Contacts of the helix formed by residues 120 - 128 (chain G) in PDB entry 6FI8
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 PRO 120 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119G ALA* 1.3 94.5 - - + +
121G LEU* 1.3 66.4 + - - +
122G ASN* 3.4 13.5 - - - +
123G VAL* 3.3 25.4 + - + -
124G VAL* 3.1 19.2 + - - +
116H VAL* 3.8 0.2 - - - -
117H GLY 3.5 6.5 - - - +
118H GLY 3.3 17.5 - - - +
120H PRO* 4.0 29.2 - - + -
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Residues in contact with LEU 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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120G PRO* 1.3 74.9 - - - +
122G ASN* 1.3 59.3 + - - +
124G VAL* 3.3 1.8 + - + -
125G LYS* 2.9 44.8 + - - +
18H LYS* 3.7 32.5 - - + -
56H ILE* 5.2 1.6 - - + -
68H LEU* 3.9 22.0 - - + -
116H VAL* 3.6 28.9 - - + -
117H GLY 2.7 23.4 + - - +
118H GLY* 3.8 9.2 + - - +
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Residues in contact with ASN 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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120G PRO* 4.0 15.4 - - - +
121G LEU* 1.3 76.4 + - - +
123G VAL* 1.3 73.4 + - - +
125G LYS* 3.8 13.7 + - + +
126G GLN* 3.2 31.2 + - - +
118H GLY 4.4 4.5 - - - +
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Residues in contact with VAL 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 ALA* 3.9 10.1 - - + -
120G PRO* 3.3 31.7 + - + +
121G LEU 3.2 0.6 - - - -
122G ASN* 1.3 85.4 - - - +
124G VAL* 1.3 60.9 + - - +
126G GLN* 3.0 41.0 + - - +
127G TYR* 3.5 30.2 + - + +
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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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119G ALA* 4.0 17.9 - - + +
120G PRO 3.1 17.1 + - - +
121G LEU* 3.3 4.9 + - + +
123G VAL* 1.3 73.8 - - - +
125G LYS* 1.3 65.1 + - - +
127G TYR* 3.0 34.0 + - + +
128G ILE* 3.9 8.0 + - + +
20H HIS* 4.2 34.1 - - + +
68H LEU* 4.7 11.7 - - + -
115H THR 5.9 0.2 - - - +
116H VAL* 3.5 25.1 - - + -
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Residues in contact with LYS 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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121G LEU* 2.9 41.6 + - + +
122G ASN* 3.9 12.8 - - + +
123G VAL 3.3 0.2 - - - -
124G VAL* 1.3 76.5 - - - +
126G GLN* 1.3 56.6 + - - +
128G ILE* 2.9 11.5 + - - +
202G CA 2.4 27.3 - - - -
56H ILE* 3.7 27.2 - - - +
57H GLU* 3.5 23.5 - - - +
68H LEU* 3.9 15.3 - - + -
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Residues in contact with GLN 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 ASN* 3.2 23.2 + - - +
123G VAL* 3.0 30.4 + - - +
125G LYS* 1.3 79.3 - - - +
127G TYR* 1.3 63.5 + - + +
128G ILE 3.2 0.9 + - - -
202G CA 4.6 0.7 - - - -
0L C 3.5 22.0 + - - -
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Residues in contact with TYR 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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119G ALA* 4.2 8.9 - - + +
123G VAL* 3.8 27.6 - - + +
124G VAL* 3.0 40.9 + - + +
126G GLN* 1.3 80.4 - - + +
128G ILE* 1.3 62.7 + - + +
20H HIS* 4.8 15.5 - + + -
66H HIS* 4.7 2.3 + - + -
0L C 3.3 39.9 - - - +
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Residues in contact with ILE 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* 4.0 13.2 - - + +
125G LYS* 2.9 3.4 + - - +
126G GLN 3.1 0.4 - - - +
127G TYR* 1.3 82.5 - - + +
129G GLU* 1.3 61.1 + - - +
202G CA 2.4 28.1 - - - -
20H HIS* 3.9 22.0 - - + +
57H GLU* 3.3 23.6 - - + +
58H MET 4.6 0.7 - - - +
59H GLN* 3.6 31.6 - - + +
66H HIS* 3.7 32.5 - - + +
68H LEU* 4.2 26.9 - - + +
0L C 3.9 10.4 + - - -
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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