Contacts of the helix formed by residues 105 - 127 (chain G) in PDB entry 5VOT
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 SER 105 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G LEU* 5.4 15.3 - - - -
101G VAL 4.0 6.7 - - - -
102G ARG 4.1 5.6 + - - -
103G ALA 2.9 9.3 + - - -
104G SER* 1.3 79.0 - - - +
106G ILE* 1.3 65.0 + - - +
108G PRO* 3.2 28.1 - - - +
109G ILE* 3.2 22.3 - - - +
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Residues in contact with ILE 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G ALA 5.0 2.2 - - - +
101G VAL* 4.2 34.8 + - + +
103G ALA 4.5 2.9 - - - +
104G SER* 3.8 19.3 - - - +
105G SER* 1.3 77.0 - - - +
107G PHE* 1.3 65.9 + - - +
109G ILE* 3.7 2.9 - - - +
110G LEU* 2.9 49.0 + - + +
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Residues in contact with PHE 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G VAL* 5.1 6.7 - - + +
106G ILE* 1.3 82.1 - - - +
108G PRO* 1.3 64.2 - - + +
110G LEU* 3.3 8.6 + - - +
111G SER* 2.9 27.4 + - - -
148G SER* 4.3 11.3 + - - +
151G ILE* 5.0 2.0 - - + -
152G GLY* 3.5 26.7 - - - +
155G VAL* 5.1 7.9 - - + -
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Residues in contact with PRO 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G MET* 6.1 0.2 - - - +
28G VAL* 5.3 12.0 - - + +
105G SER* 3.2 34.8 - - - +
107G PHE* 1.3 94.2 - - + +
109G ILE* 1.3 56.0 + - + +
111G SER* 3.0 10.1 + - - -
112G VAL* 2.9 27.5 + - - +
149G ASN* 5.2 7.0 - - - +
152G GLY* 4.6 12.8 - - - +
155G VAL* 6.4 0.4 - - + -
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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
----------------------------------------------------------
28G VAL* 5.6 13.5 - - + -
104G SER 3.2 28.0 - - - +
105G SER* 3.2 15.7 + - - +
106G ILE* 3.7 3.6 - - - +
108G PRO* 1.3 77.1 - - + +
110G LEU* 1.3 66.6 + - + +
112G VAL* 3.0 8.6 + - + +
113G ILE* 2.9 44.9 + - + +
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Residues in contact with LEU 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G ILE* 2.9 43.4 + - + +
107G PHE* 3.6 7.2 - - - +
109G ILE* 1.3 80.3 - - + +
111G SER* 1.3 56.1 + - - +
113G ILE* 4.7 9.6 - - + +
114G LEU* 2.8 33.9 + - - +
148G SER* 5.0 6.1 - - - +
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Residues in contact with SER 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G MET* 5.9 0.2 - - - -
107G PHE 2.9 13.4 + - - -
108G PRO* 3.0 13.4 + - - -
110G LEU* 1.3 74.1 - - - +
112G VAL* 1.3 59.2 + - - +
114G LEU* 3.7 2.5 - - - +
115G LEU* 2.9 38.8 + - - +
145G ALA 4.3 2.5 - - - -
148G SER* 4.2 8.9 + - - -
149G ASN* 3.7 42.0 - - - -
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Residues in contact with VAL 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G PHE* 3.5 19.6 - - + +
24G MET* 4.9 19.5 - - + +
25G THR* 5.6 4.0 - - - +
28G VAL* 5.0 12.6 - - + -
108G PRO 2.9 12.4 + - - +
109G ILE* 3.0 10.3 + - + +
111G SER* 1.3 77.7 - - - +
113G ILE* 1.3 66.4 + - + +
115G LEU* 3.2 3.7 + - - +
116G PHE 2.9 18.2 + - - -
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Residues in contact with ILE 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G PHE* 5.4 0.2 - - - -
109G ILE* 2.9 36.7 + - + +
110G LEU* 4.4 10.1 - - + +
112G VAL* 1.3 77.4 - - + +
114G LEU* 1.3 63.6 + - - +
116G PHE* 3.1 16.2 + - + +
117G MET* 2.9 21.3 + - + +
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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
----------------------------------------------------------
110G LEU 2.8 23.1 + - - +
111G SER* 3.7 1.3 - - - +
112G VAL 3.2 0.2 - - - -
113G ILE* 1.3 77.7 - - - +
115G LEU* 1.3 57.0 + - - +
117G MET* 3.0 12.0 + - - +
118G GLY* 2.9 22.5 + - - -
141G PHE* 5.1 5.2 - - - +
145G ALA* 3.5 26.5 - - + +
148G SER* 5.3 1.1 - - - +
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Residues in contact with LEU 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ALA* 5.3 4.9 - - + +
21G PHE* 4.4 20.4 - - + +
24G MET* 4.8 17.3 - - + -
111G SER* 2.9 25.4 + - - +
112G VAL* 3.7 3.6 - - - +
114G LEU* 1.3 75.7 - - - +
116G PHE* 1.3 56.9 + - - +
118G GLY* 3.0 5.0 + - - +
119G GLY* 2.9 25.1 + - - -
142G PHE* 3.8 37.9 - - + +
145G ALA* 3.8 21.8 - - + +
146G GLY* 4.4 7.2 - - - +
149G ASN* 4.9 11.7 - - - +
186G SER* 5.7 2.2 - - - +
190G ALA* 4.8 16.4 - - + -
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Residues in contact with PHE 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G PHE* 3.5 38.1 - + + -
