Contacts of the helix formed by residues 166 - 180 (chain A) in PDB entry 4D0N
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 GLY 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LYS* 5.7 0.9 - - - -
157A MET* 4.3 2.6 - - - +
158A GLU 3.7 14.4 - - - +
159A CYS* 3.6 5.1 - - - +
164A LYS 3.3 1.6 + - - -
165A ASP* 1.3 79.0 + - - +
167A VAL* 1.3 62.6 + - - +
169A GLU* 3.5 25.2 + - - +
170A VAL* 3.3 27.0 + - - +
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Residues in contact with VAL 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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21A LEU* 3.7 27.8 - - + -
24A VAL* 4.0 12.3 - - + -
25A PHE* 3.8 36.8 - - + -
159A CYS* 4.2 7.2 - - + -
160A SER 3.7 20.2 - - - +
164A LYS* 3.3 31.9 + - + +
165A ASP 3.3 0.4 - - - -
166A GLY* 1.3 75.4 - - - +
168A ARG* 1.3 67.7 + - - +
170A VAL* 3.2 11.9 + - - +
171A PHE* 3.3 14.8 - - + -
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 4.9 15.7 - - + -
46A ILE* 5.1 2.5 - - + +
164A LYS* 4.7 7.7 + - - +
167A VAL* 1.3 79.7 - - - +
169A GLU* 1.3 85.5 + - - +
171A PHE* 3.4 2.9 + - - +
172A GLU* 3.0 70.9 + - + +
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Residues in contact with GLU 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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157A MET* 3.7 27.6 - - + +
166A GLY* 3.5 24.6 + - - +
167A VAL 3.2 0.2 - - - -
168A ARG* 1.3 104.5 + - - +
170A VAL* 1.3 59.9 + - - +
172A GLU* 3.9 9.5 - - - +
173A MET* 2.9 31.5 + - - +
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Residues in contact with VAL 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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21A LEU* 4.6 4.9 - - + -
81A LEU* 3.9 32.8 - - + +
113A ILE* 4.8 2.7 - - + +
115A VAL* 3.9 20.6 - - + -
157A MET* 3.5 28.7 - - + -
159A CYS* 4.2 17.0 - - + -
166A GLY 3.3 15.9 + - - +
167A VAL* 3.2 9.3 + - - +
169A GLU* 1.3 78.4 - - - +
171A PHE* 1.3 65.6 - - + +
173A MET* 3.7 2.4 - - - +
174A ALA* 2.9 26.0 + - - +
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Residues in contact with PHE 171 (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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8A LEU* 3.9 15.5 - - + -
21A LEU* 4.0 27.4 - - + -
22A LEU* 4.0 17.7 - - + -
25A PHE* 3.4 69.5 - + + -
46A ILE* 4.2 3.8 - - + -
55A LEU* 4.5 3.0 - - + +
57A LEU* 3.9 17.0 - - + -
81A LEU* 3.8 24.2 - - + -
167A VAL 3.3 13.5 - - - -
168A ARG 3.4 3.0 + - - +
169A GLU 3.3 0.4 - - - -
170A VAL* 1.3 80.1 - - + +
172A GLU* 1.3 56.7 + - - +
174A ALA* 3.7 4.6 - - - +
175A THR* 2.6 38.3 + - - -
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Residues in contact with GLU 172 (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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46A ILE* 3.9 14.6 - - + +
47A GLU 4.9 4.5 - - - +
48A VAL* 3.8 22.1 - - + +
168A ARG* 3.0 59.0 + - + +
169A GLU* 3.9 10.2 - - - +
171A PHE* 1.3 73.8 - - - +
173A MET* 1.3 65.6 + - - +
175A THR* 3.5 2.9 + - - -
176A ARG* 3.2 46.0 + - - +
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Residues in contact with MET 173 (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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113A ILE* 3.7 24.0 - - + -
154A PHE* 3.8 15.0 - - + +
155A GLY* 4.0 25.8 - - - -
156A TYR 4.4 3.8 - - - +
157A MET* 3.7 34.1 - - + -
169A GLU 2.9 18.5 + - - +
