Contacts of the helix formed by residues 105 - 119 (chain G) in PDB entry 1GN2
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 SER 105 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99G ILE* 4.7 0.2 - - - -
100G ALA* 3.6 14.9 + - - +
103G PHE 2.9 5.1 + - - +
104G GLY* 1.3 81.4 - - - +
106G PHE* 1.3 63.9 + - - +
107G ASP* 3.2 8.2 + - - +
108G LYS* 2.8 38.4 + - - +
109G PHE* 3.0 12.7 + - - +
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Residues in contact with PHE 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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89G ASP 4.4 7.2 - - - -
90G LYS* 3.9 36.3 - - + -
91G PRO* 3.1 40.6 - - + -
96G ALA* 6.1 0.4 - - + +
99G ILE* 4.1 17.5 - - + +
100G ALA* 4.5 5.2 - - + +
105G SER* 1.3 72.3 - - - +
107G ASP* 1.3 66.6 + - - +
109G PHE* 3.6 14.6 - + - +
110G ARG* 3.1 59.2 + - - +
182G TRP* 4.6 2.5 - + - -
187G TRP* 3.5 25.8 - + - -
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Residues in contact with ASP 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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90G LYS* 4.4 13.5 + - - -
105G SER* 3.0 7.9 + - - +
106G PHE* 1.3 86.7 - - - +
108G LYS* 1.3 58.2 + - + +
110G ARG* 3.5 27.9 + - - +
111G ALA* 3.1 24.9 + - - +
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Residues in contact with LYS 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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51E ARG* 3.9 39.2 + - + +
52E ALA* 4.1 17.2 + - - +
54E GLU* 5.4 7.9 - - + -
103G PHE 3.3 22.4 - - - +
104G GLY* 4.8 4.7 - - - -
105G SER* 2.8 23.0 + - - +
107G ASP* 1.3 75.7 - - + +
109G PHE* 1.3 64.6 + - - +
111G ALA* 3.2 8.3 + - + +
112G GLN* 3.2 21.0 + - - +
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Residues in contact with PHE 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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99G ILE* 4.0 14.1 - - + -
103G PHE* 3.6 46.8 - + + +
105G SER 3.0 8.2 + - - +
106G PHE* 3.6 28.0 - + - +
108G LYS* 1.3 76.4 - - - +
110G ARG* 1.3 74.3 + - + +
112G GLN* 3.1 4.9 + - - +
113G PHE* 2.9 45.8 + + - +
128G LEU* 3.8 28.5 - - + -
139G ILE* 3.8 13.3 - - + +
157G LEU* 4.4 12.3 - - + -
182G TRP* 3.6 29.2 - + - -
187G TRP* 4.3 5.4 - + - -
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Residues in contact with ARG 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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90G LYS* 5.4 7.5 - - - +
106G PHE* 3.1 40.5 + - - +
107G ASP* 3.7 21.3 + - - +
109G PHE* 1.3 94.9 - - + +
111G ALA* 1.3 59.5 + - - +
113G PHE* 4.1 1.7 - - - +
114G HIS* 3.3 21.9 + - + +
179G LYS 5.3 0.6 + - - -
182G TRP* 3.3 65.4 - - + +
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Residues in contact with ALA 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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56E HIS* 3.9 12.9 - - + +
107G ASP 3.1 14.4 + - - +
108G LYS* 3.2 12.5 + - + +
109G PHE 3.1 0.4 - - - -
110G ARG* 1.3 74.8 - - - +
112G GLN* 1.3 68.3 + - - +
114G HIS* 3.5 7.0 + - - +
115G ALA* 3.1 21.7 + - - +
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Residues in contact with GLN 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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47E LEU* 4.0 20.1 - - - +
51E ARG* 2.7 39.5 + - + +
56E HIS* 3.5 26.2 + - + +
59E ILE* 4.0 9.4 - - + -
63E GLU* 3.4 20.4 + - - +
103G PHE* 3.8 5.1 - - - -
108G LYS 3.2 8.1 + - - +
109G PHE 3.1 7.5 + - - +
