Contacts of the helix formed by residues 119 - 128 (chain G) in PDB entry 6V01
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 GLY 119 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118G THR* 1.3 75.1 - - - +
120G TRP* 1.3 59.3 + - - -
121G LYS 3.1 2.7 - - - -
122G CYS* 2.9 26.1 + - - +
80I THR* 3.5 20.6 + - - +
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Residues in contact with TRP 120 (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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119G GLY* 1.3 69.4 - - - -
121G LYS* 1.3 91.2 + - - +
123G PHE* 4.0 20.1 + + + +
124G VAL* 3.8 17.7 + - + +
77I LEU* 5.2 13.2 - - + -
80I THR* 4.6 10.8 - - + -
81I ARG* 4.3 34.3 - - + -
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Residues in contact with LYS 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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113G PHE* 4.8 8.2 - - + -
119G GLY 3.1 0.8 - - - -
120G TRP* 1.3 114.4 + - + +
122G CYS* 1.3 61.2 + - - +
123G PHE 3.2 1.3 - - - -
124G VAL* 3.2 20.6 + - + +
125G TYR* 2.9 26.3 + - - +
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Residues in contact with CYS 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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112G ASN 4.2 0.7 - - - -
113G PHE* 3.5 44.4 - - - -
117G PRO* 3.7 24.5 - - + -
118G THR 3.3 24.5 - - - +
119G GLY 2.9 12.0 + - - +
121G LYS* 1.3 75.0 - - - +
123G PHE* 1.3 59.4 + - - +
125G TYR* 3.8 5.3 - - - +
126G HIS* 2.9 35.4 + - - +
80I THR* 4.3 3.6 - - - +
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Residues in contact with PHE 123 (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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119G GLY 3.6 3.0 + - - -
120G TRP* 4.0 24.7 - + + +
121G LYS 3.2 0.6 - - - -
122G CYS* 1.3 77.7 - - - +
124G VAL* 1.3 71.5 + - + +
127G PHE* 2.9 74.2 + + + +
73I GLY 4.1 9.9 - - - -
76I ILE* 4.3 10.1 - - + -
77I LEU* 4.1 48.9 - - + -
80I THR* 3.6 26.9 + - + +
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Residues in contact with VAL 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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120G TRP* 3.8 16.8 - - + +
121G LYS* 3.2 26.2 + - + +
123G PHE* 1.3 86.4 - - + +
125G TYR* 1.3 66.1 + - - +
127G PHE* 5.0 0.4 - - - -
128G ALA* 3.3 29.3 + - + +
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Residues in contact with TYR 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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113G PHE* 4.2 28.9 - + + -
114G LEU* 3.6 23.4 - - + +
121G LYS 2.9 16.2 + - - +
122G CYS* 3.8 4.9 - - - +
124G VAL* 1.3 78.3 - - - +
126G HIS* 1.3 84.2 + + - +
127G PHE 3.2 0.7 - - - -
128G ALA 3.9 0.5 - - - -
129G VAL* 3.2 45.1 + - + +
166G PHE* 3.4 24.2 - + - -
170G GLU* 2.9 24.9 + - - -
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Residues in contact with HIS 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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113G PHE 3.2 21.8 - - - -
114G LEU* 3.1 34.1 + - - +
117G PRO* 3.5 22.3 - - + +
122G CYS* 2.9 27.4 + - + +
123G PHE 3.8 0.2 - - - -
125G TYR* 1.3 97.6 - + - +
127G PHE* 1.3 58.1 + - - +
129G VAL* 4.4 4.7 - - + -
130G PHE* 4.0 0.9 - - - +
241G VAL* 3.3 35.8 - - + +
243G ARG* 5.3 10.5 + - + +
76I ILE* 3.4 25.4 - - + +
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Residues in contact with PHE 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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123G PHE* 2.9 51.6 + + + +
124G VAL* 5.0 1.1 - - - -
126G HIS* 1.3 78.8 - - - +
128G ALA* 1.3 58.3 + - + +
129G VAL 3.2 4.7 - - - -
130G PHE* 3.1 31.4 + + + -
131G LEU* 2.8 53.9 + - + +
69I ALA* 4.1 8.5 - - + -
73I GLY* 3.8 28.5 - - - -
76I ILE* 4.4 8.7 - - + -
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Residues in contact with ALA 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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124G VAL* 3.3 24.1 + - + +
125G TYR 3.9 2.0 - - - +
127G PHE* 1.3 76.1 - - + +
129G VAL* 1.3 60.7 + - - +
131G LEU* 4.1 13.7 - - + +
132G ILE* 3.4 21.4 - - - +
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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