Contacts of the helix formed by residues 151 - 164 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A VAL* 6.1 1.1 - - - -
121A PRO* 2.8 30.0 - - - +
122A GLY* 2.8 22.7 + - - +
123A ALA* 4.2 0.2 - - - -
150A GLU* 1.3 78.2 - - + +
152A ALA* 1.3 63.8 + - - +
153A GLU* 3.3 3.6 - - - -
154A ARG* 2.7 43.9 + - + -
155A TRP* 3.2 27.1 + - + -
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Residues in contact with ALA 152 (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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85A ALA 5.6 0.6 + - - +
87A GLY 3.3 27.1 - - - +
89A PHE* 3.9 13.0 - - + -
122A GLY 4.1 0.2 + - - -
123A ALA* 4.3 1.8 - - - -
147A VAL* 3.6 27.6 - - - +
148A GLU* 3.8 1.3 - - - -
149A GLY 3.1 16.0 + - - +
150A GLU 3.4 1.2 + - - -
151A GLU* 1.3 77.0 - - - +
153A GLU* 1.3 57.5 + - - +
156A PHE* 2.8 34.0 + - - +
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Residues in contact with GLU 153 (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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54A SER* 3.2 32.6 + - - -
56A PHE* 3.5 12.8 - - + -
81A PHE* 3.4 44.9 - - + +
82A PRO 4.2 1.2 - - - +
84A VAL* 3.8 36.0 - - + +
85A ALA 5.0 5.0 + - - +
89A PHE* 3.8 19.7 - - + -
150A GLU 5.2 0.8 + - - +
151A GLU* 3.3 1.0 - - - -
152A ALA* 1.3 76.8 - - - +
154A ARG* 1.3 65.1 + - - +
156A PHE* 3.6 1.8 - - - +
157A GLU* 3.0 25.5 + - - +
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Residues in contact with ARG 154 (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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56A PHE* 5.7 3.8 - - - -
121A PRO* 4.1 7.9 + - - +
151A GLU* 2.7 54.1 + - + +
153A GLU* 1.3 81.1 - - - +
155A TRP* 1.3 103.2 + - + +
157A GLU* 3.3 4.1 + - - +
158A ARG* 3.0 44.3 + - + +
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Residues in contact with TRP 155 (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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108A TRP* 3.7 44.9 - + + -
120A LEU* 3.6 33.6 - - + +
121A PRO* 2.8 43.0 + - + -
123A ALA* 3.7 13.2 - - + -
125A VAL* 5.0 1.3 - - + -
147A VAL* 4.2 12.6 - - + -
151A GLU* 3.2 25.2 + - + +
154A ARG* 1.3 116.3 - - - +
156A PHE* 1.3 65.9 + - - +
158A ARG* 3.2 30.2 + - + +
159A ILE* 3.0 31.1 + - - +
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Residues in contact with PHE 156 (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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6A TYR* 3.5 29.2 - + - -
81A PHE* 4.0 10.1 - + - -
89A PHE* 3.7 18.6 - - + -
90A GLU* 3.6 40.8 - - - -
91A ARG* 3.7 27.6 - - + -
93A PHE* 5.2 5.0 - + - -
145A VAL* 4.7 3.8 - - + -
147A VAL* 4.0 25.9 - - + +
152A ALA 2.8 21.3 + - - +
153A GLU* 3.6 4.9 - - - +
155A TRP* 1.3 76.2 - - - +
157A GLU* 1.3 86.8 + - - +
159A ILE* 3.3 7.4 + - + +
160A ALA* 3.1 17.8 + - - +
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Residues in contact with GLU 157 (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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56A PHE* 3.2 62.1 - - + +
59A GLY* 3.3 23.1 + - - +
79A ASP* 2.6 29.0 - - - +
81A PHE* 3.2 20.7 - - + -
153A GLU 3.0 19.2 + - - +
154A ARG 3.9 3.1 - - - +
156A PHE* 1.3 81.4 - - - +
158A ARG* 1.3 60.4 + - - +
160A ALA* 3.1 6.6 + - - +
161A PHE* 2.8 29.1 + - - +