170A VAL 3.7 4.0 - - - +
172A GLU* 1.3 74.5 - - - +
174A ALA* 1.3 67.3 + - - +
176A ARG* 3.0 16.2 + - - +
177A ALA* 2.9 20.4 + - - +
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Residues in contact with ALA 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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8A LEU* 4.0 18.6 - - + -
55A LEU* 5.3 0.7 - - + -
79A VAL* 3.6 13.5 - - + +
81A LEU* 3.8 24.2 - - + -
113A ILE* 3.9 11.0 - - - +
170A VAL 2.9 17.6 + - - +
171A PHE* 3.7 6.3 - - - +
173A MET* 1.3 76.1 - - - +
175A THR* 1.3 56.6 + - - +
177A ALA* 3.3 3.8 + - - +
178A ALA* 3.0 27.9 + - - +
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Residues in contact with THR 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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46A ILE* 3.7 22.3 - - + +
48A VAL* 3.5 23.8 - - + -
53A VAL* 3.7 35.7 - - + -
55A LEU* 3.7 13.0 - - + +
171A PHE 2.6 23.4 + - - -
172A GLU 3.6 6.5 - - - -
173A MET 3.1 0.2 - - - -
174A ALA* 1.3 74.3 - - - +
176A ARG* 1.3 65.2 + - - +
178A ALA* 3.0 8.8 + - - +
179A LEU* 3.0 23.0 + - + +
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Residues in contact with ARG 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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48A VAL* 4.0 23.6 - - + +
49A ASP* 2.8 40.3 + - - +
154A PHE* 4.3 14.6 - - + -
172A GLU* 3.2 39.1 + - - +
173A MET* 3.0 13.9 + - - +
175A THR* 1.3 76.3 - - - +
177A ALA* 1.3 64.3 + - - +
179A LEU* 3.2 17.2 + - - +
180A GLN* 3.5 11.3 + - - +
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Residues in contact with ALA 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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79A VAL* 4.1 8.7 - - + -
111A PRO* 3.5 28.4 - - + +
113A ILE* 4.1 3.6 - - + -
154A PHE* 3.7 39.4 - - + -
173A MET 2.9 10.7 + - - +
174A ALA 3.5 9.2 - - - +
175A THR 3.3 0.2 - - - -
176A ARG* 1.3 76.0 - - - +
178A ALA* 1.3 61.3 + - - +
180A GLN* 3.2 19.1 + - - +
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Residues in contact with ALA 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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6A LYS* 3.0 49.5 + - + +
55A LEU* 5.1 1.6 - - + -
78A ASP* 3.8 17.6 - - + +
79A VAL* 4.1 16.5 - - + +
174A ALA 3.0 13.4 + - - +
175A THR* 3.0 12.5 + - + +
177A ALA* 1.3 76.0 - - - +
179A LEU* 1.3 60.1 + - - +
180A GLN 3.5 4.9 + - - +
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Residues in contact with LEU 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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4A ILE* 4.1 30.1 - - + -
6A LYS* 4.4 8.5 + - + +
48A VAL* 3.8 26.5 - - + +
49A ASP* 6.0 0.7 - - + +
51A LYS* 4.3 25.1 - - + -
53A VAL* 4.0 27.1 - - + -
175A THR 3.0 17.6 + - - +
176A ARG* 3.2 10.0 + - - +
178A ALA* 1.3 73.6 - - + +
180A GLN* 1.3 64.3 + - - +
181A ALA* 5.2 0.7 - - - +
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Residues in contact with GLN 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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6A LYS* 5.0 2.6 + - - -
111A PRO* 5.5 4.8 - - + +
154A PHE* 3.5 37.2 - - - -
176A ARG 3.5 5.8 + - - +
177A ALA 3.2 15.7 + - - +
178A ALA 3.8 7.3 - - - +
179A LEU* 1.3 83.2 - - - +
181A ALA* 1.3 64.9 + - - +
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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