Contacts of the helix formed by residues 161 - 170 (chain A) in PDB entry 6UUQ
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 THR 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ASP* 4.6 3.8 + - - -
122A ARG 4.7 8.2 + - - +
123A GLY 4.7 5.7 + - - -
160A PHE* 1.3 83.6 - - + +
162A PHE* 1.3 67.3 + - - +
163A LYS 3.3 2.5 - - - -
164A GLN* 3.1 17.7 + - - +
165A GLU* 2.6 47.2 + - - +
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Residues in contact with PHE 162 (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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120A VAL* 3.9 19.3 - - + -
121A ASP* 3.2 21.1 + - - +
126A SER* 3.5 18.6 - - - -
127A ILE* 3.9 28.3 - - + -
130A VAL* 4.3 4.3 - - + -
157A THR* 3.5 29.4 + - + -
161A THR* 1.3 78.6 + - - +
163A LYS* 1.3 64.0 + - - +
165A GLU* 3.2 10.4 + - + +
166A CYS* 2.9 49.4 + - - -
175A TYR* 4.2 1.1 - + - -
178A CYS* 3.9 21.3 - - + -
179A MET* 3.8 20.0 - - + -
182A PHE* 4.0 6.7 - + - -
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Residues in contact with LYS 163 (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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157A THR 3.0 20.7 + - - +
158A GLU* 4.0 33.7 + - + +
160A PHE 5.5 0.2 - - - +
162A PHE* 1.3 75.8 - - - +
164A GLN* 1.3 66.4 + - + +
166A CYS* 3.5 2.4 + - - +
167A LYS* 3.2 52.8 + - + +
172A GLU* 5.1 6.4 + - - -
175A TYR* 3.4 51.9 - - + +
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Residues in contact with GLN 164 (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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158A GLU 5.0 3.7 - - - +
160A PHE 3.6 19.8 - - - +
161A THR* 3.1 16.3 + - - +
163A LYS* 1.3 78.8 - - + +
165A GLU* 1.3 65.0 + - + +
167A LYS* 3.3 9.7 + - + +
168A ILE* 2.9 34.0 + - + +
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Residues in contact with GLU 165 (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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123A GLY 4.2 10.0 - - - +
124A TYR* 4.8 10.2 - - - +
126A SER* 3.6 28.6 + - - -
127A ILE* 4.7 7.3 + - + -
161A THR* 2.6 40.2 + - - +
162A PHE* 3.7 11.6 - - + +
164A GLN* 1.3 76.4 - - + +
166A CYS* 1.3 61.8 + - - +
168A ILE* 4.4 5.8 - - - -
169A LYS* 2.9 42.5 + - + +
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Residues in contact with CYS 166 (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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127A ILE* 4.2 14.8 - - - -
162A PHE* 2.9 56.6 + - - +
163A LYS 3.7 1.6 - - - +
165A GLU* 1.3 76.5 - - - +
167A LYS* 1.3 56.8 + - - +
170A TYR* 2.8 34.3 + - - +
171A SER 2.9 10.7 + - - -
174A VAL* 4.7 2.9 - - + -
175A TYR* 3.6 37.7 - - + +
178A CYS* 4.7 1.6 - - - -
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Residues in contact with LYS 167 (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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163A LYS* 3.2 42.8 + - + +
164A GLN* 3.7 10.5 - - + +
166A CYS* 1.3 80.2 - - - +
168A ILE* 1.3 70.2 + - + +
170A TYR 3.6 10.7 - - - +
171A SER* 3.9 10.9 + - - +
172A GLU* 3.9 46.2 + - + +
175A TYR* 5.1 2.0 - - + -
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Residues in contact with ILE 168 (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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55A ARG* 4.4 10.0 + - - +
164A GLN* 2.9 26.2 + - + +
165A GLU* 3.6 6.5 - - - +
167A LYS* 1.3 84.4 - - + +
169A LYS* 1.3 73.8 + - + +
170A TYR 3.4 2.4 + - - +
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Residues in contact with LYS 169 (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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28A ARG* 3.4 3.8 + - - -
53A GLU* 2.8 34.3 + - - +
55A ARG* 3.1 52.4 + - + +
124A TYR 4.5 8.3 + - - -
127A ILE* 4.0 19.0 - - + +
128A GLU* 2.9 27.8 + - - +
165A GLU* 2.9 28.4 + - + +
168A ILE* 1.3 82.2 - - + +
170A TYR* 1.3 78.6 + - + +
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Residues in contact with TYR 170 (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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28A ARG* 3.7 13.4 + - - +
50A LEU* 5.1 0.7 - - - +
54A GLY 4.6 1.6 + - - -
55A ARG* 3.5 14.6 + - + +
56A LEU* 3.0 44.6 + - - +
58A GLU* 4.2 16.6 - - + +
61A ALA* 3.7 21.3 - - + -
127A ILE* 3.9 33.7 - - + -
131A LEU* 3.7 18.9 - - + +
166A CYS* 2.8 11.1 + - - +
167A LYS 3.6 8.0 - - - +
168A ILE 3.3 1.9 - - - +
169A LYS* 1.3 96.4 - - + +
171A SER* 1.3 67.7 + - - +
174A VAL* 3.7 24.2 - - + -
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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