Contacts of the helix formed by residues 111 - 128 (chain G) in PDB entry 5T0G
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 VAL 111 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G ILE* 3.8 20.4 - - + -
109G ILE* 3.0 8.8 + - - +
110G PRO* 1.3 86.0 - - - +
112G ASP* 1.3 65.8 + - - +
113G MET 3.3 1.1 - - - -
114G LEU* 3.3 24.9 + - + -
115G CYS* 3.5 15.6 + - - -
140G LEU* 3.5 28.3 - - + -
141G ILE 3.2 28.0 - - - +
142G GLY* 3.6 11.2 - - - -
150G GLN* 5.2 0.7 - - + -
152G TYR* 3.4 22.6 - - + -
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Residues in contact with ASP 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G PRO* 3.0 17.6 + - + +
111G VAL* 1.3 82.0 - - - +
113G MET* 1.3 85.7 + - + +
115G CYS* 3.9 3.8 + - - +
116G LYS* 3.4 25.9 + - - +
152G TYR* 2.5 44.5 + - - +
160G TYR* 5.0 8.5 - - - -
61H SER* 5.2 8.1 - - - +
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Residues in contact with MET 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G TRP* 4.0 33.8 - - + -
109G ILE* 4.5 2.0 - - + -
110G PRO* 4.5 16.1 - - + +
111G VAL 3.3 1.8 - - - +
112G ASP* 1.3 99.0 - - + +
114G LEU* 1.3 61.1 + - - +
115G CYS 3.4 0.2 - - - -
116G LYS* 3.2 30.6 + - + +
117G ARG* 3.0 32.8 + - - +
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Residues in contact with LEU 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ILE* 4.6 17.9 - - + -
73G THR* 5.4 1.6 - - - +
76G ILE* 5.7 0.9 - - + -
94G ALA* 4.5 21.1 - - + +
97G GLU* 4.3 6.2 - - + +
98G ALA* 4.7 4.9 - - + +
109G ILE* 3.6 37.8 - - + +
111G VAL* 3.3 21.6 + - + +
112G ASP 3.3 0.8 - - - -
113G MET* 1.3 78.4 - - - +
115G CYS* 1.3 60.5 + - - +
117G ARG* 3.4 4.3 + - - +
118G ILE* 2.9 54.6 + - + +
138G MET* 5.4 1.6 - - + -
140G LEU* 4.0 28.0 - - + -
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Residues in contact with CYS 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G VAL 3.5 11.1 + - - +
112G ASP 3.9 3.6 + - - +
113G MET 3.4 0.4 - - - -
114G LEU* 1.3 78.9 - - - +
116G LYS* 1.3 57.4 + - - +
118G ILE* 3.8 9.0 - - - +
119G ALA* 2.9 30.1 + - - +
138G MET* 5.7 1.8 - - - -
140G LEU* 4.2 25.6 - - - -
152G TYR* 3.6 32.8 - - + -
153G LYS 4.8 7.6 - - - +
154G CYS* 4.6 16.4 - - + -
160G TYR* 3.9 15.1 - - + +
161G CYS 5.0 1.3 - - - +
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Residues in contact with LYS 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G ASP* 3.4 18.6 - - - +
113G MET* 3.2 38.2 + - + +
114G LEU 3.1 1.0 - - - -
115G CYS* 1.3 75.1 - - - +
117G ARG* 1.3 65.1 + - - +
119G ALA* 3.1 4.7 + - - +
120G ASP* 2.9 30.2 + - - +
160G TYR* 3.4 55.6 + - + +
66H GLU* 5.0 15.0 + - - -
84H ARG* 3.5 12.0 + - - +
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Residues in contact with ARG 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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97G GLU* 3.1 33.9 - - + +
101G TRP* 4.4 23.0 - - - -
105G TYR* 4.9 8.5 + - - -
113G MET* 3.0 19.2 + - - +
114G LEU* 3.8 2.7 - - - +
116G LYS* 1.3 73.6 - - - +
118G ILE* 1.3 64.8 + - - +
120G ASP* 3.0 27.7 + - - +
121G ILE* 3.1 23.3 + - + +
88H HIS* 3.9 31.1 + - - -
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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
----------------------------------------------------------
90G GLN* 3.6 38.3 + - + +
93G ARG* 4.5 3.1 - - + +
94G ALA* 4.2 22.4 - - + +
97G GLU* 3.6 22.9 - - - +
114G LEU* 2.9 36.9 + - + +
115G CYS* 3.8 7.0 - - - +
117G ARG* 1.3 74.9 - - - +
119G ALA* 1.3 58.0 + - - +
121G ILE* 3.1 10.8 + - + +
122G SER* 2.9 34.4 + - - +
138G MET* 5.0 11.2 - - + -
154G CYS* 4.6 12.1 - - - -
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Residues in contact with ALA 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G CYS 2.9 20.1 + - - +
116G LYS* 3.1 3.8 + - - +
118G ILE* 1.3 77.3 - - - +
120G ASP* 1.3 56.9 + - - +
122G SER* 3.2 12.0 + - - -
123G GLN* 2.8 22.7 + - - +
154G CYS* 4.4 4.3 - - - -
158G GLY* 3.3 2.9 - - - -
159G TYR 3.4 30.3 - - - +
160G TYR 3.8 1.6 - - - +
84H ARG* 3.2 24.4 + - - +
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Residues in contact with ASP 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LYS* 2.9 21.3 + - - +
