Contacts of the helix formed by residues 164 - 174 (chain C) in PDB entry 4DOH
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 GLU 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C ARG* 4.3 2.0 - - - -
64C ILE* 3.1 24.3 + - - +
65C LEU* 3.0 44.1 + - + +
90C TYR* 4.2 1.8 - - - +
160C LYS* 3.2 24.6 + - - +
161C ALA* 3.2 10.7 + - - +
162C LEU 3.1 1.2 - - - -
163C GLY* 1.3 78.9 - - - +
165C LEU* 1.3 63.0 + - - +
166C ASP* 3.2 6.3 - - - -
167C ILE* 3.1 25.6 + - + +
168C LEU 3.3 7.6 + - - -
76E TYR* 2.4 35.8 + - - +
128E ARG* 4.0 7.2 - - - +
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ILE* 4.7 3.4 - - + -
46C PHE* 3.7 31.6 - - + -
90C TYR* 3.8 30.5 - - + -
95C PHE* 4.9 2.7 - - + -
112C LEU* 3.9 27.1 - - + -
116C PHE* 4.1 30.5 - - + -
161C ALA 3.6 1.6 + - - -
162C LEU* 3.3 23.3 + - + +
163C GLY 3.2 1.8 - - - -
164C GLU* 1.3 78.1 - - - +
166C ASP* 1.3 57.6 + - - +
168C LEU* 2.8 13.2 + - + +
169C LEU* 2.8 36.1 + - + +
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Residues in contact with ASP 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 5.6 0.3 + - - -
46C PHE* 3.9 18.9 - - + -
50C ARG* 3.7 15.3 - - - +
54C GLN* 3.7 12.5 - - - +
163C GLY 3.0 21.7 - - - +
164C GLU* 3.6 2.8 - - - -
165C LEU* 1.3 75.5 - - - +
167C ILE* 1.3 59.4 + - - +
169C LEU* 4.1 10.4 - - + +
170C GLN* 3.1 27.0 + - - +
107E GLN* 5.1 4.2 - - - +
128E ARG* 5.4 0.7 + - - -
130E TYR* 3.9 20.5 - - - +
133E LEU* 4.0 23.5 - - + +
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Residues in contact with ILE 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ARG* 3.7 36.8 - - - +
65C LEU* 3.9 12.6 - - + +
164C GLU* 3.1 36.0 + - + +
165C LEU 3.0 0.6 - - - -
166C ASP* 1.3 79.6 - - - +
168C LEU* 1.3 58.4 + - - +
170C GLN* 3.2 5.5 + - + +
171C TRP* 2.9 57.3 + - + +
76E TYR* 4.7 0.4 - - + -
107E GLN* 3.8 28.9 - - - +
130E TYR* 4.7 7.0 - - + +
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C LEU* 4.0 16.5 - - + +
71C LEU* 6.3 1.3 - - + -
83C LEU* 4.6 9.6 - - + -
86C LEU* 4.5 22.2 - - + -
87C LEU* 4.2 9.0 - - + -
90C TYR* 3.9 31.4 - - + +
116C PHE* 4.1 30.5 - - + -
164C GLU 3.3 2.4 + - - +
165C LEU* 2.8 17.5 + - + +
167C ILE* 1.3 79.1 - - - +
169C LEU* 1.3 62.4 + - + +
171C TRP* 3.0 22.7 + - + +
172C MET* 3.2 22.9 + - + +
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Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU* 4.2 13.8 - - + +
42C ILE* 3.6 37.2 - - + -
43C ARG* 3.5 48.4 + - + +
46C PHE* 5.0 6.5 - - + -
116C PHE* 4.1 6.1 - - + -
165C LEU* 2.8 30.2 + - + +
166C ASP* 4.1 7.2 - - - +
168C LEU* 1.3 73.1 - - - +
170C GLN* 1.3 58.0 + - - +
172C MET* 3.2 27.0 + - + +
173C GLU* 2.9 28.2 + - - +
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Residues in contact with GLN 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 3.3 20.1 + - - +
166C ASP 3.1 19.5 + - - +
167C ILE* 3.5 6.7 - - - +
168C LEU 3.2 0.2 - - - -
169C LEU* 1.3 74.4 - - - +
171C TRP* 1.3 69.2 - - + +
173C GLU* 4.3 10.0 - - - +
174C GLU* 2.9 60.0 + - - +
130E TYR* 3.8 19.3 - - - +
132E PHE* 3.5 29.4 - - + -
133E LEU* 3.5 16.2 - - + +
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Residues in contact with TRP 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ARG* 5.0 3.2 - - - +
65C LEU* 3.7 56.5 - - + -
66C ARG 4.2 1.6 - - - -
67C ARG* 3.9 13.9 - - - +
69C GLU* 3.4 26.5 - - + -
70C SER* 3.8 27.6 + - - -
71C LEU* 3.6 25.1 - - + +
72C GLN 4.7 0.5 + - - -
82C LEU* 5.5 0.7 - - + -
86C LEU* 4.3 16.2 - - + -
145C ILE* 4.2 8.3 - - + -
167C ILE* 2.9 35.8 + - + +
168C LEU* 3.0 16.5 + - + +
170C GLN* 1.3 81.0 - - + +
172C MET* 1.3 59.4 + - + +
174C GLU* 3.7 15.6 + - - +
175C THR* 3.1 28.4 + - - +
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Residues in contact with MET 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LYS* 4.0 1.6 + - - -
28C LEU* 3.1 39.6 - - + +
39C LEU* 4.0 22.7 - - + -
71C LEU* 4.6 5.8 - - + -
83C LEU* 4.2 28.9 - - + -
87C LEU* 4.7 2.5 - - + -
116C PHE* 3.4 34.3 - - + -
119C ILE* 4.6 11.0 - - + -
168C LEU* 3.2 28.7 + - + +
169C LEU* 3.6 25.1 - - + +
170C GLN 3.0 0.4 - - - -
171C TRP* 1.3 75.7 - - - +
173C GLU* 1.3 64.7 + - - +
174C GLU 3.1 1.6 - - - -
175C THR* 3.1 11.6 + - - -
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Residues in contact with GLU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LYS* 3.2 43.2 - - - +
39C LEU* 3.6 17.7 - - + +
43C ARG* 3.3 34.7 + - - +
169C LEU 2.9 16.1 + - - +
170C GLN* 3.3 13.7 + - - +
172C MET* 1.3 75.3 - - - +
174C GLU* 1.3 61.2 + - - +
175C THR 3.3 0.3 + - - -
176C GLU* 4.2 3.3 + - - +
178E ASN* 5.0 9.7 + - - -
223E PRO 5.4 2.3 - - - +
224E GLY* 5.8 2.0 - - - -
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C SER* 3.6 15.6 + - - -
72C GLN* 2.8 45.8 + - + +
170C GLN* 2.9 53.7 + - - +
171C TRP* 3.9 13.5 - - - +
172C MET 3.1 0.4 - - - -
173C GLU* 1.3 74.2 - - - +
175C THR* 1.3 57.1 + - - +
176C GLU* 2.9 15.0 + - - +
105E GLU* 4.3 19.9 - - - +
130E TYR* 5.3 0.3 + - - -
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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