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Residues in contact with ARG 158 (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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59A GLY 5.1 0.4 - - - -
108A TRP* 2.9 61.6 - - + +
154A ARG* 3.0 36.1 + - + +
155A TRP* 3.2 37.4 + - + +
157A GLU* 1.3 76.2 - - - +
159A ILE* 1.3 58.9 + - - +
161A PHE* 3.3 18.3 + - - +
162A ALA* 2.9 22.7 + - - +
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Residues in contact with ILE 159 (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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93A PHE* 3.9 23.8 - - + -
96A PHE* 3.9 16.7 - - + -
101A LEU* 3.9 13.7 - - + -
105A LEU* 4.6 2.0 - - + -
108A TRP* 3.7 21.8 - - + -
125A VAL* 3.8 36.1 - - + -
145A VAL* 4.1 9.0 - - + -
147A VAL* 3.9 17.0 - - + -
155A TRP* 3.0 19.4 + - + +
156A PHE* 3.5 8.7 - - + +
157A GLU 3.1 0.2 - - - -
158A ARG* 1.3 74.8 - - - +
160A ALA* 1.3 60.5 + - - +
162A ALA* 3.2 3.3 + - - +
163A ALA* 2.9 27.4 + - - +
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Residues in contact with ALA 160 (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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58A GLU 4.1 2.6 - - - +
59A GLY* 3.9 16.2 - - - +
91A ARG* 4.0 23.3 - - - +
93A PHE* 3.9 17.8 - - + -
156A PHE 3.1 12.8 + - - +
157A GLU* 3.1 13.6 + - - +
159A ILE* 1.3 75.4 - - - +
161A PHE* 1.3 63.7 + - - +
163A ALA* 3.4 2.6 + - - +
164A SER* 3.1 22.3 + - - -
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Residues in contact with PHE 161 (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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58A GLU 3.7 8.3 - - - -
59A GLY* 3.7 17.4 - - - +
60A ARG* 3.2 39.9 - - + -
157A GLU 2.8 12.8 + - - +
158A ARG* 3.4 23.1 - - - +
160A ALA* 1.3 76.7 - - - +
162A ALA* 1.3 62.8 + - - +
164A SER* 2.6 22.5 + - - -
165A ARG* 3.7 21.4 + - + +
63C ARG 3.8 14.1 - - - -
64C TYR* 3.6 38.6 - + - -
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Residues in contact with ALA 162 (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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96A PHE* 4.4 5.0 - - + -
100A LEU* 6.0 0.2 - - - +
101A LEU* 5.9 0.4 - - + -
104A TYR* 3.8 50.8 + - + -
108A TRP* 4.0 9.9 - - + -
158A ARG 2.9 13.2 + - - +
159A ILE* 3.5 8.7 - - - +
161A PHE* 1.3 76.9 - - - +
163A ALA* 1.3 63.6 + - - +
165A ARG* 3.1 24.5 + - - +
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Residues in contact with ALA 163 (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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93A PHE* 3.6 33.2 - - + -
96A PHE* 3.8 29.7 - - + -
159A ILE 2.9 16.0 + - - +
160A ALA 3.7 2.0 - - - +
161A PHE 3.3 0.4 - - - -
162A ALA* 1.3 77.3 - - - +
164A SER* 1.3 61.2 + - - +
165A ARG 3.0 5.9 + - - -
74B PRO* 5.3 0.8 - - - +
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Residues in contact with SER 164 (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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58A GLU* 4.2 4.5 - - - -
60A ARG* 3.1 34.9 + - - -
160A ALA 3.1 12.0 + - - -
161A PHE* 2.6 20.5 + - - -
163A ALA* 1.3 75.3 - - - +
165A ARG* 1.3 59.8 + - - +
23B ALA* 4.7 3.6 - - - +
72B LEU 4.6 8.3 - - - +
73B SER* 5.2 0.5 - - - -
74B PRO* 3.6 39.7 - - - +
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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