Contacts of the helix formed by residues 151 - 164 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B PRO 4.2 5.2 - - - +
122B GLY* 2.7 28.9 + - - +
150B GLU* 1.3 82.5 - - + +
152B ALA* 1.3 63.8 + - - +
153B GLU* 3.3 2.9 - - - -
154B ARG* 3.4 37.6 + - - +
155B TRP* 3.0 38.4 + - + +
64D TYR* 4.9 11.7 + - - -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLY* 5.3 3.1 - - - +
89B PHE* 4.0 14.1 - - + -
123B ALA* 4.1 2.9 - - - -
147B VAL* 3.6 27.0 - - + +
148B GLU* 3.7 6.7 - - - -
149B GLY 3.4 31.1 + - - +
150B GLU 3.5 1.0 + - - -
151B GLU* 1.3 76.9 - - - +
153B GLU* 1.3 54.0 + - - +
155B TRP 3.3 0.5 + - - -
156B PHE* 2.7 38.1 + - - +
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B SER* 3.0 29.7 + - - -
56B PHE* 3.4 13.9 - - + -
81B PHE* 3.2 47.8 - - + +
82B PRO 4.4 5.2 - - - +
89B PHE* 3.6 21.2 - - + -
151B GLU* 3.3 1.3 - - - +
152B ALA* 1.3 79.8 - - - +
154B ARG* 1.3 62.4 + - - +
156B PHE* 3.4 2.5 + - - +
157B GLU* 3.0 29.5 + - - +
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 5.0 8.3 - - + -
121B PRO* 4.9 6.0 + - - +
151B GLU* 3.4 46.7 + - - +
152B ALA 3.3 0.6 - - - -
153B GLU* 1.3 80.4 - - - +
155B TRP* 1.3 94.1 + - + +
157B GLU* 3.4 6.0 + - - +
158B ARG* 3.0 34.4 + - - +
63D ARG* 3.3 46.0 + - - +
64D TYR* 4.3 25.1 + - + +
65D LEU 6.0 1.3 - - - +
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Residues in contact with TRP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B TRP* 3.7 37.5 - + + -
120B LEU* 3.4 33.6 - - + +
121B PRO* 3.2 38.9 + - + -
123B ALA* 3.7 16.6 - - + -
125B VAL* 5.3 1.1 - - + -
147B VAL* 4.2 11.7 - - + -
151B GLU* 3.0 30.3 + - + +
152B ALA 3.9 2.0 - - - +
154B ARG* 1.3 102.5 - - + +
156B PHE* 1.3 66.3 + - - +
158B ARG* 3.1 47.1 + - - +
159B ILE* 3.0 29.9 + - - +
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Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TYR* 3.6 36.1 - + - -
81B PHE* 4.0 9.9 - + - -
89B PHE* 3.9 20.9 - - + -
90B GLU* 3.6 31.0 - - - -
91B ARG* 3.8 28.3 - - + -
93B PHE* 5.3 6.6 - + - -
145B VAL* 4.6 3.8 - - + -
147B VAL* 4.0 23.3 - - + +
152B ALA 2.7 24.1 + - - +
153B GLU* 3.7 3.6 - - - +
155B TRP* 1.3 72.6 - - - +
157B GLU* 1.3 78.6 + - - +
159B ILE* 3.3 8.2 + - + +
160B ALA* 3.0 24.0 + - + +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 3.1 58.5 - - + +
59B GLY* 3.3 28.5 + - - +
79B ASP* 2.6 29.5 - - - +
81B PHE* 3.2 22.5 - - + -
153B GLU 3.0 20.2 + - - +
154B ARG 3.7 4.0 - - - +
156B PHE* 1.3 84.0 - - - +
158B ARG* 1.3 59.9 + - - +
160B ALA* 3.1 3.9 + - - +
161B PHE 2.9 23.0 + - - -
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Residues in contact with ARG 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLY 4.5 2.7 + - - -
