Contacts of the helix formed by residues 151 - 165 (chain D) in PDB entry 1V8C
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 151 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PRO 3.8 12.6 - - - +
122D GLY* 2.7 22.5 + - - +
150D GLU* 1.3 87.4 - - + +
152D ALA* 1.3 63.4 + - - +
153D GLU* 3.2 3.3 + - - -
154D ARG* 2.7 49.4 + - + +
155D TRP* 3.2 39.8 + - + +
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D GLY 4.9 0.4 - - - +
87D GLY* 3.9 10.5 - - - -
89D PHE* 3.9 11.7 - - + -
122D GLY 4.0 0.2 + - - -
123D ALA* 4.4 1.1 - - - -
147D VAL* 3.6 34.3 - - - +
148D GLU 3.8 0.7 - - - -
149D GLY 3.1 28.3 + - - +
150D GLU 3.3 1.4 + - - -
151D GLU* 1.3 77.7 - - - +
153D GLU* 1.3 58.3 + - - +
156D PHE* 2.9 33.6 + - - +
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Residues in contact with GLU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D SER* 3.3 30.3 + - - -
56D PHE* 3.6 10.0 - - + -
81D PHE* 3.4 33.7 - - + +
82D PRO 4.6 1.7 - - - +
83D PRO 5.6 0.9 - - - +
85D ALA* 3.3 24.6 - - - +
86D GLY 5.2 2.2 + - - +
89D PHE* 3.6 17.5 - - + -
150D GLU 5.1 1.3 + - - +
151D GLU* 3.2 1.3 - - - -
152D ALA* 1.3 80.4 - - - +
154D ARG* 1.3 66.3 + - + +
156D PHE* 3.5 2.0 - - - +
157D GLU* 3.0 24.6 + - - +
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Residues in contact with ARG 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D PHE* 4.9 13.9 - - + -
151D GLU* 2.7 46.1 + - + +
152D ALA 3.5 0.2 - - - -
153D GLU* 1.3 81.4 - - + +
155D TRP* 1.3 60.4 + - + +
157D GLU* 3.4 6.7 + - - +
158D ARG* 2.9 35.5 + - + +
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Residues in contact with TRP 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D TRP* 3.9 43.1 - + + -
120D LEU* 3.5 30.4 - - + +
121D PRO* 3.1 41.6 + - + -
123D ALA* 3.6 18.2 - - + -
125D VAL* 5.4 0.9 - - + -
147D VAL* 4.3 11.9 - - + -
151D GLU* 3.2 32.6 + - + +
152D ALA 4.2 1.1 - - - +
154D ARG* 1.3 75.6 - - + +
156D PHE* 1.3 67.5 + - - +
158D ARG* 3.2 38.2 + - + +
159D ILE* 3.0 29.4 + - - +
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Residues in contact with PHE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D TYR* 3.8 19.5 - + - -
79D ASP* 4.0 0.2 - - - -
81D PHE* 4.4 5.8 - + - -
89D PHE* 3.8 28.9 - - + -
90D GLU* 3.8 28.3 - - - -
91D ARG* 3.8 41.5 - - + -
93D PHE* 4.7 9.5 - + - -
145D VAL* 4.8 3.8 - - + -
147D VAL* 4.1 21.0 - - + +
152D ALA 2.9 21.7 + - - +
153D GLU* 3.5 3.4 - - - +
155D TRP* 1.3 77.6 - - - +
157D GLU* 1.3 81.3 + - + +
159D ILE* 3.3 7.6 + - + +
160D ALA* 3.0 22.4 + - + +
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Residues in contact with GLU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D PHE* 3.3 60.6 - - + +
59D GLY* 3.3 27.0 + - - +
79D ASP* 2.6 28.7 - - - +
81D PHE* 3.2 21.3 - - + -
153D GLU 3.0 19.7 + - - +
154D ARG 3.8 3.6 - - - +
156D PHE* 1.3 82.1 - - + +
158D ARG* 1.3 61.0 + - - +
160D ALA* 3.1 4.7 + - - +
161D PHE 2.8 24.4 + - - -
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Residues in contact with ARG 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLY 5.0 1.1 - - - -
