Contacts of the helix formed by residues 114 - 128 (chain G) in PDB entry 4ADV
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 114 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1239A A 3.8 16.6 - - - -
1240A U 3.3 20.6 - - - -
1297A G 3.6 9.5 + - - -
113G LYS* 1.3 86.6 + - - +
115G MET* 1.3 54.0 + - - +
116G ALA* 4.3 4.5 + - - +
117G LEU* 2.6 19.6 + - - +
118G ARG* 2.5 41.6 + - - +
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Residues in contact with MET 115 (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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1240A U 2.9 55.2 + - + +
29G LEU* 3.9 26.0 - - + -
41G ILE* 4.0 15.9 - - + +
104G VAL* 4.5 7.0 - - + -
107G ALA* 4.5 7.0 - - + +
108G ARG* 4.0 31.4 - - + -
114G SER* 1.3 69.2 - - - +
116G ALA* 1.3 61.9 + - - +
118G ARG* 3.6 13.4 - - - +
119G LEU* 3.2 50.1 + - + +
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Residues in contact with ALA 116 (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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1240A U 3.7 6.6 + - - +
40G SER 5.3 0.9 - - - +
41G ILE* 3.5 36.7 - - + +
44G SER* 4.4 8.5 - - - +
45G ALA* 3.0 30.5 - - - +
114G SER* 2.7 9.6 + - - +
115G MET* 1.3 78.1 - - - +
117G LEU* 1.3 59.3 + - + +
119G LEU* 4.0 0.5 - - - +
120G ALA 3.8 1.2 + - - -
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Residues in contact with LEU 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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45G ALA* 5.8 0.2 - - + -
48G THR* 5.0 7.6 - - + +
52G ARG* 5.8 9.0 - - - +
112G ASP* 4.6 6.5 - - + +
113G LYS* 4.7 22.4 - - + -
114G SER* 2.6 22.0 + - - +
116G ALA* 1.3 72.7 - - + +
118G ARG* 1.3 56.6 + - - +
119G LEU 2.7 15.6 + - - -
120G ALA* 2.8 29.1 + - + -
121G ASN* 3.2 41.8 + - - +
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Residues in contact with ARG 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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1239A A 4.6 25.4 + - - -
1298A U 3.5 25.1 + - - -
107G ALA 3.6 20.9 - - - +
108G ARG* 4.1 14.1 + - - +
110G ARG* 3.3 28.7 + - + +
111G GLY* 3.6 21.6 - - - +
112G ASP* 2.8 61.3 + - + +
113G LYS 3.9 3.0 + - - -
114G SER* 2.5 36.9 + - - +
115G MET* 3.7 9.6 - - - +
117G LEU* 1.3 71.9 - - - +
119G LEU* 1.3 55.2 + - - +
121G ASN* 5.4 0.4 - - - -
122G GLU* 4.0 1.2 - - - +
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Residues in contact with LEU 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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25G PHE* 5.5 4.3 - - + -
41G ILE 5.3 0.7 - - - +
42G VAL* 3.9 26.9 - - + +
45G ALA* 3.6 20.4 - - + -
46G LEU* 5.2 3.1 - - + +
103G ILE* 4.2 13.9 - - + +
104G VAL* 5.0 7.9 - - + -
107G ALA* 4.1 20.2 - - + -
115G MET* 3.2 37.4 + - + +
116G ALA 4.0 2.0 - - - +
117G LEU 2.7 1.4 + - - -
118G ARG* 1.3 78.4 - - - +
120G ALA* 1.3 68.8 + - - +
122G GLU* 3.0 12.9 + - + +
123G LEU* 2.9 39.2 - - + +
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Residues in contact with ALA 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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45G ALA* 3.5 29.4 - - + +
48G THR* 3.8 11.0 - - - +
49G LEU* 4.6 7.1 - - + +
52G ARG* 6.1 4.9 - - + -
116G ALA 3.8 0.8 + - - -
117G LEU* 2.8 32.2 + - + +
119G LEU* 1.3 77.6 - - - +
121G ASN* 1.3 66.4 + - - +
123G LEU* 2.9 24.8 + - - +
124G SER* 3.5 5.5 + - - -
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Residues in contact with ASN 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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52G ARG* 4.7 20.0 - - - +