111G ALA* 1.3 78.9 - - - +
113G PHE* 1.3 64.9 + - - +
115G ALA* 2.9 5.5 + - - +
116G ALA* 2.9 20.4 + - - +
139G ILE* 3.5 27.4 + - + +
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Residues in contact with PHE 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 PHE* 2.9 33.2 + + + +
110G ARG* 4.1 5.2 - - - +
112G GLN* 1.3 76.7 - - - +
114G HIS* 1.3 62.9 + - - +
116G ALA* 3.4 7.1 + - - +
117G ALA* 3.0 20.6 + - - +
126G ALA* 3.6 25.4 - - + +
127G ALA 4.0 4.0 - - - -
128G LEU* 3.9 26.9 - - + -
139G ILE* 3.9 19.7 - - + +
157G LEU* 4.2 22.0 - - + -
159G LEU* 3.8 33.7 - - + -
181G PHE* 4.2 8.3 - + - -
182G TRP* 3.7 23.8 - + + -
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Residues in contact with HIS 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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110G ARG* 3.3 17.9 + - + +
111G ALA* 3.7 7.0 + - - +
112G GLN 3.1 0.6 - - - -
113G PHE* 1.3 82.3 - - - +
115G ALA* 1.3 58.5 + - - +
117G ALA* 3.4 3.3 + - - +
118G THR* 2.7 51.3 + - + +
159G LEU* 6.1 1.3 - - - -
175G VAL* 3.8 27.4 + - + -
178G ALA* 3.7 31.0 - - + -
179G LYS* 4.0 29.5 + - + -
182G TRP* 5.0 7.9 - - - +
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Residues in contact with ALA 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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56E HIS* 3.8 31.0 - - + -
59E ILE* 4.1 12.8 - - + -
111G ALA 3.1 13.8 + - - +
112G GLN 2.9 10.5 + - - +
114G HIS* 1.3 81.3 + - - +
116G ALA* 1.3 61.6 + - - +
118G THR* 3.4 4.6 + - - -
119G THR* 3.1 33.5 + - + +
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Residues in contact with ALA 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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59E ILE* 4.0 7.8 - - + +
63E GLU* 4.2 10.8 - - - +
112G GLN 2.9 11.6 + - - +
113G PHE 3.6 7.4 - - - +
114G HIS 3.3 0.2 - - - -
115G ALA* 1.3 76.1 - - - +
117G ALA* 1.3 60.5 + - - +
120G VAL* 3.6 3.5 - - - +
126G ALA* 4.3 9.2 - - + +
139G ILE* 4.1 22.9 - - + -
140G PHE 4.8 0.2 - - - +
141G GLN* 3.0 46.4 + - + +
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Residues in contact with ALA 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 PHE 3.0 12.9 + - - +
114G HIS* 4.1 3.6 - - - +
116G ALA* 1.3 78.5 - - - +
118G THR* 1.3 64.1 + - + +
119G THR 3.4 0.7 + - - -
120G VAL* 3.7 11.4 + - - +
126G ALA* 3.4 25.1 - - + +
159G LEU* 4.1 13.7 - - + -
161G MET* 3.2 45.3 - - + +
174G LYS* 4.9 1.6 - - - -
178G ALA* 5.1 0.9 - - + -
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Residues in contact with THR 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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114G HIS* 2.7 37.7 + - - +
115G ALA* 3.4 7.8 + - - -
117G ALA* 1.3 78.5 - - - +
119G THR* 1.3 60.8 + - - +
120G VAL 3.6 0.7 - - - -
161G MET* 4.8 1.3 - - + -
174G LYS* 3.0 31.9 + - + +
175G VAL* 4.1 26.0 - - + +
178G ALA* 3.8 27.1 - - + -
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Residues in contact with THR 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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56E HIS 5.7 0.2 - - - +
59E ILE* 3.5 24.1 - - + +
60E LEU* 3.6 19.6 + - - +
115G ALA* 3.1 19.3 + - + +
117G ALA 3.4 0.6 - - - -
118G THR* 1.3 82.4 - - - +
120G VAL* 1.3 67.4 + - - +
121G GLN* 3.3 6.6 + - - +
141G GLN* 2.7 25.9 + - - -
174G LYS* 5.1 0.7 - - - +
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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