Contacts of the helix formed by residues 118 - 128 (chain D) in PDB entry 3B4V
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 ASP 118 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D PRO 3.7 8.5 - - - +
104D ALA* 4.5 2.8 - - - -
105D ARG* 3.3 27.6 + - - +
106D LEU 3.0 15.7 - - - +
107D GLN* 4.6 0.2 - - - +
108D VAL* 3.9 10.4 - - - +
116D TYR* 3.3 3.3 - - - +
117D ARG* 1.3 85.5 + - - +
119D GLU* 1.3 68.7 + - - +
120D CYS* 3.0 12.6 + - - +
121D GLU* 3.1 34.0 + - - +
122D LEU 3.5 6.8 + - - -
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Residues in contact with GLU 119 (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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102D LEU* 3.7 28.1 - - + +
103D PRO* 4.6 8.6 + - + +
106D LEU 4.1 2.4 + - - -
108D VAL* 4.0 16.0 - - + +
118D ASP* 1.3 73.6 - - - +
120D CYS* 1.3 57.2 + - - +
122D LEU* 3.0 4.7 + - + +
123D ARG* 2.7 72.9 + - - +
135D VAL* 3.7 15.9 - - + +
138D ARG* 2.7 40.6 + - - +
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Residues in contact with CYS 120 (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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97D PRO* 3.9 3.7 - - - +
99D CYS* 2.0 52.3 - - + -
102D LEU* 3.8 10.1 - - + +
118D ASP* 3.0 15.3 + - + +
119D GLU* 1.3 78.5 - - - +
121D GLU* 1.3 65.8 + - + +
123D ARG* 3.3 6.0 + - - +
124D ALA* 3.1 19.9 + - - +
152G ARG* 5.8 5.4 - - - -
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Residues in contact with GLU 121 (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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116D TYR* 4.3 13.3 - - + -
117D ARG* 2.5 41.6 + - + +
118D ASP* 3.1 21.5 + - - +
120D CYS* 1.3 76.5 - - - +
122D LEU* 1.3 60.7 + - - +
124D ALA* 3.2 12.1 + - - +
125D ALA* 2.8 29.3 + - - +
128D ARG* 4.8 0.7 + - - -
155G SER* 4.9 0.7 + - - -
204G PHE* 3.3 48.5 - - + +
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Residues in contact with LEU 122 (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 VAL* 4.1 14.1 - - + -
110D GLY* 3.7 18.8 - - - -
116D TYR* 4.0 26.6 - - + -
118D ASP 3.5 5.3 + - - +
119D GLU 3.0 11.5 + - - +
121D GLU* 1.3 76.2 - - - +
123D ARG* 1.3 77.1 + - - +
125D ALA 3.3 0.8 + - - +
126D ARG* 2.8 29.6 + - - +
133D LEU* 3.7 18.3 - - + +
134D SER* 3.6 42.4 - - - +
135D VAL* 4.0 14.4 - - + +
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Residues in contact with ARG 123 (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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97D PRO* 3.7 24.3 - - + +
98D ASP 5.2 4.0 - - - +
99D CYS* 4.9 0.2 - - - -
102D LEU* 3.8 29.1 - - + +
119D GLU* 2.7 56.1 + - - +
120D CYS 3.5 6.3 - - - +
122D LEU* 1.3 78.7 - - - +
124D ALA* 1.3 57.8 + - - +
126D ARG* 3.0 51.6 + - - +
127D CYS* 3.0 28.4 + - - +
134D SER* 5.8 0.4 - - - -
135D VAL* 4.3 12.5 - - - +
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Residues in contact with ALA 124 (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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95D CYS* 4.2 3.0 - - + +
97D PRO* 3.6 21.5 - - + +
120D CYS* 3.1 12.9 + - - +
121D GLU* 3.2 17.0 + - - +
123D ARG* 1.3 73.7 - - - +
125D ALA* 1.3 64.0 + - - +
127D CYS* 3.2 7.7 + - - +
128D ARG* 3.0 50.4 + - - +
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Residues in contact with ALA 125 (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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116D TYR* 3.7 26.9 - - + +
121D GLU 2.8 19.4 + - - +
122D LEU 3.9 0.2 - - - +
124D ALA* 1.3 69.7 - - - +
126D ARG* 1.3 67.2 + - - +
128D ARG* 3.4 26.8 + - - +
130D HIS* 3.4 15.3 + - + +
133D LEU* 3.8 11.4 - - + -
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Residues in contact with ARG 126 (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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122D LEU* 2.8 20.4 + - + +
123D ARG* 3.0 55.3 + - - +
125D ALA* 1.3 76.1 - - - +
127D CYS* 1.3 60.9 + - - +
129D GLY 3.4 0.2 + - - -
130D HIS* 2.8 47.6 + - - +
131D PRO* 3.7 20.5 - - + +
133D LEU* 3.2 29.6 + - + +
134D SER* 4.4 9.9 - - - +
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Residues in contact with CYS 127 (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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80D PRO 5.6 1.1 - - - -
81D GLY* 4.3 8.5 - - - +
82D LYS* 3.7 23.2 + - - -
95D CYS* 2.0 52.9 - - + -
97D PRO* 5.3 4.0 - - + -
123D ARG 3.0 13.7 + - - +
124D ALA* 3.4 7.9 - - - +
126D ARG* 1.3 78.3 - - - +
128D ARG* 1.3 54.9 + - - +
129D GLY 3.0 7.6 + - - -
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Residues in contact with ARG 128 (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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95D CYS* 4.0 23.8 + - - +
121D GLU* 4.8 1.2 + - - -
124D ALA* 3.0 47.5 + - - +
125D ALA* 3.6 17.8 - - - +
126D ARG 3.1 1.2 + - - -
127D CYS* 1.3 72.7 - - - +
129D GLY* 1.3 60.9 + - - +
130D HIS* 3.4 12.1 + - - +
171G ALA* 2.8 34.0 + - - +
172G ALA 4.5 2.0 - - - -
173G PRO* 4.6 28.5 - - + +
200G GLN* 3.7 26.2 - - - +
204G PHE* 3.1 46.7 - - - -
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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