Contacts of the helix formed by residues 164 - 175 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ARG* 3.7 0.6 - - - -
64A ILE* 3.2 26.8 + - - +
65A LEU* 2.9 36.5 + - + +
90A TYR* 4.1 7.0 - - - +
160A LYS* 3.2 20.4 + - - +
161A ALA* 3.0 8.9 + - - +
162A LEU 3.0 1.4 - - - -
163A GLY* 1.3 79.7 - - - +
165A LEU* 1.3 64.1 + - - +
166A ASP* 3.1 6.1 - - - -
167A ILE* 3.0 33.7 + - + +
168A LEU* 3.2 10.7 + - - +
76R TYR* 2.6 31.2 + - - +
128R ARG* 4.1 6.1 - - - +
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Residues in contact with LEU 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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42A ILE* 4.8 2.9 - - + -
46A PHE* 3.9 19.7 - - + -
90A TYR* 3.4 33.4 - - + -
95A PHE* 4.2 6.3 - - + -
112A LEU* 3.7 34.5 - - + -
116A PHE* 3.8 24.7 - - + -
161A ALA 3.5 0.4 + - - -
162A LEU* 3.3 18.7 + - + +
163A GLY 3.5 0.4 - - - -
164A GLU* 1.3 77.3 - - - +
166A ASP* 1.3 57.8 + - - +
168A LEU* 3.2 17.8 + - + -
169A LEU* 2.8 37.9 + - + +
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Residues in contact with ASP 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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43A ARG* 4.9 0.7 + - - -
46A PHE* 3.6 19.4 - - + -
50A ARG* 4.0 13.4 - - - +
54A GLN* 3.4 17.4 + - - +
163A GLY 3.3 15.8 - - - +
164A GLU* 3.8 3.5 - - - -
165A LEU* 1.3 74.4 - - - +
167A ILE* 1.3 64.4 + - - +
169A LEU* 4.1 5.5 - - - +
170A GLN* 3.1 23.7 + - - +
107R GLN* 4.1 8.6 - - - +
128R ARG* 5.7 0.2 - - - -
130R TYR* 3.7 24.7 - - - +
133R LEU* 3.8 21.5 - - + +
134R GLU* 5.2 0.2 - - - +
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Residues in contact with ILE 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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63A ARG* 3.8 27.6 - - - +
65A LEU* 3.8 14.8 - - + +
164A GLU* 3.0 33.7 + - + +
166A ASP* 1.3 75.6 + - - +
168A LEU* 1.3 60.3 + - - +
170A GLN* 3.1 5.0 + - - +
171A TRP* 2.8 58.4 + - + +
76R TYR* 4.8 1.1 - - + -
107R GLN* 3.6 39.5 - - - +
130R TYR* 4.4 8.5 - - + +
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Residues in contact with LEU 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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65A LEU* 3.8 22.8 - - + +
83A LEU* 4.6 12.6 - - + -
86A LEU* 4.8 13.2 - - + -
87A LEU* 4.5 7.9 - - + -
90A TYR* 4.4 17.3 - - + +
116A PHE* 3.9 34.5 - - + -
164A GLU 3.2 6.8 + - - +
165A LEU* 3.5 17.9 - - + +
167A ILE* 1.3 79.0 - - - +
169A LEU* 1.3 62.3 + - - +
171A TRP* 3.2 16.5 + - + +
172A MET* 3.1 36.3 + - + +
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Residues in contact with LEU 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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39A LEU* 4.2 14.6 - - + +
42A ILE* 3.7 40.8 - - + +
43A ARG* 3.8 40.7 + - + +
46A PHE* 4.7 7.9 - - + -
116A PHE* 4.2 7.6 - - + -
165A LEU* 2.8 36.8 + - + +
166A ASP* 4.3 4.7 - - - +
168A LEU* 1.3 72.5 - - - +
170A GLN* 1.3 57.3 + - - +
172A MET* 3.3 27.8 + - + +
173A GLU* 3.0 26.3 + - - +
