Contacts of the helix formed by residues 98 - 111 (chain G) in PDB entry 1G9N
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 ASN 98 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G ASN 2.9 5.5 + - - +
95G MET* 3.3 26.1 + - + +
97G LYS* 1.3 78.2 - - - +
99G ASN* 1.3 65.2 + - - +
100G MET* 2.7 49.0 + - - +
101G VAL* 3.3 27.6 - - + +
102G GLU* 4.2 2.6 + - - +
480G ARG* 5.6 2.6 + - - +
483G LEU* 3.4 13.7 + - - +
486G TYR 2.6 30.3 + - - -
487G LYS* 4.1 5.1 - - - +
488G VAL* 5.2 0.3 + - - +
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Residues in contact with ASN 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G LYS 3.4 5.7 + - - +
98G ASN* 1.3 72.9 + - - +
100G MET* 1.3 66.5 + - + +
101G VAL 3.1 2.2 - - - -
102G GLU* 3.3 13.5 + - - +
103G GLN* 3.2 19.2 + - - +
488G VAL* 5.7 6.1 - - + -
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Residues in contact with MET 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G ASN* 2.7 35.5 + - - +
99G ASN* 1.3 72.3 - - - +
101G VAL* 1.3 64.8 + - - +
103G GLN* 2.9 10.2 + - + +
104G MET* 2.8 25.6 + - - +
217G TYR* 5.5 10.1 - - + -
225G ILE* 4.8 10.8 - - - -
248G THR* 5.0 7.6 - - - -
483G LEU* 3.7 17.7 - - + -
486G TYR* 3.1 17.3 - - + -
487G LYS* 3.0 32.1 - - - +
488G VAL* 3.3 35.0 - - + -
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Residues in contact with VAL 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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95G MET 4.1 0.9 - - - +
98G ASN* 3.3 34.3 - - + +
100G MET* 1.3 78.7 - - - +
102G GLU* 1.3 52.8 + - - +
104G MET* 3.2 0.3 + - - -
105G HIS* 2.8 36.3 + - - +
476G ARG* 3.3 41.7 - - + +
479G TRP* 3.6 12.9 - - + -
480G ARG* 3.8 30.1 - - + +
483G LEU* 3.5 19.0 - - + +
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Residues in contact with GLU 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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22C LYS* 5.3 4.5 + - - -
98G ASN 4.2 1.5 + - - +
99G ASN* 3.3 19.6 + - - +
100G MET 3.2 0.2 - - - -
101G VAL* 1.3 80.6 - - - +
103G GLN* 1.3 59.4 + - - +
105G HIS* 4.0 9.5 - - - -
106G GLU* 3.3 29.9 + - - +
476G ARG* 2.5 49.9 + - - +
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Residues in contact with GLN 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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99G ASN* 3.2 12.8 + - - +
100G MET* 2.9 15.2 + - + +
102G GLU* 1.3 78.5 - - - +
104G MET* 1.3 62.9 + - - +
106G GLU* 4.2 14.9 - - - +
107G ASP* 3.4 20.0 + - - +
217G TYR* 3.8 25.3 + - + -
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Residues in contact with MET 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 MET 2.8 13.3 + - - +
101G VAL 3.8 3.1 - - - +
103G GLN* 1.3 76.9 - - - +
105G HIS* 1.3 54.7 + - - +
107G ASP* 2.7 5.5 + - - +
108G ILE* 2.6 51.4 + - + +
215G ILE* 3.4 15.3 - - + -
217G TYR* 2.9 50.0 - - + +
251G ILE* 3.7 31.0 - - + -
253G PRO* 5.4 0.7 - - - -
479G TRP* 4.0 35.9 - - - -
482G GLU* 5.5 0.4 - - + -
483G LEU* 4.0 13.7 - - + -
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Residues in contact with HIS 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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101G VAL 2.8 18.4 + - - +
102G GLU* 4.0 12.1 - - - +
104G MET* 1.3 78.1 - - - +
106G GLU* 1.3 64.4 + - - +
108G ILE* 3.2 2.3 + - - +
109G ILE* 3.0 45.0 + - + +
427G TRP* 3.7 34.3 + + - -
428G GLN 5.3 1.4 + - - -
474G ASP* 5.4 0.4 - - - -
475G MET* 4.3 7.4 - - + -
476G ARG* 3.7 50.5 + - + +
479G TRP* 3.0 34.6 + - + +
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Residues in contact with GLU 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 GLU* 3.3 23.2 + - + +
103G GLN* 4.2 15.3 - - - +
104G MET 3.2 0.2 - - - -
105G HIS* 1.3 80.1 - - - +
107G ASP* 1.3 59.5 + - - +
109G ILE* 3.7 13.1 + - + +
110G SER* 2.9 28.6 + - - +
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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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103G GLN* 3.4 16.1 + - - +
104G MET 2.7 13.3 + - - +
106G GLU* 1.3 77.3 - - - +
108G ILE* 1.3 55.8 + - + +
109G ILE 3.0 1.8 - - - -
110G SER* 2.9 9.3 + - - -
111G LEU* 2.7 43.5 + - - +
215G ILE* 6.0 3.2 - - - +
217G TYR* 3.4 24.6 + - - +
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Residues in contact with ILE 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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104G MET* 2.6 43.9 + - + +
105G HIS 3.6 4.5 - - - +
107G ASP* 1.3 78.2 - - - +
109G ILE* 1.3 62.9 + - - +
111G LEU* 3.2 9.8 + - + +
112G TRP* 3.1 31.1 + - + +
215G ILE* 4.0 8.7 - - + -
253G PRO* 3.3 34.1 - - + +
255G VAL* 4.0 7.6 - - + -
427G TRP* 3.9 10.8 - - + -
479G TRP* 3.6 37.9 - - + -
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Residues in contact with ILE 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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105G HIS* 3.0 41.2 + - + +
106G GLU* 3.8 11.4 - - + +
107G ASP 3.0 0.2 - - - -
108G ILE* 1.3 76.9 - - - +
110G SER* 1.3 57.7 + - - +
112G TRP* 2.7 23.1 + - - +
113G ASP* 3.0 29.9 + - - +
427G TRP* 3.8 21.1 - - + -
428G GLN* 3.6 38.8 - - + +
429G GLU* 6.0 0.9 - - - +
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Residues in contact with SER 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G GLU* 2.9 17.6 + - - +
107G ASP* 2.9 11.7 + - - -
109G ILE* 1.3 74.8 - - - +
111G LEU* 1.3 58.4 + - - +
112G TRP 3.0 6.1 + - - -
113G ASP* 3.7 13.4 + - - +
114G GLN* 3.5 22.2 + - - +
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Residues in contact with LEU 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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107G ASP* 2.7 20.6 + - - +
108G ILE* 3.4 18.6 - - + +
109G ILE 3.0 0.2 - - - -
110G SER* 1.3 77.9 - - - +
112G TRP* 1.3 54.9 + - + +
114G GLN* 4.6 16.0 - - + +
115G SER* 2.4 28.7 + - - -
210G PHE* 4.0 16.9 - - + -
212G PRO* 6.0 0.4 - - + -
213G ILE* 5.1 17.5 - - + +
215G ILE* 5.1 6.5 - - + -
253G PRO* 4.3 24.2 - - + -
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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