Contacts of the helix formed by residues 105 - 118 (chain G) in PDB entry 5UQ9
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 GLU 105 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103G ASN 4.0 1.2 + - - -
104G SER* 1.3 73.9 - - - +
106G TYR* 1.3 89.3 + - + +
107G ARG* 3.1 31.5 + - + +
108G ASP* 3.0 31.8 + - - +
109G THR* 3.4 8.7 + - - -
185G MET* 4.7 1.5 - - - +
266G TRP* 4.0 48.2 + - - +
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Residues in contact with TYR 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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104G SER 3.5 2.0 + - - -
105G GLU* 1.3 91.1 - - - +
107G ARG* 1.3 94.1 + - + +
109G THR* 3.1 4.3 + - - -
110G THR* 2.9 35.0 + - + +
178G GLY 3.9 8.9 - - - +
181G HIS* 4.1 11.5 + - - +
182G PHE* 3.7 56.7 - + + +
185G MET* 4.2 16.6 - - + -
270G SER* 4.5 3.3 - - - -
273G GLU* 4.0 2.1 + - - -
274G TYR* 3.1 22.4 + - - -
349G PHE* 3.8 24.9 - + - -
351G TRP* 3.8 13.5 - + - -
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Residues in contact with ARG 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G GLU* 3.1 24.6 + - + -
106G TYR* 1.3 112.3 + - + +
108G ASP* 1.3 59.8 + - - +
110G THR* 2.7 22.1 + - - -
111G ARG* 3.2 11.4 + - - +
266G TRP* 5.9 6.3 - - - -
269G ILE* 5.1 2.6 - - - +
270G SER* 5.5 1.0 - - - +
273G GLU* 2.7 43.9 + - - -
274G TYR* 5.2 1.6 + - - -
349G PHE* 5.9 1.1 - - + -
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Residues in contact with ASP 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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78G GLY* 5.4 7.6 - - - -
82G ASP* 5.0 0.7 - - - +
104G SER* 5.6 0.2 - - - -
105G GLU* 3.0 26.8 + - - +
107G ARG* 1.3 77.3 - - - +
109G THR* 1.3 59.9 + - - +
111G ARG* 3.2 24.3 + - - +
112G ARG* 2.8 62.7 + - - +
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Residues in contact with THR 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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100G ASP* 4.9 0.7 + - - -
104G SER* 4.1 5.4 - - - -
105G GLU 3.4 8.3 + - - -
106G TYR* 3.1 8.8 + - - -
108G ASP* 1.3 78.1 - - - +
110G THR* 1.3 61.4 + - - +
112G ARG* 4.0 3.1 + - - +
113G CYS* 3.0 24.1 + - - +
123G PHE* 3.5 27.6 - - + -
125G GLY* 3.7 12.8 - - - +
145G GLY* 5.8 0.2 - - - -
178G GLY* 3.6 24.6 + - - +
181G HIS* 2.7 35.4 + - + +
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Residues in contact with THR 110 (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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106G TYR* 2.9 16.1 + - + +
107G ARG* 2.7 26.2 + - - -
109G THR* 1.3 74.1 - - - +
111G ARG* 1.3 66.6 + - - +
113G CYS* 3.2 3.0 + - - +
114G ARG* 3.0 40.4 + - - +
177G GLU* 3.1 44.1 - - + +
178G GLY* 4.4 1.3 - - - -
349G PHE* 5.8 4.3 - - + -
351G TRP* 3.6 18.8 - - + -
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Residues in contact with ARG 111 (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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82G ASP* 2.8 41.4 + - - -
107G ARG 3.2 13.1 + - - +
108G ASP* 3.2 21.3 + - - +
110G THR* 1.3 80.9 + - - +
112G ARG* 1.3 77.2 + - - +
114G ARG* 3.4 8.1 + - - +
115G ASP* 2.9 62.9 + - - +
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Residues in contact with ARG 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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78G GLY* 3.5 19.2 + - - -
81G VAL* 3.9 12.5 - - - +
82G ASP* 2.6 57.8 + - - +
85G ILE* 3.5 22.0 - - + -
100G ASP* 4.2 2.6 + - - -
104G SER* 3.7 26.1 + - - -
108G ASP* 2.8 48.8 + - - +
109G THR* 4.0 1.4 - - - +
111G ARG* 1.3 84.3 - - - +
113G CYS* 1.3 62.7 + - - +
115G ASP* 3.2 5.0 + - - +
116G LEU* 3.0 36.7 + - + +
123G PHE* 3.9 25.9 - - + -
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Residues in contact with CYS 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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109G THR 3.0 19.0 + - - +
110G THR 3.2 4.0 + - - +
112G ARG* 1.3 75.1 - - - +
114G ARG* 1.3 62.4 + - - +
116G LEU* 4.3 0.5 - - - +
117G LYS* 3.2 28.0 + - - +
123G PHE* 4.0 25.5 - - + +
145G GLY* 3.2 31.4 - - - -
146G ASN* 4.6 9.6 - - - -
177G GLU* 4.2 17.0 - - + -
178G GLY 4.9 2.0 - - - +
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Residues in contact with ARG 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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401A ASN* 6.2 2.0 - - - -
110G THR* 3.0 29.3 + - - +
111G ARG* 3.8 4.5 - - - +
113G CYS* 1.3 79.5 - - - +
115G ASP* 1.3 69.0 + - - +
116G LEU 3.1 4.8 + - - -
117G LYS* 3.6 8.9 + - - +
118G ALA* 4.0 11.6 + - - +
177G GLU* 2.1 48.9 + - + +
349G PHE* 5.0 13.9 - - - -
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Residues in contact with ASP 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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111G ARG* 2.9 47.6 + - - +
112G ARG* 3.2 4.7 + - - +
114G ARG* 1.3 83.0 - - - +
116G LEU* 1.3 54.7 + - - +
118G ALA* 5.1 2.9 - - - -
119G LYS* 2.2 42.0 + - - +
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Residues in contact with LEU 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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85G ILE* 4.2 26.0 - - + -
89G VAL* 5.3 4.5 - - + -
98G ILE* 6.0 1.6 - - + -
112G ARG* 3.0 25.9 + - + +
113G CYS 4.5 1.8 - - - +
114G ARG 3.2 0.2 - - - -
115G ASP* 1.3 79.7 - - - +
117G LYS* 1.3 64.5 + - - +
118G ALA 3.2 2.0 - - - -
119G LYS* 3.0 28.9 + - + +
121G ILE* 3.1 67.1 + - + +
123G PHE* 3.5 43.3 - - + +
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Residues in contact with LYS 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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113G CYS* 3.2 23.8 + - - +
114G ARG* 3.6 4.9 + - - +
116G LEU* 1.3 77.5 - - + +
118G ALA* 1.3 59.0 + - - +
120G GLY* 3.0 19.3 + - - -
121G ILE 3.2 12.3 - - - +
122G LEU* 4.1 9.8 - - + +
123G PHE 5.8 0.2 - - - +
146G ASN* 3.3 31.6 - - - +
148G GLU* 5.7 0.9 - - + -
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Residues in contact with ALA 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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404A ASP* 4.2 10.5 - - - +
408A ARG* 5.9 1.1 - - - +
309B LYS* 3.5 40.5 + - - +
114G ARG 4.0 10.4 + - - +
115G ASP* 5.6 1.8 - - - -
116G LEU 3.2 0.6 - - - +
117G LYS* 1.3 79.8 - - - +
119G LYS* 1.3 58.9 + - + +
120G GLY 3.1 3.4 + - - -
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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