Contacts of the helix formed by residues 173 - 181 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A VAL 3.3 27.4 - - - -
142A ALA 4.1 7.0 + - - -
143A ASN 4.8 0.7 - - - -
144A GLU* 3.8 27.5 + - + +
168A ALA* 3.1 14.1 + - + +
171A LYS* 3.7 46.8 + - + +
172A GLY* 1.3 76.9 - - - +
174A VAL* 1.3 63.9 + - - +
175A ARG 3.4 1.8 - - - -
176A ILE* 3.9 24.9 - - + -
177A VAL* 3.1 26.8 + - - +
234A ILE* 4.9 0.4 - - - -
882A GLY 5.1 4.9 + - - -
885A LYS* 4.9 3.6 + - - -
886A GLU* 3.7 33.2 + - - +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLY 3.4 13.2 + - - +
173A TYR* 1.3 71.4 - - - +
175A ARG* 1.3 61.4 + - + +
177A VAL* 3.4 6.7 + - + +
178A GLU* 2.9 30.8 + - + +
231A GLU* 5.6 2.0 - - - +
233A GLU* 3.6 46.2 - - + +
234A ILE* 4.4 19.5 - - + -
237A THR* 5.6 2.2 - - - +
108B TYR* 5.1 9.6 - - - +
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Residues in contact with ARG 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLU* 5.2 9.1 + - - +
146A LEU* 3.5 38.4 - - + +
173A TYR* 3.4 0.4 - - - +
174A VAL* 1.3 74.3 - - + +
176A ILE* 1.3 61.5 + - + +
178A GLU* 3.4 6.3 + - - +
179A ALA* 2.9 29.3 + - - +
104B ASP* 5.6 4.4 + - - +
108B TYR* 3.7 61.3 - - + +
892B SER* 4.9 6.1 + - - -
896B TYR* 3.4 24.9 + - - -
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ALA 4.4 0.7 - - - +
141A VAL* 3.9 21.1 - - + +
144A GLU* 3.7 36.1 - - + +
145A HIS 4.1 8.7 - - - +
146A LEU* 4.3 21.3 - - + -
149A THR* 4.4 10.3 - - + +
168A ALA* 3.8 13.0 - - + -
173A TYR* 3.6 26.6 + - + -
174A VAL 3.3 0.4 - - - -
175A ARG* 1.3 75.1 - - + +
177A VAL* 1.3 60.7 + - - +
179A ALA* 3.3 2.4 + - - +
180A ILE* 2.9 48.8 + - + +
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 4.5 9.4 - - + +
168A ALA* 3.7 20.4 - - + +
169A ILE* 3.7 25.1 - - + -
173A TYR 3.1 19.8 + - - +
174A VAL* 3.7 7.4 - - + +
176A ILE* 1.3 77.2 - - - +
178A GLU* 1.3 56.9 + - - +
180A ILE* 3.3 4.9 + - - +
181A LEU* 2.9 51.3 + - + +
234A ILE* 4.2 25.8 - - + -
237A THR* 5.5 4.3 - - + -
238A LEU* 5.9 0.2 - - + -
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A VAL* 2.9 20.0 + - + +
175A ARG* 3.9 6.1 - - - +
177A VAL* 1.3 77.6 - - + +
179A ALA* 1.3 58.1 + - - +
181A LEU* 4.2 8.3 - - - +
182A SER* 4.1 15.1 + - - -
237A THR* 5.9 5.6 - - + -
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 4.1 8.5 - - + -
149A THR* 5.2 2.7 - - + -
150A GLU* 4.0 31.2 - - + +
153A LEU* 3.5 18.4 - - + +
175A ARG 2.9 17.4 + - - +
176A ILE* 3.8 4.5 - - - +
177A VAL 3.2 0.4 - - - -
178A GLU* 1.3 77.3 - - - +
180A ILE* 1.3 63.1 + - - +
181A LEU 3.4 0.2 - - - -
182A SER* 3.3 19.4 + - - -
183A HIS 4.1 1.4 + - - -
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 5.5 0.9 - - + -
141A VAL* 4.0 11.4 - - + -
149A THR* 4.3 4.5 - - + -
153A LEU* 3.9 23.1 - - + -
161A VAL* 4.1 16.8 - - + +
164A ALA* 3.9 29.6 - - + +
165A LEU* 3.8 31.2 - - + +
168A ALA* 4.6 1.1 - - + -
176A ILE* 2.9 37.1 + - + +
177A VAL* 3.3 3.1 + - - +
179A ALA* 1.3 71.9 - - - +
181A LEU* 1.3 58.3 + - - +
182A SER 3.1 4.9 - - - -
183A HIS* 3.1 25.3 + - - +
186A PHE* 3.6 12.1 - - + -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.8 19.5 - - + -
177A VAL* 2.9 36.1 + - + +
178A GLU* 4.6 7.0 - - - +
179A ALA 3.4 0.4 - - - -
180A ILE* 1.3 75.9 - - - +
182A SER* 1.3 55.9 + - - +
183A HIS 3.4 1.8 - - - -
186A PHE* 3.9 34.3 - - + +
192A LEU* 3.8 32.3 - - + -
237A THR* 4.1 11.0 - - + -
238A LEU* 4.1 15.0 - - + -
241A LYS* 3.8 32.7 + - + +
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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