +
179B ALA* 2.9 29.1 + - - +
104C ASP* 5.6 4.2 + - - +
108C TYR* 3.7 63.5 - - + +
892C SER* 4.9 5.9 + - - -
896C TYR* 3.4 24.9 + - - -
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Residues in contact with ILE 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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140B ALA 4.4 0.4 - - - +
141B VAL* 3.9 21.8 - - + +
144B GLU* 3.7 35.4 - - + +
145B HIS 4.1 9.2 - - - +
146B LEU* 4.3 21.8 - - + -
149B THR* 4.4 10.8 - - + +
168B ALA* 3.8 13.5 - - + -
173B TYR* 3.6 25.9 + - + -
174B VAL 3.3 0.2 - - - -
175B ARG* 1.3 74.8 - - + +
177B VAL* 1.3 61.0 + - - +
179B ALA* 3.3 2.1 + - - +
180B ILE* 2.9 48.1 + - + +
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Residues in contact with VAL 177 (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 LEU* 4.4 9.1 - - + +
168B ALA* 3.7 20.6 - - + +
169B ILE* 3.7 25.8 - - + -
173B TYR 3.1 18.9 + - - +
174B VAL* 3.7 7.4 - - + +
176B ILE* 1.3 77.3 - - - +
178B GLU* 1.3 57.4 + - - +
180B ILE* 3.3 4.9 + - - +
181B LEU* 2.9 49.9 + - + +
234B ILE* 4.2 25.4 - - + -
237B THR* 5.5 5.2 - - + -
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Residues in contact with GLU 178 (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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174B VAL* 2.9 19.7 + - + +
175B ARG* 3.7 6.3 - - - +
177B VAL* 1.3 78.4 - - + +
179B ALA* 1.3 59.9 + - - +
181B LEU* 4.2 8.1 + - - +
182B SER* 4.1 15.1 + - - -
237B THR* 5.9 6.3 - - + -
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Residues in contact with ALA 179 (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* 4.1 9.0 - - + -
149B THR* 5.2 2.7 - - + -
150B GLU* 4.0 32.8 - - + +
153B LEU* 3.5 16.5 - - + +
175B ARG 2.9 16.9 + - - +
176B ILE* 3.8 4.5 - - - +
177B VAL 3.2 0.2 - - - -
178B GLU* 1.3 78.6 - - - +
180B ILE* 1.3 62.6 + - - +
181B LEU 3.4 0.7 - - - -
182B SER* 3.3 18.2 + - - -
183B HIS 4.1 1.7 + - - -
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Residues in contact with ILE 180 (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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137B LEU* 5.5 1.3 - - + -
141B VAL* 4.0 11.4 - - + -
149B THR* 4.3 4.0 - - + -
153B LEU* 3.9 22.4 - - + -
161B VAL* 4.1 16.2 - - + +
164B ALA* 3.9 28.7 - - + +
165B LEU* 3.8 31.2 - - + +
168B ALA* 4.6 1.3 - - + -
176B ILE* 2.9 37.9 + - + +
177B VAL* 4.0 2.7 - - - +
179B ALA* 1.3 72.3 - - - +
181B LEU* 1.3 57.9 + - - +
182B SER 3.1 4.7 - - - -
183B HIS* 3.1 25.3 + - - +
186B PHE* 3.6 12.0 - - + -
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Residues in contact with LEU 181 (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 LEU* 3.8 19.3 - - + -
177B VAL* 2.9 36.4 + - + +
178B GLU* 4.2 6.5 - - - +
179B ALA 3.4 0.4 - - - -
180B ILE* 1.3 75.2 - - - +
182B SER* 1.3 56.3 + - - +
183B HIS 3.4 1.8 - - - -
186B PHE* 3.9 34.5 - - + +
192B LEU* 3.8 32.1 - - + -
237B THR* 4.1 10.8 - - + -
238B LEU* 4.1 15.5 - - + -
241B LYS* 3.8 32.1 + - + -
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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