Contacts of the helix formed by residues 118 - 128 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103G PRO 3.6 8.1 - - - +
104G ALA* 3.3 10.8 - - - +
105G ARG* 3.0 28.2 + - - +
106G LEU 3.1 16.4 - - - +
108G VAL* 3.6 10.0 - - - +
116G TYR* 3.2 3.5 + - - +
117G ARG* 1.3 80.1 - - - +
119G GLU* 1.3 66.3 + - - +
120G CYS* 3.0 15.0 + - - +
121G GLU* 3.1 32.9 + - - +
122G LEU 3.4 7.6 + - - -
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Residues in contact with GLU 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G LEU* 3.8 29.9 - - + +
103G PRO* 4.2 9.4 + - + +
106G LEU 4.2 2.4 + - - -
108G VAL* 3.6 16.5 - - + +
118G ASP* 1.3 73.9 - - - +
120G CYS* 1.3 62.1 + - - +
122G LEU* 3.2 5.9 + - + +
123G ARG* 2.7 55.2 + - - +
135G VAL* 4.0 16.8 - - + +
138G ARG* 3.1 40.3 + - - +
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Residues in contact with CYS 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G PRO* 4.0 1.5 - - - +
99G CYS* 2.0 56.2 - - + -
102G LEU* 3.7 12.9 - - + +
103G PRO 6.5 0.2 - - - -
104G ALA* 6.1 1.1 - - - -
118G ASP* 3.0 17.2 + - - +
119G GLU* 1.3 78.6 - - - +
121G GLU* 1.3 64.8 + - - +
123G ARG* 3.3 6.6 + - - +
124G ALA* 3.2 17.7 + - - +
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Residues in contact with GLU 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G TYR* 4.5 9.0 - - + -
117G ARG* 3.4 53.9 + - + +
118G ASP* 3.1 22.9 + - - +
120G CYS* 1.3 74.4 - - + +
122G LEU* 1.3 55.7 + - - +
124G ALA* 3.0 10.2 + - - +
125G ALA* 2.8 33.6 + - - +
128G ARG* 4.9 10.0 + - - -
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Residues in contact with LEU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G VAL* 4.5 6.1 - - + -
110G GLY* 4.0 19.1 - - - -
116G TYR* 4.0 25.4 - - + -
118G ASP 3.4 7.5 + - - +
119G GLU* 3.2 13.1 + - + +
121G GLU* 1.3 78.1 - - - +
123G ARG* 1.3 61.0 + - + +
125G ALA* 3.2 3.9 + - - +
126G ARG* 2.8 45.0 + - - +
133G LEU* 4.0 15.0 - - + +
134G SER* 3.8 30.5 - - - +
135G VAL* 3.9 29.2 - - + +
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Residues in contact with ARG 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G PRO* 3.8 21.3 - - + +
98G ASP 4.4 9.3 + - - +
102G LEU* 3.5 34.9 - - + +
119G GLU* 2.7 52.1 + - + +
120G CYS* 3.4 8.5 - - - +
121G GLU 3.3 0.2 - - - -
122G LEU* 1.3 79.3 - - + +
124G ALA* 1.3 60.3 + - - +
126G ARG* 3.2 43.9 + - - +
127G CYS* 3.1 21.7 + - - +
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Residues in contact with ALA 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G CYS* 4.1 7.5 - - + +
97G PRO* 3.7 25.0 - - + +
120G CYS 3.2 5.0 + - - +
121G GLU* 3.0 15.5 + - - +
123G ARG* 1.3 77.3 - - - +
125G ALA* 1.3 64.8 + - - +
127G CYS* 3.1 16.8 + - - +
128G ARG* 3.2 38.1 + - - +
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Residues in contact with ALA 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G TYR* 3.6 28.0 - - + +
121G GLU 2.8 16.1 + - - +
122G LEU 3.6 7.6 - - - +
124G ALA* 1.3 73.1 - - - +
126G ARG* 1.3 62.4 + - - +
128G ARG* 3.4 27.9 + - - +
130G HIS* 3.5 21.0 + - - +
133G LEU* 3.7 9.6 - - + -
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Residues in contact with ARG 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G LEU* 2.8 24.9 + - + +
123G ARG* 3.2 46.8 + - - +
124G ALA 3.1 0.2 - - - -
125G ALA* 1.3 70.5 - - - +
127G CYS* 1.3 67.0 + - - +
129G GLY 3.5 0.7 + - - -
130G HIS* 3.0 43.8 + - - +
131G PRO* 3.8 19.7 - - + +
133G LEU* 3.1 31.4 + - + +
134G SER* 4.3 12.9 - - - +
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Residues in contact with CYS 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G PRO 5.4 2.0 - - - -
81G GLY* 4.1 8.5 - - - +
82G LYS* 3.5 31.6 + - - -
95G CYS* 2.0 51.4 - - + -
97G PRO* 5.5 2.9 - - + -
123G ARG 3.1 10.1 + - - +
124G ALA* 3.1 7.8 + - - +
126G ARG* 1.3 80.6 - - - +
128G ARG* 1.3 55.4 + - - +
129G GLY 3.1 6.3 + - - -
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Residues in contact with ARG 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G LYS* 5.5 0.4 - - - +
95G CYS* 3.7 19.7 + - - +
121G GLU* 4.9 7.1 + - - -
124G ALA* 3.2 29.3 + - - +
125G ALA* 3.4 36.9 - - - +
126G ARG 3.1 1.6 - - - -
127G CYS* 1.3 72.6 - - - +
129G GLY* 1.3 57.5 + - - +
130G HIS* 3.1 22.4 + - - +
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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