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Residues in contact with GLN 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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43A ARG* 2.9 24.3 + - - +
166A ASP 3.1 20.5 + - - +
167A ILE* 3.6 4.0 - - - +
169A LEU* 1.3 75.7 - - - +
171A TRP* 1.3 67.6 + - + +
173A GLU* 4.2 9.5 - - - +
174A GLU* 2.8 56.6 + - - +
130R TYR* 4.0 20.0 - - - +
132R PHE* 3.6 27.6 - - + -
133R LEU* 3.2 14.4 - - + +
225R PRO* 5.4 0.2 - - - +
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Residues in contact with TRP 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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63A ARG* 4.7 4.4 - - - +
65A LEU* 3.6 55.4 - - + -
66A ARG 4.1 1.8 - - - -
67A ARG* 3.8 10.5 - - - +
69A GLU* 3.5 26.7 - - + -
70A SER* 3.5 28.0 - - - -
71A LEU* 4.0 20.8 - - + +
82A LEU* 5.4 0.4 - - + -
86A LEU* 4.4 13.9 - - + -
145A ILE* 4.3 8.5 - - + -
167A ILE* 2.8 35.8 + - + +
168A LEU* 3.2 19.0 + - + +
170A GLN* 1.3 75.9 - - + +
172A MET* 1.3 59.7 + - + +
174A GLU* 3.4 30.7 - - - +
175A THR* 3.1 24.6 - - - +
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Residues in contact with MET 172 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LYS* 3.5 5.4 + - - -
28A LEU* 3.4 25.9 - - + +
39A LEU* 4.1 22.6 - - + +
71A LEU* 4.7 6.1 - - + -
83A LEU* 4.2 33.7 - - + -
87A LEU* 5.5 1.1 - - - -
116A PHE* 3.8 22.2 - - + -
119A ILE* 4.9 11.4 - - + -
168A LEU* 3.1 25.7 + - + +
169A LEU* 3.6 37.0 - - + +
170A GLN 3.1 0.6 - - - -
171A TRP* 1.3 76.5 - - + +
173A GLU* 1.3 63.3 + - - +
175A THR* 3.2 18.7 + - - -
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Residues in contact with GLU 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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26A LYS* 3.5 35.7 - - - +
39A LEU* 3.3 22.9 - - + +
43A ARG* 3.0 32.1 + - - +
169A LEU 3.0 11.8 + - - +
170A GLN* 3.1 15.9 + - - +
172A MET* 1.3 73.6 - - - +
174A GLU* 1.3 64.3 + - - +
175A THR 3.3 1.0 + - - -
176A GLU* 4.2 2.9 + - - +
178R ASN* 5.5 4.9 + - - -
223R PRO 5.6 1.9 - - - +
224R GLY* 5.5 4.7 - - - -
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Residues in contact with GLU 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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70A SER* 3.4 22.9 + - - -
72A GLN* 3.9 35.2 + - + +
170A GLN* 2.8 48.5 + - - +
171A TRP* 3.4 23.0 - - - +
173A GLU* 1.3 74.5 - - - +
175A THR* 1.3 50.8 + - - +
176A GLU* 2.6 20.2 + - - +
105R GLU* 5.4 9.7 - - - +
130R TYR* 5.4 0.9 + - - -
132R PHE* 5.9 0.3 - - - -
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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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26A LYS* 3.4 4.5 + - - -
28A LEU* 2.9 27.9 - - - +
29A ASN* 3.7 14.1 + - - -
30A LEU* 5.6 0.4 - - - -
71A LEU* 3.6 33.6 - - + +
72A GLN* 3.8 15.7 - - - +
79A ARG* 4.5 9.9 - - - +
171A TRP 3.1 19.5 - - - +
172A MET 3.2 1.1 + - - +
173A GLU 3.2 1.4 - - - -
174A GLU* 1.3 69.8 - - - +
176A GLU* 1.3 86.4 + - - +
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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