Contacts of the helix formed by residues 90 - 97 (chain G) in PDB entry 6FQ6
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 90 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65G LEU* 4.8 11.3 - - + +
86G ALA 3.5 10.6 + - - +
87G VAL 3.3 2.3 + - - +
88G ARG 3.4 0.9 - - - -
89G ASN* 1.3 77.6 - - - +
91G GLU* 1.3 58.8 + - - +
92G GLU* 3.3 12.6 + - - +
93G LEU* 2.9 48.4 + - + +
94G ASN* 2.8 38.1 + - - +
103H LEU* 3.7 6.8 - - - +
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Residues in contact with GLU 91 (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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89G ASN 4.0 3.0 + - - -
90G ASP* 1.3 73.6 + - - +
92G GLU* 1.3 67.0 + - + +
94G ASN* 3.8 5.1 - - - +
95G LYS* 2.9 41.6 + - - +
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Residues in contact with GLU 92 (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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90G ASP* 3.3 10.3 + - - +
91G GLU* 1.3 84.7 - - + +
93G LEU* 1.3 61.5 + - - +
95G LYS* 3.4 7.8 + - - +
96G LEU* 2.9 26.2 + - - +
100H PRO* 2.9 50.1 - - + +
101H GLY* 3.6 6.1 + - - -
102H GLU* 3.5 17.1 + - - +
103H LEU* 3.3 33.1 + - + +
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Residues in contact with LEU 93 (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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58G LEU* 4.6 11.9 - - + +
61G GLU* 5.2 9.6 - - + -
62G ILE* 3.7 37.9 - - + -
65G LEU* 5.4 3.8 - - + -
86G ALA 4.9 5.4 - - - +
87G VAL* 4.1 14.1 - - + +
90G ASP* 2.9 35.5 + - + +
92G GLU* 1.3 74.6 - - - +
94G ASN* 1.3 54.0 + - - +
95G LYS 3.1 0.2 - - - -
96G LEU* 3.0 26.4 + - + +
97G LEU* 2.5 41.0 + - + +
62H PHE* 4.7 6.7 - - + -
103H LEU* 4.1 16.6 - - + -
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Residues in contact with ASN 94 (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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87G VAL* 3.7 12.6 + - - +
88G ARG* 3.7 40.6 + - - +
90G ASP 2.8 23.0 + - - +
91G GLU* 3.9 5.2 - - - +
93G LEU* 1.3 71.2 - - - +
95G LYS* 1.3 58.0 + - - +
97G LEU* 4.1 4.5 - - - +
98G GLY* 2.9 35.0 + - - -
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Residues in contact with LYS 95 (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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132E GLY 5.4 10.9 - - - -
91G GLU* 2.9 32.2 + - - +
92G GLU* 3.5 7.2 - - - +
94G ASN* 1.3 77.0 - - - +
96G LEU* 1.3 61.8 + - - +
97G LEU 3.6 0.2 + - - -
98G GLY* 4.2 3.8 + - - -
100H PRO* 3.8 25.1 - - + -
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Residues in contact with LEU 96 (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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58G LEU* 5.2 2.9 - - + -
92G GLU 2.9 15.9 + - - +
93G LEU* 3.3 29.2 - - + +
95G LYS* 1.3 79.9 - - - +
97G LEU* 1.3 65.4 + - + +
98G GLY 3.7 1.5 + - - -
62H PHE* 4.7 3.8 - - + -
66H VAL* 4.4 27.1 - - + -
69H ARG* 2.8 48.5 + - - +
98H LEU* 4.7 23.6 - - + +
99H LEU* 4.2 22.0 - - + -
100H PRO* 5.4 1.8 - - + +
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Residues in contact with LEU 97 (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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98B TYR* 3.9 24.9 - - + +
87G VAL* 3.7 34.3 - - + -
88G ARG* 3.4 19.6 + - - +
93G LEU* 2.5 24.9 + - + +
94G ASN* 3.2 4.7 + - - +
96G LEU* 1.3 96.1 - - + +
98G GLY* 1.3 60.4 + - - +
99G ARG 3.4 2.8 + - - -
100G VAL* 3.8 26.0 + - + +
102G ILE* 5.7 2.2 - - + -
62H PHE* 3.6 30.3 - - + -
66H VAL* 4.5 4.7 - - + -
69H ARG* 4.6 4.3 - - - +
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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