Contacts of the helix formed by residues 131 - 145 (chain G) in PDB entry 4UNA
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 ASN 131 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19G ILE* 6.1 1.2 - - - +
129G ASN* 3.1 20.0 + - - +
130G LYS* 1.3 74.5 - - - +
132G LYS* 1.3 63.6 + - - +
133G ALA* 3.1 13.0 + - - +
134G LEU* 2.8 47.1 + - + +
135G LEU* 3.2 15.9 + - - +
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Residues in contact with LYS 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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130G LYS 3.1 7.5 + - - -
131G ASN* 1.3 72.0 + - - +
133G ALA* 1.3 57.9 + - - +
135G LEU* 3.0 9.6 + - - +
136G GLU* 2.8 53.6 + - + +
151G ILE* 4.9 10.8 - - + -
161G TYR* 3.8 55.6 + - + +
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Residues in contact with ALA 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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99G ARG* 4.9 13.9 - - - +
131G ASN* 3.1 9.5 + - - +
132G LYS* 1.3 78.1 - - - +
134G LEU* 1.3 63.4 + - - +
136G GLU* 3.3 17.0 + - - +
137G ILE* 3.2 28.6 + - + +
140G ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ILE* 3.6 30.5 - - + -
95G LEU* 5.7 3.4 - - + -
98G ILE* 4.0 15.0 - - + -
109G PHE* 3.7 28.9 - - + -
113G LEU* 4.5 19.7 - - + -
129G ASN* 4.3 18.6 - - + +
131G ASN* 2.8 30.7 + - + +
133G ALA* 1.3 76.8 - - - +
135G LEU* 1.3 64.9 + - + +
137G ILE* 3.3 11.2 + - + +
138G VAL* 3.1 23.1 + - + +
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Residues in contact with LEU 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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113G LEU* 4.8 9.9 - - + -
127G ILE* 4.1 19.1 - - + +
129G ASN* 4.0 23.6 - - + +
131G ASN 3.2 9.6 + - - +
132G LYS* 3.0 9.2 + - - +
134G LEU* 1.3 78.3 - - + +
136G GLU* 1.3 51.9 + - - +
138G VAL* 3.2 5.8 + - + +
139G SER* 2.7 35.7 + - - -
151G ILE* 3.5 18.0 - - + +
161G TYR* 3.8 35.9 - - + +
162G VAL 4.0 1.6 - - - +
163G LEU* 3.6 36.8 - - + +
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Residues in contact with GLU 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 LYS* 2.8 47.9 + - + +
133G ALA* 3.6 16.9 - - - +
134G LEU 3.3 0.2 - - - -
135G LEU* 1.3 75.8 - - - +
137G ILE* 1.3 61.9 + - - +
139G SER* 3.3 3.2 + - - -
140G ARG* 3.1 52.1 + - - +
151G ILE* 3.7 15.5 - - + -
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Residues in contact with ILE 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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98G ILE* 4.0 21.1 - - + +
99G ARG* 3.9 43.5 - - + +
133G ALA* 3.2 18.2 + - + +
134G LEU* 3.6 11.0 - - + +
135G LEU 3.2 0.2 - - - -
136G GLU* 1.3 75.3 - - - +
138G VAL* 1.3 66.8 + - + +
140G ARG* 3.3 26.1 + - - +
141G TRP* 3.1 60.8 + - + +
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Residues in contact with VAL 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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109G PHE* 4.0 29.6 - - + -
110G ILE* 4.1 18.8 - - + -
113G LEU* 4.1 15.0 - - + -
127G ILE* 4.5 13.9 - - + -
134G LEU* 3.1 15.1 + - + +
135G LEU* 3.6 8.7 - - + +
137G ILE* 1.3 76.0 - - + +
139G SER* 1.3 57.7 + - - +
141G TRP* 3.5 12.1 + - + +
142G LEU* 2.9 39.7 + - + +
163G LEU* 3.8 16.8 - - + -
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Residues in contact with SER 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 LEU 2.7 20.8 + - - -
136G GLU* 3.4 7.0 - - - -
137G ILE 3.1 0.2 - - - -
138G VAL* 1.3 74.4 - - - +
140G ARG* 1.3 58.2 + - - +
142G LEU 3.2 1.2 + - - -
143G ASN* 2.9 35.1 + - - +
149G ASN* 2.7 34.6 + - - +
151G ILE* 3.7 16.6 - - - +
163G LEU* 4.0 5.6 - - - -
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Residues in contact with ARG 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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99G ARG* 5.1 7.7 - - - +
133G ALA 5.4 0.2 + - - -
136G GLU* 3.1 38.0 + - - +
137G ILE* 3.7 29.3 - - - +
139G SER* 1.3 74.0 - - - +
141G TRP* 1.3 68.8 + - + +
143G ASN* 3.2 7.5 + - - +
144G ASN* 3.0 37.4 + - - +
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Residues in contact with TRP 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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98G ILE* 3.2 45.1 - - + -
99G ARG* 4.8 7.4 + - - +
101G PHE* 3.8 19.4 + + + -
106G GLN* 3.5 48.8 - - + +
109G PHE* 3.6 27.4 - + - -
110G ILE* 3.8 26.9 - - + -
137G ILE* 3.1 31.0 + - + +
138G VAL* 3.7 13.7 - - + +
140G ARG* 1.3 78.4 - - + +
142G LEU* 1.3 63.0 + - - +
144G ASN* 3.3 7.4 + - - +
145G LEU* 3.0 30.2 + - + +
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Residues in contact with LEU 142 (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 ILE* 4.4 15.5 - - + -
127G ILE* 5.3 0.9 - - + -
138G VAL* 2.9 36.2 + - + +
139G SER 3.2 0.2 + - - -
141G TRP* 1.3 73.1 - - - +
143G ASN* 1.3 55.8 + - - +
145G LEU* 3.1 6.9 + - + -
146G GLY 3.1 4.7 + - - -
147G VAL* 2.7 44.4 + - + +
149G ASN* 3.5 17.0 - - + +
163G LEU* 3.9 17.0 - - + -
165G ILE* 3.8 29.2 - - + -
173G PHE* 3.9 29.4 - - + -
177G ILE* 4.4 8.7 - - + -
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Residues in contact with ASN 143 (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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139G SER* 2.9 28.8 + - - +
140G ARG* 3.2 8.9 + - - +
142G LEU* 1.3 76.4 - - - +
144G ASN* 1.3 65.3 + - - +
146G GLY* 2.9 18.5 + - - -
147G VAL 3.5 12.3 - - - +
148G ARG* 3.8 18.0 - - - +
149G ASN* 3.8 10.5 + - - +
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Residues in contact with ASN 144 (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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140G ARG* 3.0 24.3 + - - +
141G TRP* 3.7 6.9 - - - +
143G ASN* 1.3 83.5 - - - +
145G LEU* 1.3 63.7 + - + +
146G GLY 3.2 1.6 + - - -
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Residues in contact with LEU 145 (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 MET* 3.7 39.3 - - + -
106G GLN* 4.5 12.8 - - + +
107G ILE* 4.0 14.4 - - + -
110G ILE* 4.9 6.7 - - + -
141G TRP 3.0 22.8 + - - +
142G LEU* 3.1 8.3 + - + +
144G ASN* 1.3 81.2 - - + +
146G GLY* 1.3 61.7 + - - +
147G VAL* 3.4 8.0 + - + +
172G LYS* 3.5 15.4 - - - +
176G THR* 5.5 5.1 + - - +
177G ILE* 4.0 26.7 - - + -
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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