112G VAL 2.9 8.1 + - - +
113G ILE* 3.2 18.6 - - + +
115G LEU* 1.3 77.2 - - - +
117G MET* 1.3 65.7 + - - +
119G GLY* 3.0 4.9 + - - +
120G LEU* 2.9 28.3 + - + +
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Residues in contact with MET 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G ILE* 2.9 11.9 + - + +
114G LEU* 3.0 13.2 + - - +
116G PHE* 1.3 79.1 - - + +
118G GLY* 1.3 56.7 + - - +
120G LEU* 3.3 10.1 + - - +
121G CYS* 2.9 27.4 + - - +
141G PHE* 5.9 10.3 - - + -
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Residues in contact with GLY 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ALA* 6.0 0.2 - - - -
114G LEU 2.9 12.7 + - - -
115G LEU* 3.0 5.7 + - - -
117G MET* 1.3 77.9 - - - +
119G GLY* 1.3 55.7 + - - +
121G CYS* 3.0 9.4 + - - +
122G ILE* 2.9 29.2 + - - +
138G ALA* 4.7 4.3 - - - +
141G PHE* 5.4 4.0 - - - +
142G PHE* 4.4 29.7 - - - +
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Residues in contact with GLY 119 (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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17G ALA* 4.9 15.4 - - - +
18G PHE* 5.7 9.3 - - - -
115G LEU 2.9 13.1 + - - -
116G PHE* 3.0 4.4 + - - -
118G GLY* 1.3 75.0 - - - +
120G LEU* 1.3 57.9 + - - +
122G ILE* 4.1 5.1 - - - +
123G ALA* 2.9 33.4 + - - +
142G PHE* 5.3 0.8 - - - -
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Residues in contact with LEU 120 (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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116G PHE* 2.9 21.3 + - + +
117G MET* 3.5 12.3 - - - +
119G GLY* 1.3 76.1 - - - +
121G CYS* 1.3 57.9 + - - +
123G ALA* 4.3 3.7 - - - +
124G ALA* 2.9 32.4 + - - +
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Residues in contact with CYS 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 MET 2.9 13.6 + - - +
118G GLY* 3.0 10.3 + - - +
120G LEU* 1.3 75.5 - - - +
122G ILE* 1.3 60.1 + - - +
124G ALA* 3.5 4.4 + - - +
125G SER* 2.9 29.3 + - - -
134G ILE* 5.1 4.9 - - + +
137G SER* 4.9 5.8 - - - +
138G ALA* 3.6 29.9 - - + +
141G PHE* 5.6 5.6 - - + -
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Residues in contact with ILE 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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13G THR* 4.4 22.4 - - + -
17G ALA* 5.6 5.4 - - + -
118G GLY 2.9 13.9 + - - +
119G GLY* 4.1 6.1 - - - +
121G CYS* 1.3 74.1 - - - +
123G ALA* 1.3 61.9 + - - +
125G SER* 2.8 21.8 + - - -
126G GLU* 2.9 15.6 + - - +
138G ALA* 4.3 9.4 - - + +
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Residues in contact with ALA 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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18G PHE* 5.8 8.7 - - + -
119G GLY 2.9 18.0 + - - +
120G LEU* 4.3 3.1 - - - +
122G ILE* 1.3 77.3 - - - +
124G ALA* 1.3 61.0 + - - +
125G SER 3.4 0.3 + - - -
126G GLU* 3.6 12.1 + - - +
127G PHE* 3.7 13.2 + - - +
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Residues in contact with ALA 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 LEU 2.9 23.4 + - - +
121G CYS* 3.6 5.4 - - - +
123G ALA* 1.3 76.1 - - - +
125G SER* 1.3 53.7 + - - +
127G PHE* 2.7 26.3 - - - +
128G TYR* 4.9 1.9 - - - +
134G ILE* 5.8 2.7 - - + +
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Residues in contact with SER 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G CYS 2.9 16.3 + - - -
122G ILE* 2.8 10.1 + - - -
124G ALA* 1.3 75.8 - - - +
126G GLU* 1.3 65.4 + - - +
127G PHE 3.2 6.9 + - - +
128G TYR 5.0 0.3 - - - +
129G LYS* 4.5 12.8 - - - +
134G ILE* 4.9 7.6 - - - -
135G ILE* 4.6 27.6 - - - -
138G ALA* 5.6 0.4 - - - -
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Residues in contact with GLU 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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10G MET* 6.4 2.7 - - + -
122G ILE 2.9 12.9 + - - +
123G ALA* 4.1 7.0 - - - +
124G ALA 3.6 0.2 - - - -
125G SER* 1.3 77.3 - - - +
127G PHE* 1.3 58.1 + - - +
129G LYS* 4.6 8.1 - - - +
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Residues in contact with PHE 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G ALA 3.7 12.2 + - - +
124G ALA* 2.7 22.8 - - - +
125G SER 3.2 3.1 - - - +
126G GLU* 1.3 78.6 - - + +
128G TYR* 1.3 73.1 + - + +
129G LYS 3.4 0.2 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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