Contacts of the helix formed by residues 104 - 118 (chain G) in PDB entry 5GJQ
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 PRO 104 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G ARG* 4.0 16.6 - - - +
102G PRO 3.3 9.8 - - - +
103G LEU* 1.3 97.6 - - + +
105G VAL* 1.3 65.9 + - - +
106G SER* 4.5 3.8 - - - +
107G ARG* 3.2 39.5 + - + +
108G LEU 3.2 8.8 + - - -
138G ASP* 4.0 11.9 - - + +
139G ASP* 6.3 0.7 - - - -
81g HIS* 3.4 36.6 - - + +
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Residues in contact with VAL 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G HIS* 4.6 2.5 - - + -
70G ILE* 3.7 33.7 - - + -
104G PRO* 1.3 71.7 - - - +
106G SER* 1.3 64.9 + - - +
108G LEU* 3.1 4.5 + - + +
109G VAL* 3.0 22.3 + - + +
134G ILE* 4.1 22.9 - - + +
136G GLY* 4.1 17.3 - - - +
137G TYR 4.1 7.2 - - - +
138G ASP* 3.2 22.6 + - + +
143G HIS* 4.3 9.2 - - + -
145G PHE* 3.9 25.1 - - + -
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Residues in contact with SER 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G PRO* 4.5 5.5 - - - +
105G VAL* 1.3 81.0 - - - +
107G ARG* 1.3 58.2 + - - +
109G VAL* 3.4 3.6 + - - +
110G SER* 2.9 30.5 + - - -
138G ASP* 4.4 3.0 + - - -
143G HIS* 5.5 7.1 - - - -
145G PHE* 4.0 25.6 - - - -
153G TYR* 5.4 1.7 - - - -
79g ASP* 3.9 27.2 + - - +
81g HIS* 5.0 2.3 + - - -
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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
----------------------------------------------------------
101G ARG* 4.0 21.6 - - - +
103G LEU* 4.3 12.6 - - + -
104G PRO* 3.2 27.2 + - + +
106G SER* 1.3 75.2 + - - +
108G LEU* 1.3 67.0 + - - +
110G SER* 3.5 7.5 - - - -
111G LEU* 2.9 30.6 + - + +
74g GLU* 3.0 47.8 + - - +
77g LEU* 3.5 22.8 - - + +
79g ASP* 2.7 40.2 + - - +
81g HIS* 3.6 12.6 - - - +
83g TYR* 4.4 5.3 + - - -
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Residues in contact with LEU 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G VAL* 4.2 0.4 - - + -
70G ILE* 3.6 31.6 - - + -
87G PHE* 5.3 0.9 - - + -
88G MET* 3.6 61.2 - - + +
91G GLU* 4.2 10.1 - - + -
92G CYS* 4.2 10.5 - - - -
103G LEU* 4.0 22.7 - - + +
104G PRO 3.2 8.9 + - - +
105G VAL* 3.1 10.9 + - - +
107G ARG* 1.3 77.7 - - - +
109G VAL* 1.3 63.0 - - + +
111G LEU* 3.2 10.3 + - + +
112G ILE* 3.0 26.0 + - + +
134G ILE* 5.3 2.5 - - + -
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Residues in contact with VAL 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G VAL* 3.0 21.2 + - + +
106G SER 3.6 7.6 - - - +
108G LEU* 1.3 78.3 - - + +
110G SER* 1.3 62.8 + - - +
112G ILE* 3.0 10.4 + - - +
113G GLY* 2.9 19.2 + - - -
134G ILE* 3.8 19.7 - - + -
145G PHE* 3.6 35.4 - - + -
147G THR* 4.4 10.8 - - + -
153G TYR* 3.5 41.9 - - + -
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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 SER 2.9 16.7 + - - -
107G ARG* 3.2 12.5 + - - +
109G VAL* 1.3 77.0 - - - +
111G LEU* 1.3 58.5 + - - +
113G GLY* 3.2 2.4 + - - -
114G SER* 3.0 30.4 + - - -
153G TYR* 3.4 27.2 + - - -
77g LEU* 5.8 3.8 - - - +
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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
----------------------------------------------------------
