Contacts of the helix formed by residues 151 - 165 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A TYR* 4.8 10.1 + - - -
1001A EDO 3.9 21.9 - - - +
121C PRO 3.9 10.8 - - - +
122C GLY* 2.8 22.4 + - - +
150C GLU* 1.3 86.4 - - + +
152C ALA* 1.3 63.1 + - - +
153C GLU* 3.3 3.7 + - - -
154C ARG* 3.4 22.0 + - - +
155C TRP* 3.1 38.8 + - + +
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Residues in contact with ALA 152 (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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87C GLY 4.1 4.3 - - - +
89C PHE* 3.9 14.4 - - + -
122C GLY 4.1 0.4 + - - -
123C ALA* 4.4 1.3 - - - -
147C VAL* 3.5 38.1 - - - +
148C GLU* 3.8 10.5 - - - -
149C GLY 3.0 19.0 + - - +
150C GLU 3.4 1.0 + - - -
151C GLU* 1.3 77.4 - - - +
153C GLU* 1.3 57.0 + - - +
156C PHE* 2.8 34.1 + - - +
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Residues in contact with GLU 153 (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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54C SER* 2.9 34.7 + - - -
56C PHE* 3.6 9.1 - - + -
81C PHE* 3.3 46.3 - - + +
82C PRO 4.7 2.1 - - - +
85C ALA* 3.7 11.8 - - - +
89C PHE* 3.5 19.3 - - + -
150C GLU 5.1 1.5 + - - +
151C GLU* 3.3 1.0 - - - +
152C ALA* 1.3 79.7 - - - +
154C ARG* 1.3 68.0 + - + +
156C PHE* 3.6 2.1 - - - +
157C GLU* 3.0 28.6 + - - +
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Residues in contact with ARG 154 (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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64A TYR* 3.5 44.3 + - - +
1001A EDO 3.4 26.5 + - - +
54C SER* 4.6 10.4 + - - -
56C PHE* 3.9 21.5 - - + -
61C ASP* 3.0 32.1 + - - +
63C ARG* 6.1 1.0 - - - +
64C TYR* 4.5 10.6 + - - -
151C GLU* 3.4 18.8 + - - +
152C ALA 3.4 0.2 - - - -
153C GLU* 1.3 84.9 - - + +
155C TRP* 1.3 57.9 + - - +
157C GLU* 3.3 6.6 + - - +
158C ARG* 2.9 28.2 + - - +
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Residues in contact with TRP 155 (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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1001A EDO 3.6 23.4 - - - -
108C TRP* 3.6 35.2 - + + -
120C LEU* 3.5 29.5 - - + +
121C PRO* 2.8 42.2 + - + -
123C ALA* 3.6 17.9 - - + -
125C VAL* 5.2 1.3 - - + -
147C VAL* 4.1 13.9 - - + -
151C GLU* 3.1 27.3 + - + +
152C ALA 4.1 1.6 - - - +
154C ARG* 1.3 73.9 - - - +
156C PHE* 1.3 66.2 + - - +
158C ARG* 3.2 49.5 + - - +
159C ILE* 3.0 29.3 + - - +
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Residues in contact with PHE 156 (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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6C TYR* 3.6 27.6 - + - -
81C PHE* 4.3 7.9 - + - -
89C PHE* 3.8 26.2 - + + -
90C GLU* 3.7 26.2 - - - -
91C ARG* 3.7 35.7 - - + -
93C PHE* 4.8 9.1 - + - -
145C VAL* 4.6 5.6 - - + -
147C VAL* 4.0 21.2 - - + +
152C ALA 2.8 21.5 + - - +
153C GLU* 3.6 2.5 - - - +
155C TRP* 1.3 75.9 - - - +
157C GLU* 1.3 78.5 + - - +
159C ILE* 3.2 7.6 + - + +
160C ALA* 3.0 24.7 + - + +
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Residues in contact with GLU 157 (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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56C PHE* 3.1 62.2 - - + +
59C GLY* 3.3 28.5 + - - +
79C ASP* 2.5 30.4 - - - +
81C PHE* 3.3 19.1 - - + -
153C GLU 3.0 21.0 + - - +
154C ARG 3.7 3.1 - - - +
156C PHE* 1.3 82.8 - - - +
158C ARG* 1.3 59.4 + - - +
160C ALA* 3.1 5.1 + - - +
161C PHE* 2.9 23.7 + - - +
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Residues in contact with ARG 158 (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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63A ARG* 3.1 30.5 + - - +
65A LEU 4.0 5.7 + - - +
66A GLN* 3.5 32.6 + - + +
67A GLY* 3.5 18.4 - - - +
