Contacts of the helix formed by residues 114 - 132 (chain G) in PDB entry 4D1Q
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 GLY 114 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G SER 3.5 12.9 + - - -
111G ALA 3.8 0.9 + - - -
112G VAL 3.0 3.4 - - - -
113G SER* 1.3 76.4 - - - +
115G SER* 1.3 59.6 + - - -
117G PHE* 3.0 22.0 - - - +
118G ILE* 3.1 11.3 + - - +
105H ASP* 3.5 24.2 - - - -
107H ARG* 5.3 1.3 - - - -
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Residues in contact with SER 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G SER 3.2 4.9 + - - -
114G GLY* 1.3 66.6 - - - -
116G GLY* 1.3 64.3 + - - +
117G PHE 3.0 5.9 + - - -
118G ILE* 3.1 17.8 + - - +
119G ASP* 3.1 17.9 + - - +
104H ARG* 3.0 25.6 - - - -
105H ASP* 3.5 3.2 + - - -
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Residues in contact with GLY 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G SER* 1.3 78.1 - - - +
117G PHE* 1.3 58.9 + - - +
119G ASP* 3.9 4.3 - - - +
120G MET* 3.4 20.4 + - - +
97H LYS 4.1 2.1 - - - +
100H GLN* 5.4 0.9 - - - +
101H TRP* 3.6 17.1 + - - +
104H ARG* 3.3 41.7 - - - +
105H ASP* 3.3 6.8 + - - -
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Residues in contact with PHE 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G CYS* 5.4 0.2 - - - -
101G TRP* 4.0 21.3 - + - -
111G ALA 3.2 9.9 - - - +
112G VAL* 2.8 52.9 - - + -
114G GLY 3.0 10.5 - - - +
116G GLY* 1.3 77.2 - - - +
118G ILE* 1.3 54.4 + - + +
120G MET* 2.8 13.4 + - + +
121G ILE* 2.8 66.4 + - + +
101H TRP* 3.5 25.8 - + + +
105H ASP* 3.1 18.7 + - - +
117H PHE* 4.9 4.3 - + - -
120H MET* 4.3 15.5 - - + -
124H PHE* 5.2 0.4 - + - -
141H LEU* 4.6 9.6 - - + -
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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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112G VAL 3.8 12.1 - - - +
113G SER* 3.9 17.5 - - - +
114G GLY 3.1 16.2 - - - +
115G SER* 3.1 9.6 + - - +
117G PHE* 1.3 75.8 - - - +
119G ASP* 1.3 63.4 + - - +
121G ILE* 3.2 10.7 + - - +
122G LYS* 3.0 39.4 + - - +
137H VAL* 3.9 21.3 - - + -
138H GLU* 4.3 16.6 - - + +
141H LEU* 4.0 13.0 - - + -
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Residues in contact with ASP 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G SER* 3.1 12.6 + - - +
116G GLY 3.9 9.2 - - - +
117G PHE 3.2 0.2 - - - -
118G ILE* 1.3 79.8 - - - +
120G MET* 1.3 60.3 + - - +
122G LYS* 3.6 18.0 + - - +
123G PHE 3.2 14.9 + - - -
97H LYS* 3.4 29.5 + - - +
100H GLN* 6.1 0.9 - - - +
104H ARG* 3.8 20.7 + - - +
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Residues in contact with MET 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G GLY 3.4 11.7 + - - +
117G PHE* 2.8 13.6 + - + +
119G ASP* 1.3 77.6 - - - +
121G ILE* 1.3 69.8 + - + +
123G PHE* 2.8 24.6 + - - +
124G PHE* 3.0 35.6 + - + -
97H LYS* 3.6 22.6 + - + +
98H CYS* 2.9 46.0 - - + +
101H TRP* 3.5 33.9 - - + -
117H PHE* 4.0 18.4 - - + -
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Residues in contact with ILE 121 (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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117G PHE* 2.8 58.6 + - + +
118G ILE* 3.3 10.8 - - - +
120G MET* 1.3 82.3 - - + +
122G LYS* 1.3 60.7 + - - +
124G PHE* 3.1 9.6 + - + +
125G ILE* 3.0 28.0 + - + +
120H MET* 4.6 0.2 - - + -
121H ILE* 4.4 13.5 - - + -
124H PHE* 3.7 32.5 - - + +
137H VAL* 3.9 12.3 - - + -
141H LEU* 3.7 24.5 - - + -
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Residues in contact with LYS 122 (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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118G ILE* 3.0 26.5 + - - +
119G ASP* 3.6 20.7 + - - +
121G ILE* 1.3 75.1 - - - +
123G PHE* 1.3 64.9 + - - +
125G ILE* 2.9 17.9 + - - +
126G LYS* 2.9 13.1 + - - +
135H VAL 5.1 2.7 - - - -
137H VAL* 3.5 31.6 - - + +
138H GLU* 2.7 32.7 + - - -
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Residues in contact with PHE 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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119G ASP 3.2 3.0 + - - -
120G MET 2.8 14.7 + - - +
122G LYS* 1.3 74.8 - - - +
124G PHE* 1.3 83.3 + + - -
126G LYS* 3.5 16.4 + - + +
127G VAL* 2.8 53.5 + - + +
140G LEU* 5.3 1.1 - - + -