110G ARG* 3.1 23.0 + - - +
112G ASP* 3.6 13.9 - - - +
117G LEU* 3.2 40.1 + - + +
120G ALA* 1.3 79.4 - - - +
122G GLU* 1.3 62.3 + - - +
124G SER* 3.0 11.2 + - - +
125G ASP* 2.9 28.5 + - - +
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Residues in contact with GLU 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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103G ILE* 3.7 27.6 - - + +
106G ALA 4.6 4.2 - - - +
107G ALA* 4.0 11.0 - - + +
110G ARG* 3.0 40.9 + - - +
118G ARG 4.0 4.3 - - - +
119G LEU 3.0 14.2 + - - +
121G ASN* 1.3 74.3 - - - +
123G LEU* 1.3 53.2 + - + +
125G ASP* 3.1 7.1 + - - +
126G ALA* 2.7 28.9 + - + +
130G LYS 3.3 17.8 - - - +
131G GLY* 4.0 13.2 - - - -
132G THR 4.9 0.9 + - - -
133G ALA* 4.0 18.8 + - + +
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Residues in contact with LEU 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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25G PHE* 5.3 3.1 - - + -
45G ALA 6.0 0.9 - - - +
46G LEU* 5.3 10.1 - - + -
49G LEU* 4.7 16.6 - - + -
61G PHE* 4.5 15.5 - - + -
64G ALA* 3.5 26.0 - - + +
65G LEU* 4.5 11.4 - - + -
103G ILE* 4.1 18.6 - - + -
119G LEU* 2.9 57.9 - - + +
120G ALA* 2.9 11.8 + - - +
122G GLU* 1.3 76.5 - - + +
124G SER* 1.3 63.5 + - - +
126G ALA* 3.0 20.6 + - + +
127G ALA* 3.4 6.1 + - - +
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Residues in contact with SER 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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49G LEU* 4.5 9.4 - - - +
52G ARG* 4.2 21.0 - - - +
120G ALA 3.5 4.6 + - - -
121G ASN* 3.0 13.6 + - - -
123G LEU* 1.3 78.4 - - - +
125G ASP* 1.3 63.8 + - - +
127G ALA* 3.9 3.6 + - - +
128G GLU* 3.1 33.9 + - - +
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Residues in contact with ASP 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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110G ARG* 3.4 29.8 + - - -
121G ASN* 2.9 18.1 + - - +
122G GLU* 3.4 15.1 - - - +
124G SER* 1.3 80.3 - - - +
126G ALA* 1.3 55.3 + - - +
128G GLU* 3.7 6.5 - - - +
129G ASN 2.7 27.0 + - - -
130G LYS* 2.7 56.1 + - + +
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Residues in contact with ALA 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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64G ALA* 3.1 26.0 - - + +
65G LEU* 6.0 0.2 - - + -
67G ASN* 2.9 18.1 - - - +
68G VAL* 3.9 14.8 - - + -
103G ILE* 5.6 5.6 - - + -
122G GLU* 2.7 16.6 + - - +
123G LEU* 3.0 17.9 + - + +
125G ASP* 1.3 77.2 - - - +
127G ALA* 1.3 58.1 + - - +
129G ASN* 2.9 18.2 + - - +
130G LYS 4.9 2.0 - - - +
133G ALA* 5.9 2.5 - - + -
134G VAL* 4.8 2.7 - - - +
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Residues in contact with ALA 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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63G VAL* 4.0 13.2 - - + +
64G ALA* 3.6 24.8 + - + +
67G ASN* 2.7 29.3 + - - +
123G LEU 3.4 4.8 + - - +
124G SER* 4.5 3.4 - - - +
126G ALA* 1.3 78.7 - - - +
128G GLU* 1.3 57.6 + - + +
129G ASN* 3.3 2.8 - - - +
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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 SER* 3.1 26.0 + - - +
125G ASP* 3.2 6.3 - - - +
126G ALA 3.1 1.0 - - - -
127G ALA* 1.3 74.5 - - + +
129G ASN* 1.3 75.3 + - - +
130G LYS* 4.7 1.0 - - + +
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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