108B TRP* 3.3 52.1 - - + -
154B ARG* 3.0 25.2 + - - +
155B TRP* 3.1 33.3 + - - +
157B GLU* 1.3 76.9 - - - +
159B ILE* 1.3 58.0 + - - +
161B PHE* 3.3 6.9 + - + +
162B ALA* 2.9 21.8 + - - +
1003B CL 3.3 26.3 - - - +
63D ARG* 3.1 29.5 + - - +
65D LEU 4.0 6.3 + - - +
66D GLN* 3.5 41.3 + - + +
67D GLY* 3.6 9.1 - - - +
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PHE* 4.0 24.0 - - + -
96B PHE* 4.0 16.4 - - + -
101B LEU* 4.1 11.2 - - + -
105B LEU* 4.4 5.2 - - + -
108B TRP* 3.9 22.0 - - + -
120B LEU* 5.5 0.4 - - + -
125B VAL* 3.9 35.2 - - + -
145B VAL* 4.2 8.3 - - + -
147B VAL* 4.1 16.2 - - + -
155B TRP* 3.0 20.3 + - + +
156B PHE* 3.5 8.3 - - + +
158B ARG* 1.3 73.9 - - - +
160B ALA* 1.3 64.8 + - - +
162B ALA* 3.2 3.5 + - - +
163B ALA* 2.9 22.9 + - - +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLU 4.7 2.6 - - - -
59B GLY* 4.4 5.4 - - - +
79B ASP* 4.7 1.6 - - - +
91B ARG* 3.8 25.8 - - - +
93B PHE* 4.0 15.6 - - + -
156B PHE* 3.0 14.9 + - + +
157B GLU* 3.1 21.5 + - - +
159B ILE* 1.3 77.8 - - - +
161B PHE* 1.3 62.4 + - - +
163B ALA* 3.4 2.8 + - - +
164B SER* 3.2 23.6 + - - -
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Residues in contact with PHE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLU 3.6 17.3 - - - +
59B GLY* 4.0 6.7 - - - +
60B ARG* 3.7 37.2 - - + -
104B TYR* 5.9 2.7 - + - -
108B TRP* 5.7 0.2 - + - -
157B GLU 2.9 12.5 + - - +
158B ARG* 3.3 14.1 - - + +
159B ILE 3.2 0.2 - - - -
160B ALA* 1.3 77.1 - - - +
162B ALA* 1.3 69.9 + - + +
164B SER* 2.7 24.7 + - - -
66D GLN* 3.6 24.2 - - + -
69D SER* 3.9 19.7 - - - -
71D PRO* 3.6 30.7 - - + -
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B PHE* 4.4 9.3 - - + -
100B LEU* 5.6 1.6 - - - +
101B LEU* 6.1 0.4 - - + -
104B TYR* 3.8 52.1 + - + -
108B TRP* 3.9 10.8 - - + -
158B ARG 2.9 16.7 + - - +
159B ILE* 3.2 6.0 + - - +
161B PHE* 1.3 85.1 - - + +
163B ALA* 1.3 62.1 + - - +
164B SER 3.4 4.0 + - - -
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 5.0 4.2 - - - +
93B PHE* 3.5 34.8 - - + -
96B PHE* 3.8 30.2 - - + -
159B ILE 2.9 14.2 + - - +
160B ALA 3.7 2.5 - - - +
162B ALA* 1.3 76.9 - - - +
164B SER* 1.3 61.6 + - - +
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Residues in contact with SER 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.1 31.6 - - - +
72A LEU 4.7 5.6 - - - +
73A SER* 5.8 0.4 - - - -
74A PRO* 4.4 30.1 - - - -
58B GLU* 4.1 16.8 + - - +
160B ALA 3.2 13.2 + - - -
161B PHE* 2.7 30.8 + - - -
162B ALA 4.2 3.4 - - - -
163B ALA* 1.3 80.3 - - - +
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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