90H CYS* 3.7 13.2 - - - -
93H GLU* 3.5 46.7 - - + +
94H ALA* 3.4 36.8 - - + -
97H LYS* 3.2 32.5 - - + -
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Residues in contact with PHE 124 (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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120G MET* 3.0 53.9 + - + -
121G ILE* 3.5 7.9 - - - +
122G LYS 2.9 0.6 + - - -
123G PHE* 1.3 103.5 - + - +
125G ILE* 1.3 65.4 + - - +
127G VAL* 3.0 15.7 + - + +
128G GLY 3.1 9.2 + - - -
140G LEU* 3.8 27.1 - - + -
141G LEU* 3.4 26.0 - - + -
94H ALA* 5.1 1.3 - - + -
98H CYS* 4.2 4.5 - - - -
117H PHE* 4.8 0.2 - + - -
121H ILE* 4.0 35.4 - - + -
124H PHE* 4.5 13.5 - - + -
125H ILE* 3.9 18.4 - - + +
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Residues in contact with ILE 125 (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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121G ILE* 3.0 16.4 + - + +
122G LYS* 2.9 7.6 + - - +
124G PHE* 1.3 73.9 - - - +
126G LYS* 1.3 57.9 + - - +
128G GLY 2.9 17.0 + - - -
129G ALA* 3.2 5.2 + - - +
124H PHE* 3.8 25.4 - - + +
127H VAL* 5.0 3.6 - - + -
128H GLY* 3.2 30.1 - - - +
133H GLU* 4.0 14.6 - - - +
135H VAL* 3.9 28.0 - - + -
137H VAL* 3.7 30.1 - - + -
140H LEU* 4.0 22.4 - - + -
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Residues in contact with LYS 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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122G LYS 2.9 15.3 + - - +
123G PHE* 3.6 17.9 - - - +
125G ILE* 1.3 78.2 - - - +
127G VAL* 1.3 58.0 + - + +
129G ALA* 4.2 2.1 - - - +
130G GLU* 3.5 29.2 + - + +
93H GLU* 3.1 31.6 + - - +
133H GLU* 3.4 39.6 - - + +
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Residues in contact with VAL 127 (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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123G PHE* 2.8 55.9 - - + +
124G PHE* 3.0 13.3 + - + +
126G LYS* 1.3 76.7 - - + +
128G GLY* 1.3 59.3 + - - +
130G GLU* 3.5 0.4 + - - -
131G TYR* 3.0 47.3 + - + +
135G VAL* 5.1 2.2 - - + -
140G LEU* 4.5 10.5 - - + -
86H VAL* 4.6 7.2 - - + -
90H CYS* 4.4 12.6 - - - -
125H ILE* 4.4 17.9 - - + +
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Residues in contact with GLY 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 PHE 3.1 6.4 + - - -
125G ILE 2.9 7.9 + - - -
127G VAL* 1.3 74.4 - - - +
129G ALA* 1.3 59.7 + - - +
131G TYR 3.0 0.2 + - - -
132G GLY 2.8 38.4 + - - +
125H ILE* 3.4 30.2 - - - +
129H ALA* 3.3 11.7 - - - +
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Residues in contact with ALA 129 (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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125G ILE 3.2 8.6 + - - +
126G LYS 4.4 2.0 - - - +
127G VAL 3.5 0.2 - - - -
128G GLY* 1.3 77.0 - - - +
130G GLU* 1.3 60.2 + - - +
131G TYR 3.4 0.3 + - - -
132G GLY 4.4 2.3 + - - -
128H GLY 3.2 20.7 + - - +
129H ALA* 4.0 4.8 - - - +
132H GLY* 3.8 6.1 - - - -
133H GLU* 3.4 33.0 - - + +
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Residues in contact with GLU 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 LYS* 3.5 24.4 + - + +
127G VAL* 5.9 0.2 - - - -
128G GLY 3.3 0.4 - - - -
129G ALA* 1.3 78.8 - - - +
131G TYR* 1.3 91.6 + - + +
132G GLY 4.0 0.2 - - - -
90H CYS* 5.8 1.0 - - - +
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Residues in contact with TYR 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 VAL* 3.0 31.6 + - + +
130G GLU* 1.3 120.3 + - + +
132G GLY* 1.3 63.9 + - - +
135G VAL* 4.6 10.6 - - + +
84H LYS* 3.0 40.4 - - + +
85H THR 4.6 2.5 - - - -
86H VAL* 3.4 39.6 - - + +
87H SER* 2.9 36.3 + - - -
90H CYS* 3.8 12.6 - - + +
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Residues in contact with GLY 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 GLY* 2.8 30.6 + - - +
129G ALA 4.4 2.6 + - - -
130G GLU 4.0 0.4 - - - -
131G TYR* 1.3 76.9 - - - +
133G GLU* 1.3 60.8 + - - +
135G VAL* 4.3 1.3 - - - +
84H LYS* 4.3 5.4 - - - -
125H ILE* 4.1 3.1 - - - +
129H ALA* 3.3 14.8 - - - +
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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
------------------------------------------------------------
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