117G ARG* 3.0 26.4 + - - +
119G ALA* 1.3 73.8 - - - +
121G ILE* 1.3 65.3 + - + +
123G GLN* 2.8 29.0 + - - +
124G VAL* 3.1 11.0 + - - +
84H ARG* 2.6 38.5 + - - +
85H VAL* 5.0 6.0 + - + +
88H HIS* 5.7 8.0 - - - +
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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
----------------------------------------------------------
90G GLN* 5.5 5.4 - - - +
93G ARG* 3.3 43.3 - - - +
97G GLU* 3.5 21.5 - - - +
117G ARG* 3.1 32.2 + - + +
118G ILE* 3.1 11.4 + - + +
120G ASP* 1.3 81.1 - - + +
122G SER* 1.3 57.9 + - - +
124G VAL* 3.0 27.7 + - + +
125G TYR* 3.0 31.6 + - + -
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Residues in contact with SER 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G GLN* 5.2 4.7 + - - -
118G ILE* 2.9 22.3 + - - +
119G ALA* 3.3 14.1 - - - -
121G ILE* 1.3 77.6 - - - +
123G GLN* 1.3 51.0 + - - +
125G TYR* 3.3 15.8 + - - +
126G THR* 2.6 36.5 + - - -
133G PRO 5.1 2.1 - - - +
154G CYS* 4.6 4.9 - - - -
155G ASP 5.1 1.6 - - - -
156G PRO* 5.0 10.8 - - - +
158G GLY* 3.7 15.9 - - - -
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Residues in contact with GLN 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G ALA 2.8 11.2 + - - +
120G ASP* 2.8 18.4 + - - +
122G SER* 1.3 73.9 - - - +
124G VAL* 1.3 59.9 + - + +
126G THR* 2.8 17.0 + - - +
127G GLN* 2.7 37.1 + - + +
157G ALA 4.3 3.6 + - - -
158G GLY* 3.8 4.8 + - - +
81H PRO* 3.3 32.7 - - - +
82H ASP* 2.9 27.0 + - - +
84H ARG* 5.0 0.4 - - - +
85H VAL* 3.5 24.7 - - + -
121H TYR* 5.8 2.5 - - - +
128H ARG* 3.7 9.3 + - - +
130H PHE* 6.0 0.4 - - + -
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Residues in contact with VAL 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 ASP 3.1 13.3 + - - +
121G ILE* 3.0 16.5 + - + +
123G GLN* 1.3 77.5 - - + +
125G TYR* 1.3 65.5 + - + +
127G GLN* 3.0 16.6 + - + +
128G ASN* 3.2 19.9 + - + +
131G MET* 4.2 10.9 - - - +
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Residues in contact with TYR 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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14G THR* 5.0 0.5 - - - +
90G GLN* 4.5 11.5 + - - -
93G ARG* 2.6 30.1 + - - -
121G ILE* 3.0 33.7 + - + -
122G SER* 3.6 14.6 - - - +
124G VAL* 1.3 78.9 - - + +
126G THR* 1.3 61.3 + - - +
127G GLN 3.6 0.2 + - - -
128G ASN 3.7 11.6 - - - +
131G MET* 3.4 40.8 - - + +
132G ARG 3.9 7.4 - - - +
133G PRO* 3.4 43.4 - - + +
134G LEU* 3.6 32.0 - - + +
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Residues in contact with THR 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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14G THR* 3.4 14.4 - - - +
22G LEU* 5.0 3.4 - - + -
25G VAL* 3.8 27.8 - - + +
122G SER 2.6 20.1 + - - -
123G GLN* 2.8 18.0 + - - +
125G TYR* 1.3 78.0 - - - +
127G GLN* 1.3 54.7 + - - +
128G ASN 4.5 0.2 - - - -
133G PRO* 5.1 7.6 + - - +
156G PRO 4.0 14.0 + - - -
157G ALA* 4.2 13.0 - - - +
128H ARG* 2.5 45.3 + - - +
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Residues in contact with GLN 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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14G THR* 2.7 22.2 + - - +
123G GLN* 2.7 23.0 + - + +
124G VAL* 3.0 8.9 + - + +
126G THR* 1.3 76.7 - - - +
128G ASN* 1.3 61.5 + - - +
129G ALA* 3.3 1.4 + - - +
82H ASP* 4.6 7.3 + - - -
121H TYR* 3.1 30.0 + - + +
126H GLY 4.3 4.3 - - - +
127H VAL* 3.2 19.1 - - + -
128H ARG* 2.4 66.6 + - - +
129H PRO 5.1 0.2 + - - -
130H PHE* 5.4 0.2 - - - -
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Residues in contact with ASN 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G THR* 3.8 4.7 + - - +
124G VAL* 3.2 12.6 + - + +
125G TYR 3.7 13.7 - - - +
127G GLN* 1.3 78.9 - - - +
129G ALA* 1.3 60.8 + - - +
130G GLU* 2.4 39.0 + - - +
131G MET* 3.7 36.9 - - + +
3H GLU* 3.3 33.3 + - - +
6H TYR* 2.6 16.3 + - - -
126H GLY 4.3 6.5 - - - -
127H VAL* 4.5 6.1 - - + -
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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
------------------------------------------------------------
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