87G PHE* 4.1 17.3 - - + -
91G GLU* 3.4 38.4 - - + +
103G LEU* 5.0 6.7 - - + -
107G ARG* 2.9 20.8 + - + +
108G LEU* 3.4 13.0 - - + +
110G SER* 1.3 77.6 - - - +
112G ILE* 1.3 58.5 + - - +
114G SER* 3.3 12.5 + - - +
115G LYS* 2.9 29.5 + - - +
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Residues in contact with ILE 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G LEU* 4.1 19.1 - - + -
87G PHE* 4.7 9.6 - - + -
88G MET* 3.5 49.4 - - + -
108G LEU* 3.0 15.5 + - + +
109G VAL* 3.0 10.3 + - - +
111G LEU* 1.3 73.4 - - - +
113G GLY* 1.3 55.2 + - - +
115G LYS* 3.7 5.1 - - - +
116G THR* 2.6 52.4 + - + +
132G LEU* 4.5 2.7 - - + -
134G ILE* 3.9 17.9 - - + -
147G THR* 4.8 16.2 - - + +
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Residues in contact with GLY 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 VAL 2.9 12.9 + - - -
110G SER 3.2 4.0 + - - -
112G ILE* 1.3 75.5 - - - +
114G SER* 1.3 64.7 - - - +
116G THR* 3.2 6.8 + - - -
117G GLN* 2.9 27.8 + - - +
151G ALA* 3.9 17.5 - - - +
153G TYR* 4.4 12.5 - - - -
85X ARG* 6.2 2.0 - - - -
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Residues in contact with SER 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G SER 3.0 15.5 + - - -
111G LEU* 3.6 17.0 - - - +
113G GLY* 1.3 76.2 - - - +
115G LYS* 1.3 63.6 + - - +
117G GLN* 3.4 11.2 + - - +
118G ILE* 3.5 20.4 + - - +
86X SER* 6.3 3.1 - - - +
89X ASP* 3.4 22.4 + - - -
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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
----------------------------------------------------------
83G LEU* 5.1 8.5 - - - +
84G LEU* 4.3 12.1 - - + -
87G PHE* 3.6 55.1 - - + -
111G LEU 2.9 17.9 + - - +
112G ILE* 3.7 5.8 - - - +
114G SER* 1.3 78.4 - - - +
116G THR* 1.3 61.7 + - + +
118G ILE* 3.7 13.6 + - + +
119G PRO* 3.4 15.8 - - - +
128G TYR* 3.4 28.1 + - + +
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Residues in contact with THR 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G LEU* 4.1 21.8 - - + -
112G ILE* 2.6 31.1 + - + +
113G GLY* 3.2 9.0 + - - -
115G LYS* 1.3 74.6 - - - +
117G GLN* 1.3 64.4 + - - +
118G ILE 3.3 0.4 - - - -
119G PRO* 3.3 12.7 - - - +
120G THR* 3.7 12.0 - - - +
127G PRO* 5.6 0.7 - - - +
128G TYR* 3.6 37.1 + - + -
148G CYS 5.3 2.6 + - - +
149G PRO* 5.4 2.9 - - - +
151G ALA* 3.3 22.7 - - - +
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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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113G GLY 2.9 18.3 + - - +
114G SER* 3.7 6.7 - - - +
115G LYS 3.3 0.4 - - - -
116G THR* 1.3 78.0 + - - +
118G ILE* 1.3 76.2 + - - +
120G THR* 2.7 30.8 + - - +
121G GLN* 3.0 29.3 + - - +
151G ALA* 3.6 9.9 - - + -
82X ALA* 3.8 31.6 - - + +
83X ASP* 3.2 19.6 + - - +
86X SER* 3.8 24.3 + - - -
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Residues in contact with ILE 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 SER* 3.5 17.9 - - - +
115G LYS* 3.8 11.9 - - + +
117G GLN* 1.3 86.6 - - - +
119G PRO* 1.3 66.1 - - + +
120G THR 3.1 4.3 + - - -
121G GLN* 3.2 15.0 + - - +
122G ARG* 3.7 46.1 + - - +
125G ARG* 4.2 10.5 - - - +
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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