108D TRP* 2.9 60.9 - - + +
154D ARG* 2.9 27.5 + - + +
155D TRP* 3.2 39.4 + - + +
157D GLU* 1.3 76.7 - - - +
159D ILE* 1.3 58.1 + - - +
161D PHE* 3.3 17.2 + - - +
162D ALA* 3.0 22.9 + - - +
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Residues in contact with ILE 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D PHE* 4.0 23.6 - - + -
96D PHE* 4.0 18.8 - - + -
101D LEU* 4.1 12.8 - - + -
105D LEU* 4.5 2.5 - - + -
108D TRP* 3.8 22.7 - - + -
120D LEU* 5.8 0.4 - - + -
125D VAL* 3.9 34.1 - - + -
145D VAL* 4.1 8.1 - - + -
147D VAL* 4.0 17.0 - - + -
155D TRP* 3.0 19.0 + - + +
156D PHE* 3.4 7.6 - - + +
157D GLU 3.2 0.2 - - - -
158D ARG* 1.3 74.7 - - - +
160D ALA* 1.3 59.7 + - - +
162D ALA* 3.2 3.5 + - - +
163D ALA* 2.8 27.4 + - - +
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLU* 4.0 4.4 - - - +
59D GLY* 3.9 13.0 - - - +
79D ASP* 5.0 0.2 - - - +
91D ARG* 4.2 20.6 - - - +
93D PHE* 4.0 17.4 - - + -
156D PHE* 3.0 14.2 + - + +
157D GLU* 3.1 17.2 + - - +
159D ILE* 1.3 76.0 - - - +
161D PHE* 1.3 57.5 + - - +
163D ALA* 3.7 1.0 - - - +
164D SER* 2.9 30.3 + - - -
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Residues in contact with PHE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ARG 4.3 6.1 - - - -
64B TYR* 4.6 10.8 - + - -
58D GLU 3.5 7.4 - - - -
59D GLY* 3.7 12.0 - - - +
60D ARG* 3.1 57.9 - - + -
108D TRP* 6.1 1.8 - + - -
157D GLU 2.8 12.9 + - - +
158D ARG* 3.5 20.4 - - - +
160D ALA* 1.3 77.2 - - - +
162D ALA* 1.3 65.9 + - + +
164D SER* 2.6 20.4 + - - -
165D ARG* 3.1 36.9 + - + +
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D PHE* 4.3 8.2 - - + -
100D LEU* 5.6 1.2 - - - +
104D TYR* 3.7 50.1 + - + -
108D TRP* 4.1 9.9 - - + -
158D ARG 3.0 13.0 + - - +
159D ILE* 3.5 7.9 - - - +
161D PHE* 1.3 81.3 - - + +
163D ALA* 1.3 60.6 + - - +
165D ARG* 3.3 23.4 - - - +
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Residues in contact with ALA 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D PHE* 3.7 29.8 - - + -
94D GLY 5.3 4.6 - - - +
95D ALA 5.6 1.4 - - - +
96D PHE* 3.7 34.3 - - + +
159D ILE 2.8 17.5 + - - +
160D ALA 3.8 2.5 - - - +
162D ALA* 1.3 72.4 - - - +
164D SER* 1.3 65.3 + - - +
165D ARG 3.1 7.7 + - - -
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Residues in contact with SER 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ALA* 5.5 0.7 - - - +
74C PRO* 3.7 33.8 - - - +
58D GLU* 3.9 17.3 - - - -
60D ARG* 3.3 24.9 + - - -
160D ALA 2.9 15.4 + - - -
161D PHE 2.6 19.1 + - - -
163D ALA* 1.3 77.9 - - - +
165D ARG* 1.3 63.7 + - - +
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Residues in contact with ARG 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ARG 2.9 28.1 + - - -
64B TYR 4.1 0.8 - - - -
65B LEU 2.5 28.0 + - - -
66B GLN* 4.1 9.7 - - - +
22C GLY 5.4 0.3 - - - -
23C ALA* 3.1 32.4 - - - +
60D ARG* 3.8 13.9 - - - +
104D TYR* 4.4 12.3 - - - +
161D PHE* 3.1 42.1 - - + +
162D ALA* 3.3 19.3 - - - +
163D ALA 3.1 6.8 - - - -
164D SER* 1.3 87.1 + - - +
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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