1001A EDO 4.1 4.9 + - - -
1002A CL 3.2 27.3 - - - +
59C GLY 4.4 2.7 + - - -
108C TRP* 3.3 47.7 - - + -
154C ARG 2.9 17.5 + - - +
155C TRP* 3.2 33.5 + - - +
157C GLU* 1.3 75.7 - - - +
159C ILE* 1.3 57.2 + - - +
161C PHE* 3.2 9.7 + - + +
162C ALA* 2.9 26.7 + - - +
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Residues in contact with ILE 159 (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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93C PHE* 4.1 17.5 - - + -
96C PHE* 3.9 23.5 - - + -
101C LEU* 4.1 13.2 - - + -
105C LEU* 4.5 3.1 - - + -
108C TRP* 3.8 21.5 - - + -
120C LEU* 5.7 0.4 - - + -
125C VAL* 3.9 33.7 - - + -
145C VAL* 4.0 14.8 - - + -
147C VAL* 4.1 10.8 - - + -
155C TRP* 3.0 19.2 + - + +
156C PHE* 3.5 8.3 - - + +
158C ARG* 1.3 74.9 - - - +
160C ALA* 1.3 64.0 + - - +
162C ALA* 3.1 3.9 + - - +
163C ALA* 2.9 21.8 + - - +
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Residues in contact with ALA 160 (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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58C GLU 4.7 3.1 - - - -
59C GLY* 4.4 9.4 - - - +
79C ASP* 5.0 0.4 - - - +
91C ARG* 3.9 25.1 - - - +
93C PHE* 4.0 16.9 - - + -
156C PHE* 3.0 13.7 + - + +
157C GLU* 3.1 17.7 + - - +
159C ILE* 1.3 76.6 - - - +
161C PHE* 1.3 63.2 + - - +
163C ALA* 3.4 2.9 + - - +
164C SER* 3.1 23.2 + - - -
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Residues in contact with PHE 161 (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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66A GLN* 3.5 31.9 - - + -
69A SER* 4.0 19.3 - - - -
71A PRO* 3.7 28.5 - - + -
58C GLU 3.6 16.8 - - - +
59C GLY* 4.1 6.4 - - - +
60C ARG* 3.9 26.2 - - + -
104C TYR* 5.6 1.8 - + - -
108C TRP* 5.7 0.7 - + - -
157C GLU 2.9 12.5 + - - +
158C ARG* 3.3 15.0 - - + +
159C ILE 3.2 0.2 - - - -
160C ALA* 1.3 76.9 - - - +
162C ALA* 1.3 68.8 + - + +
164C SER* 2.6 22.8 + - - -
165C ARG* 3.2 45.0 - - + +
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Residues in contact with ALA 162 (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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96C PHE* 4.1 9.9 - - + -
100C LEU* 5.7 1.7 - - - +
104C TYR* 3.7 47.3 + - + -
108C TRP* 4.2 7.6 - - + -
158C ARG 2.9 14.0 + - - +
159C ILE 3.1 8.3 + - - +
161C PHE* 1.3 83.6 - - + +
163C ALA* 1.3 62.3 + - - +
165C ARG* 3.1 22.7 + - - +
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Residues in contact with ALA 163 (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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93C PHE* 3.5 32.1 - - + -
96C PHE* 3.7 32.0 - - + +
159C ILE 2.9 14.9 + - - +
160C ALA 3.7 3.6 - - - +
162C ALA* 1.3 76.9 - - - +
164C SER* 1.3 62.6 + - - +
165C ARG 3.2 5.0 + - - -
23D ALA* 5.4 0.9 - - - +
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Residues in contact with SER 164 (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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58C GLU* 4.2 27.5 + - - +
160C ALA 3.1 12.6 + - - -
161C PHE* 2.6 25.9 + - - -
163C ALA* 1.3 75.5 - - - +
165C ARG* 1.3 64.1 + - - +
23D ALA* 3.5 15.3 - - - +
72D LEU 4.6 7.1 - - - +
74D PRO* 4.4 21.4 - - - +
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Residues in contact with ARG 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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24A THR* 5.2 7.9 - - - +
69A SER 5.2 0.6 + - - -
71A PRO* 3.3 36.4 - - - +
104C TYR* 4.0 14.3 + - - +
161C PHE* 3.2 45.3 - - + +
162C ALA* 3.3 14.1 - - - +
163C ALA 3.1 6.0 - - - -
164C SER* 1.3 84.5 - - - +
23D ALA* 3.4 21.8 - - - +
24D THR* 6.0 0.3 - - - +
27D GLU* 5.2 3.6 - - - +
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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