Contacts of the helix formed by residues 100 - 109 (chain G) in PDB entry 6PB4
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 LYS 100 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99G TYR* 1.3 78.1 - - + +
101G LYS* 1.3 55.9 - - - +
102G PHE 3.0 1.3 - - - -
103G ARG* 3.5 40.1 - - + +
104G GLN* 2.7 36.0 + - - +
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Residues in contact with LYS 101 (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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859C GLU* 4.7 12.9 + - - +
863C SER* 4.4 29.6 - - - -
17G HIS 5.9 1.6 - - - +
97G ILE* 5.0 9.6 - - + +
98G SER* 3.5 33.4 - - - +
99G TYR 2.3 20.4 + - - +
100G LYS* 1.3 69.7 - - - +
102G PHE* 1.3 57.1 + - - +
104G GLN* 3.3 7.6 - - - +
105G LEU* 3.0 37.5 + - + +
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Residues in contact with PHE 102 (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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14G PHE* 4.0 24.5 - + - -
39G LEU* 3.7 18.8 - - + -
69G PHE* 5.3 4.7 - + - -
75G LEU* 3.4 34.8 - - + -
97G ILE* 3.6 15.0 - - + -
98G SER 3.2 19.7 - - - +
99G TYR* 3.1 5.5 + - - +
100G LYS 3.0 0.2 - - - -
101G LYS* 1.3 79.5 - - - +
103G ARG* 1.3 60.7 + - + +
105G LEU* 3.0 12.2 + - + +
106G ILE* 2.9 63.2 + - + +
112G ILE* 4.0 22.2 - - + -
116G LEU* 5.5 4.5 - - + -
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Residues in contact with ARG 103 (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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75G LEU* 3.6 38.0 + - + +
76G PHE* 4.5 10.5 + - - +
77G GLU* 5.4 3.4 - - - +
99G TYR* 5.1 9.2 - - + +
100G LYS* 3.1 44.6 + - + +
102G PHE* 1.3 77.1 - - + +
104G GLN* 1.3 63.8 + - - +
106G ILE* 3.2 11.1 + - - +
107G GLN* 3.0 19.8 + - - +
114H MET* 6.3 2.6 - - + +
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Residues in contact with GLN 104 (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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100G LYS 2.7 16.3 + - - +
101G LYS* 3.3 12.8 - - - +
103G ARG* 1.3 72.6 - - - +
105G LEU* 1.3 64.5 + - + +
107G GLN* 2.9 48.7 + - - +
108G VAL* 3.0 20.7 + - + +
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Residues in contact with LEU 105 (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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13G TRP* 5.3 6.5 - - + +
14G PHE* 6.2 3.4 - - + -
17G HIS* 4.1 45.1 - - + +
97G ILE* 6.2 2.5 - - + -
101G LYS* 3.0 26.6 + - + +
102G PHE* 3.0 13.2 + - + +
104G GLN* 1.3 81.9 - - + +
106G ILE* 1.3 54.2 + - + +
108G VAL* 2.8 23.9 + - + +
109G ASN* 2.6 40.3 + - + +
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Residues in contact with ILE 106 (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 PHE* 2.9 70.9 + - + +
103G ARG* 3.2 10.1 + - - +
105G LEU* 1.3 73.7 - - + +
107G GLN* 1.3 67.7 + - - +
109G ASN 3.0 21.1 + - - +
112G ILE* 3.7 25.1 - - + -
113G LEU* 5.6 9.2 - - + -
114H MET* 5.4 12.3 - - - -
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Residues in contact with GLN 107 (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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103G ARG 3.0 10.6 + - - +
104G GLN* 2.9 31.7 + - - +
106G ILE* 1.3 80.0 - - - +
108G VAL* 1.3 68.1 + - - +
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Residues in contact with VAL 108 (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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13G TRP* 6.0 4.7 - - + +
104G GLN* 3.4 20.6 - - + +
105G LEU* 2.8 28.6 + - + +
107G GLN* 1.3 93.3 - - - +
109G ASN* 1.3 61.0 + - + +
110G PRO* 4.2 4.2 - - - +
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Residues in contact with ASN 109 (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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10G THR* 4.2 18.8 - - - +
13G TRP* 4.1 26.0 - - + +
105G LEU* 2.6 18.8 + - + +
106G ILE* 3.0 28.9 - - - +
107G GLN 3.5 0.6 - - - -
108G VAL* 1.3 79.4 - - + +
110G PRO* 1.4 91.6 + - - +
111G ASP* 5.1 1.4 - - - +
112G ILE* 5.0 8.8 - - + +
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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