Contacts of the helix formed by residues 119 - 141 (chain G) in PDB entry 4GTU
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 PHE 119 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113G VAL* 3.9 21.8 - - + +
114G CYS* 4.3 5.4 - - - -
116G SER 3.1 9.6 + - - +
117G PRO 2.9 5.8 + - - +
118G ASP* 1.3 71.9 - - - +
120G GLU* 1.3 88.2 + - - +
122G LEU* 2.8 4.9 + - - +
123G LYS* 2.8 68.7 + - + +
169G PHE* 4.3 10.8 - + - -
213G VAL* 3.5 34.5 - - + -
214G TRP* 3.0 50.3 - + + -
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Residues in contact with GLU 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G PRO 5.2 2.1 - - - +
118G ASP 3.5 0.4 - - - -
119G PHE* 1.3 110.1 - - - +
121G LYS* 1.3 60.7 + - + +
123G LYS* 3.5 8.7 + - + +
124G PRO* 2.9 23.4 - - - +
213G VAL* 4.8 4.3 - - - +
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Residues in contact with LYS 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G ASP* 2.9 34.7 + - + +
120G GLU* 1.3 78.5 - - + +
122G LEU* 1.3 64.5 + - + +
124G PRO* 3.0 22.8 - - - +
125G GLU* 3.2 11.0 - - - +
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Residues in contact with LEU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G VAL* 4.1 36.5 - - + +
116G SER* 3.6 31.4 - - - +
118G ASP* 2.8 36.0 + - + +
119G PHE* 3.6 3.8 - - - +
121G LYS* 1.3 81.4 - - + +
123G LYS* 1.3 65.8 + - - +
124G PRO 3.5 0.2 - - - -
125G GLU* 3.4 26.5 + - - +
126G TYR* 3.4 7.3 + - - +
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Residues in contact with LYS 123 (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 VAL* 6.0 2.2 - - - -
119G PHE* 2.8 43.8 + - + +
120G GLU* 3.6 7.2 - - + +
122G LEU* 1.3 76.3 - - - +
124G PRO* 1.3 71.0 - - + +
126G TYR* 2.9 19.5 + - - +
127G LEU* 2.9 33.8 + - + +
169G PHE* 3.6 43.4 + - + -
214G TRP* 4.5 9.5 - - - +
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Residues in contact with PRO 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G GLU 2.9 27.1 - - - +
121G LYS* 3.0 19.1 - - - +
123G LYS* 1.3 81.2 - - + +
125G GLU* 1.3 69.4 + - - +
127G LEU* 3.7 14.2 - - + +
128G GLU* 3.3 29.2 + - - +
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Residues in contact with GLU 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G LYS 3.2 21.2 - - - +
122G LEU* 3.4 19.5 + - + +
123G LYS 2.9 0.8 + - - -
124G PRO* 1.3 87.8 - - - +
126G TYR* 1.3 65.6 + - - +
127G LEU 3.3 0.3 + - - -
128G GLU* 3.4 13.9 - - - +
129G GLU* 2.9 38.6 - - - +
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Residues in contact with TYR 126 (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 VAL* 3.8 12.5 + - - +
109G GLN* 4.0 33.8 - - + +
110G LEU* 4.0 16.7 - - + +
113G VAL* 4.6 16.6 - - + -
122G LEU 3.4 6.7 + - - +
123G LYS* 2.9 11.2 + - - +
125G GLU* 1.3 80.0 - - - +
127G LEU* 1.3 51.3 + - + +
129G GLU* 3.2 8.4 + - - +
130G LEU* 2.7 57.6 + - + +
133G MET* 3.4 30.3 - - + +
166G HIS* 2.9 37.9 + + - -
169G PHE* 4.8 13.7 - + + -
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Residues in contact with LEU 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G LYS* 2.9 36.6 + - + +
124G PRO* 3.7 14.8 - - + +
125G GLU 3.2 0.2 - - - -
126G TYR* 1.3 76.5 - - + +
128G GLU* 1.3 56.9 - - - +
