Contacts of the helix formed by residues 111 - 122 (chain G) in PDB entry 6CP3
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 111 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78G THR* 3.4 19.3 - - - -
79G SER 3.4 3.4 - - - -
80G ASP* 3.4 12.1 - - - -
109G THR* 4.2 2.4 + - - -
110G ILE* 1.3 75.1 - - - +
112G ASP* 1.3 64.6 + - - -
113G LYS 3.4 2.5 - - - -
114G ILE* 3.8 3.3 - - - +
115G LYS* 3.5 19.8 + - - +
129G SER* 6.0 0.2 - - - -
130G ILE 3.1 15.7 + - - +
133G ILE* 5.1 2.4 - - - +
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Residues in contact with ASP 112 (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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411C ASP* 3.7 20.8 - - - +
79G SER 3.0 2.8 + - - -
80G ASP* 2.8 35.6 + - + +
111G GLY* 1.3 74.3 - - - -
113G LYS* 1.3 59.4 + - - +
115G LYS* 3.2 27.0 + - - +
116G MET* 2.9 44.0 + - - +
131G ASN* 4.2 19.6 + - - +
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Residues in contact with LYS 113 (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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408C PHE* 5.1 11.3 + - - -
409C GLY 4.4 12.3 + - - -
410C SER* 6.0 0.4 - - - +
78G THR* 4.6 0.9 - - - +
79G SER 3.1 14.5 + - - +
80G ASP 4.5 2.4 + - - +
81G LYS 4.1 6.7 - - - +
82G GLY* 4.2 25.4 - - - +
88G HIS* 3.3 42.4 - - + +
112G ASP* 1.3 79.1 - - - +
114G ILE* 1.3 58.5 + - - +
116G MET* 3.3 26.4 + - + +
117G GLN* 2.9 33.9 + - + +
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Residues in contact with ILE 114 (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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76G ALA* 4.4 18.4 - - + -
78G THR* 3.3 39.8 + - + +
88G HIS* 4.0 10.3 - - - +
91G LEU* 4.4 3.6 - - + -
92G ALA* 3.7 38.8 - - + +
95G VAL* 5.4 1.3 - - + -
109G THR* 3.7 24.5 - - + +
110G ILE 4.5 4.7 - - - +
111G GLY 3.8 6.3 - - - +
113G LYS* 1.3 76.1 - - - +
115G LYS* 1.3 62.5 + - - +
117G GLN* 4.0 2.5 - - + -
118G LEU* 2.9 44.2 + - + +
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Residues in contact with LYS 115 (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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109G THR* 3.7 14.6 - - - +
111G GLY 3.5 10.2 + - - +
112G ASP* 3.2 30.9 + - - +
114G ILE* 1.3 82.4 - - - +
116G MET* 1.3 68.3 + - - +
119G LEU* 2.8 45.9 + - + +
126G ILE* 4.3 4.6 - - + +
129G SER* 3.5 30.5 - - - +
131G ASN* 5.5 7.0 - - - +
47I TYR* 3.0 36.1 + - + +
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Residues in contact with MET 116 (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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409C GLY 5.1 9.2 - - - +
410C SER* 5.3 5.4 - - - +
411C ASP* 5.2 16.8 - - + +
80G ASP 5.6 1.6 - - - +
112G ASP* 2.9 46.4 + - - +
113G LYS* 3.3 30.7 + - + +
115G LYS* 1.3 82.2 - - - +
117G GLN* 1.3 67.8 + - - +
119G LEU* 4.4 6.7 - - + -
120G ARG* 3.6 19.6 + - - +
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Residues in contact with GLN 117 (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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398F GLU* 3.4 40.1 + - - +
88G HIS* 3.6 27.9 + - - +
89G SER* 4.5 4.4 + - - -
92G ALA* 4.2 11.0 - - + +
113G LYS* 2.9 28.3 + - + +
114G ILE* 3.4 19.3 - - + +
115G LYS 3.1 0.2 - - - -
116G MET* 1.3 78.8 + - - +
118G LEU* 1.3 67.2 + - + +
120G ARG* 3.2 34.0 + - - +
121G THR* 3.5 9.2 + - - +
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Residues in contact with LEU 118 (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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92G ALA* 4.4 8.7 - - + +
95G VAL* 3.7 33.7 - - + -
99G LEU* 5.1 3.4 - - + -
107G ILE* 3.7 37.2 - - + -
109G THR* 4.4 6.7 - - + -
114G ILE* 2.9 46.0 + - + +
117G GLN* 1.3 75.1 - - + +
119G LEU* 1.3 57.8 + - - +
121G THR* 3.5 12.2 - - + +
122G HIS* 2.6 39.1 + - + +
126G ILE* 3.7 12.8 - - + -
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Residues in contact with LEU 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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115G LYS* 2.8 27.7 + - + +
116G MET* 4.7 4.7 - - + -
118G LEU* 1.3 76.4 - - - +
120G ARG* 1.3 61.9 + - - +
121G THR 3.5 0.3 + - - -
122G HIS 4.3 1.3 - - - -
123G PRO* 3.6 30.5 - - + +
126G ILE* 3.5 13.1 - - + +
47I TYR* 4.1 34.1 - - + +
51I THR* 3.7 30.5 - - - +
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Residues in contact with ARG 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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398F GLU* 3.6 47.4 + - - +
399F GLN 5.7 0.4 - - - +
96G ARG* 4.8 7.3 - - - +
116G MET 3.6 13.9 + - - +
117G GLN* 3.2 24.8 + - - +
118G LEU 3.2 0.6 - - - -
119G LEU* 1.3 81.3 - - - +
121G THR* 1.3 67.9 + - - +
123G PRO* 5.0 1.6 - - - +
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Residues in contact with THR 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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96G ARG* 3.1 35.5 + - - +
99G LEU* 6.4 0.2 - - + -
117G GLN 3.6 11.9 - - - +
118G LEU* 3.5 20.0 - - + +
120G ARG* 1.3 89.7 - - - +
122G HIS* 1.3 88.2 + - + +
123G PRO* 3.9 5.5 - - - +
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Residues in contact with HIS 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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96G ARG* 4.3 20.2 + - - -
99G LEU* 4.4 16.2 - - + +
100G ASN* 5.6 4.5 + - - -
103G PRO* 5.6 4.7 - - + +
107G ILE* 5.6 1.1 - - + -
118G LEU* 2.6 25.0 + - + +
121G THR* 1.3 106.5 + - + +
123G PRO* 1.3 63.7 - - - +
124G ASN* 3.1 7.6 + - + +
125G ASN* 3.3 39.2 + - + +
126G ILE* 3.9 12.6 - - - +
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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