130G LEU* 3.3 9.3 + - + +
131G PRO* 3.0 25.1 - - - +
169G PHE* 4.3 25.4 - - + -
170G GLU* 3.7 32.1 - - + +
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Residues in contact with GLU 128 (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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124G PRO* 3.3 19.0 + - - +
125G GLU* 3.4 17.3 - - - +
127G LEU* 1.3 77.2 - - - +
129G GLU* 1.3 65.0 + - + +
131G PRO* 3.4 17.7 - - - +
132G THR* 4.9 2.9 - - - +
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Residues in contact with GLU 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G GLU* 2.9 39.1 - - - +
126G TYR* 3.2 7.7 + - - +
127G LEU 3.1 0.6 - - - -
128G GLU* 1.3 87.2 - - + +
130G LEU* 1.3 64.5 + - - +
131G PRO* 3.4 1.6 - - - -
132G THR* 3.2 14.6 - - + +
133G MET* 3.2 32.5 + - + +
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Residues in contact with LEU 130 (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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126G TYR* 2.7 31.8 + - + +
127G LEU* 3.5 9.4 - - + +
129G GLU* 1.3 73.7 - - - +
131G PRO* 1.3 68.3 - - + +
133G MET* 3.0 25.3 - - - +
134G MET* 2.9 39.5 + - + +
166G HIS* 3.5 34.1 - - + +
169G PHE* 5.3 2.7 - - + -
170G GLU* 4.0 22.0 - - + -
173G CYS* 3.8 27.1 - - + -
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Residues in contact with PRO 131 (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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127G LEU 3.0 25.8 - - - +
128G GLU* 3.4 15.3 - - - +
129G GLU 3.5 0.4 - - - -
130G LEU* 1.3 82.1 - - + +
132G THR* 1.3 62.5 + - - +
134G MET* 3.2 3.1 + - + -
135G GLN 3.0 18.4 + - - -
173G CYS* 5.7 4.3 - - + +
177G PHE* 3.1 24.9 - - + -
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Residues in contact with THR 132 (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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128G GLU 4.9 2.5 - - - +
129G GLU* 3.2 23.6 - - + +
131G PRO* 1.3 78.9 - - - +
133G MET* 1.3 55.1 + - - +
135G GLN* 3.3 13.6 + - - +
136G HIS* 2.8 43.8 + - + -
50H PHE* 4.8 10.4 - - - -
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Residues in contact with MET 133 (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 VAL* 4.6 21.3 - - + -
109G GLN* 4.3 13.0 - - - +
126G TYR* 3.4 42.8 - - + -
129G GLU* 3.2 26.0 + - + +
130G LEU* 3.0 32.1 - - - +
132G THR* 1.3 77.9 - - + +
134G MET* 1.3 64.9 + - - +
136G HIS* 3.3 24.1 + - - +
137G PHE* 3.8 8.7 + - + -
166G HIS* 4.8 2.0 - - - -
56H PHE* 5.1 0.9 - - - -
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Residues in contact with MET 134 (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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130G LEU* 2.9 38.5 + - + +
131G PRO* 3.6 1.1 - - + +
133G MET* 1.3 79.6 - - - +
135G GLN* 1.3 65.5 + - - +
136G HIS 3.0 2.7 - - - -
137G PHE* 2.9 34.5 + - + +
138G SER* 3.2 9.5 + - - -
162G VAL* 5.5 1.8 - - + -
163G LEU* 3.4 33.4 - - + -
166G HIS* 5.1 13.7 - - + +
173G CYS* 4.6 10.1 - - + -
174G LEU* 3.5 14.8 - - + -
177G PHE* 3.3 27.1 - - + -
180G LEU* 3.9 7.2 - - + +
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Residues in contact with GLN 135 (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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131G PRO 3.0 9.6 + - - +
132G THR* 3.3 14.9 + - - +
134G MET* 1.3 75.6 - - - +
136G HIS* 1.3 86.5 + - - +
138G SER* 3.3 4.5 + - - -
139G GLN* 3.1 60.9 + - - +
177G PHE* 3.4 28.6 - - + -
50H PHE* 5.8 0.3 - - - -
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Residues in contact with HIS 136 (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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132G THR* 2.8 36.8 + - + -
133G MET* 3.4 11.2 - - - +
134G MET 3.0 0.4 - - - -
135G GLN* 1.3 90.2 + - - +
137G PHE* 1.3 66.2 + - - +
139G GLN* 3.1 19.8 + - - +
140G PHE* 3.2 12.3 + - - +
50H PHE* 4.2 16.9 - + - -
55H ASP 3.9 8.6 - - - +
56H PHE* 3.6 25.5 - + + -
57H PRO* 3.2 40.4 - - + +
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Residues in contact with PHE 137 (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 LEU* 3.8 25.8 - - + -
102G GLN* 4.5 5.4 - - + -
103G ALA* 4.4 19.5 - - + -
106G VAL* 4.3 20.6 - - + -
133G MET* 3.8 9.2 + - + -
134G MET* 2.9 36.4 + - + +
136G HIS* 1.3 77.9 - - - +
138G SER* 1.3 63.9 + - - +
140G PHE* 3.1 13.9 + - - +
141G LEU* 3.2 10.0 + - - +
147G PHE* 3.5 19.1 - + + -
159G ALA* 6.1 1.6 - - + -
162G VAL* 4.2 20.0 - - + -
163G LEU* 5.0 4.7 - - + -
180G LEU* 4.1 17.5 - - + -
56H PHE* 3.4 29.8 - + - -
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Residues in contact with SER 138 (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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134G MET 3.2 5.6 + - - -
135G GLN 3.6 8.5 - - - -
137G PHE* 1.3 78.5 - - - +
139G GLN* 1.3 55.2 + - - +
141G LEU* 3.1 4.0 + - - +
142G GLY* 2.7 34.0 + - - -
177G PHE* 3.9 22.2 - - - +
179G ASN* 3.3 27.0 + - - +
180G LEU* 3.8 19.7 - - - +
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Residues in contact with GLN 139 (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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135G GLN* 3.1 43.0 + - - +
136G HIS* 3.1 11.0 + - - +
138G SER* 1.3 77.6 - - - +
140G PHE* 1.3 62.0 + - - +
142G GLY* 3.9 7.7 + - - +
144G ARG* 4.1 6.6 + - - -
55H ASP* 5.1 10.4 - - + +
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Residues in contact with PHE 140 (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 ARG* 2.9 75.6 + - + +
98G ILE* 4.2 18.6 - - + -
99G LEU* 3.7 22.0 - - + -
136G HIS 3.2 6.6 + - - +
137G PHE 3.1 10.9 + - - +
139G GLN* 1.3 79.5 - - - +
141G LEU* 1.3 57.1 + - - +
144G ARG* 3.0 13.2 + - - -
147G PHE* 3.5 37.7 - + + -
55H ASP* 3.7 38.5 + - + +
56H PHE* 3.7 18.2 - + + -
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Residues in contact with LEU 141 (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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137G PHE 3.2 7.3 + - - +
138G SER* 3.1 8.1 + - - +
140G PHE* 1.3 79.8 - - - +
142G GLY* 1.3 54.1 + - - +
143G LYS 2.7 18.5 + - - -
144G ARG* 3.0 48.2 + - - +
145G PRO 4.1 3.1 - - - +
146G TRP* 3.6 6.1 - - - +
147G PHE* 3.3 52.0 - - + +
179G ASN* 3.4 39.7 - - + +
180G LEU* 4.6 4.3 - - + -
183G PHE* 4.1 18.4 - - + -
186G ARG* 4.6 2.5 - - - +
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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